Tensor voting for image correction by global and local intensity alignment.

PubMed

Jia, Jiaya; Tang, Chi-Keung

2005-01-01

This paper presents a voting method to perform image correction by global and local intensity alignment. The key to our modeless approach is the estimation of global and local replacement functions by reducing the complex estimation problem to the robust 2D tensor voting in the corresponding voting spaces. No complicated model for replacement function (curve) is assumed. Subject to the monotonic constraint only, we vote for an optimal replacement function by propagating the curve smoothness constraint using a dense tensor field. Our method effectively infers missing curve segments and rejects image outliers. Applications using our tensor voting approach are proposed and described. The first application consists of image mosaicking of static scenes, where the voted replacement functions are used in our iterative registration algorithm for computing the best warping matrix. In the presence of occlusion, our replacement function can be employed to construct a visually acceptable mosaic by detecting occlusion which has large and piecewise constant color. Furthermore, by the simultaneous consideration of color matches and spatial constraints in the voting space, we perform image intensity compensation and high contrast image correction using our voting framework, when only two defective input images are given.

Seismic moment tensor for anisotropic media: implication for Non-double-couple earthquakes

NASA Astrophysics Data System (ADS)

Cai, X.; Chen, X.; Chen, Y.; Cai, M.

2008-12-01

It is often found that the inversion results of seismic moment tensor from real seismic recorded data show the trace of seismic moment tensor M is not zero, a phenomenon called non-double-couple earthquake sources mechanism. Recently we have derived the analytical expressions of M in transversely isotropic media with the titled axis of symmetry and the results shows even only pure shear-motion of fault can lead to the implosive components determined by several combined anisotropic elastic constants. Many non-double-couple earthquakes from observations often appear in volcanic and geothermal areas (Julian, 1998), where there exist a mount of stress-aligned fluid-saturated parallel vertical micro-cracks identical to transversely isotropic media (Crampin, 2008), this stress-aligned crack will modify the seismic moment tensor. In another word, non-double-couple earthquakes don't mean to have a seismic failure movement perpendicular to the fault plane, while traditional research of seismic moment tensor focus on the case of isotropy, which cannot provide correct interpretation of seismic source mechanism. Reference: Julian, B.R., Miller, A.D. and Foulger, G.R., 1998. Non-double-couple earthquakes,1. Theory, Rev. Geophys., 36, 525¨C549. Crampin,S., Peacock,S., 2008, A review of the current understanding of seismic shear-wave splitting in the Earth's crust and common fallacies in interpretation, wave motion, 45,675-722

Analytical structure, dynamics, and coarse graining of a kinetic model of an active fluid

NASA Astrophysics Data System (ADS)

Gao, Tong; Betterton, Meredith D.; Jhang, An-Sheng; Shelley, Michael J.

2017-09-01

We analyze one of the simplest active suspensions with complex dynamics: a suspension of immotile "extensor" particles that exert active extensile dipolar stresses on the fluid in which they are immersed. This is relevant to several experimental systems, such as recently studied tripartite rods that create extensile flows by consuming a chemical fuel. We first describe the system through a Doi-Onsager kinetic theory based on microscopic modeling. This theory captures the active stresses produced by the particles that can drive hydrodynamic instabilities, as well as the steric interactions of rodlike particles that lead to nematic alignment. This active nematic system yields complex flows and disclination defect dynamics very similar to phenomenological Landau-deGennes Q -tensor theories for active nematic fluids, as well as by more complex Doi-Onsager theories for polar microtubule-motor-protein systems. We apply the quasiequilibrium Bingham closure, used to study suspensions of passive microscopic rods, to develop a nonstandard Q -tensor theory. We demonstrate through simulation that this B Q -tensor theory gives an excellent analytical and statistical accounting of the suspension's complex dynamics, at a far reduced computational cost. Finally, we apply the B Q -tensor model to study the dynamics of extensor suspensions in circular and biconcave domains. In circular domains, we reproduce previous results for systems with weak nematic alignment, but for strong alignment we find unusual dynamics with activity-controlled defect production and absorption at the boundaries of the domain. In biconcave domains, a Fredericks-like transition occurs as the width of the neck connecting the two disks is varied.

Evolution of the shock front and turbulence structures in the shock/turbulence interaction

NASA Technical Reports Server (NTRS)

Kevlahan, N.; Mahesh, K.; Lee, S.

1992-01-01

The interaction of a weak shock front with isotropic turbulence has been investigated using Direct Numerical Simulation (DNS). Two problems were considered: the ability of the field equation (the equation for a propagating surface) to model the shock; and a quantitative study of the evolution of turbulence structure using the database generated by Lee et al. Field equation model predictions for front shape have been compared with DNS results; good agreement is found for shock wave interaction with 2D turbulence and for a single steady vorticity wave. In the interaction of 3D isotropic turbulence with a normal shock, strong alignment of vorticity with the intermediate eigenvector of the rate of strain tensor (S(sup *)(sub ij) = S(sub ij) - (1/3)(delta(sub ij))(S(sub kk))) is seen to develop upstream of the shock and to be further amplified on passage through the shock. Vorticity tends to align at 90 deg to the largest eigenvector, but there is no preferred alignment with the smallest eigenvector. Upstream of the shock, the alignments continue to develop even after the velocity derivative skewness saturates. There is a significant tendency, which increases with time throughout the computational domain, for velocity to align with vorticity. The alignment between velocity and vorticity is strongest in eddy regions and weakest in convergence regions.

Joint Data Management for MOVINT Data-to-Decision Making

DTIC Science & Technology

2011-07-01

flux tensor , aligned motion history images, and related approaches have been shown to be versatile approaches [12, 16, 17, 18]. Scaling these...methods include voting , neural networks, fuzzy logic, neuro-dynamic programming, support vector machines, Bayesian and Dempster-Shafer methods. One way...Information Fusion, 2010. [16] F. Bunyak, K. Palaniappan, S. K. Nath, G. Seetharaman, “Flux tensor constrained geodesic active contours with sensor fusion

Why do galactic spins flip in the cosmic web? A Theory of Tidal Torques near saddles

NASA Astrophysics Data System (ADS)

Pichon, Christophe; Codis, Sandrine; Pogosyan, Dmitry; Dubois, Yohan; Desjacques, Vincent; Devriendt, Julien

2016-10-01

Filaments of the cosmic web drive spin acquisition of disc galaxies. The point process of filament-type saddle represent best this environment and can be used to revisit the Tidal Torque Theory in the context of an anisotropic peak (saddle) background split. The constrained misalignment between the tidal tensor and the Hessian of the density field generated in the vicinity of filament saddle points simply explains the corresponding transverse and longitudinal point-reflection symmetric geometry of spin distribution. It predicts in particular an azimuthal orientation of the spins of more massive galaxies and spin alignment with the filament for less massive galaxies. Its scale dependence also allows us to relate the transition mass corresponding to the alignment of dark matter halos' spin relative to the direction of their neighboring filament to this geometry, and to predict accordingly it's scaling with the mass of non linearity, as was measured in simulations.

Exact solutions to quadratic gravity

NASA Astrophysics Data System (ADS)

Pravda, V.; Pravdová, A.; Podolský, J.; Švarc, R.

2017-04-01

Since all Einstein spacetimes are vacuum solutions to quadratic gravity in four dimensions, in this paper we study various aspects of non-Einstein vacuum solutions to this theory. Most such known solutions are of traceless Ricci and Petrov type N with a constant Ricci scalar. Thus we assume the Ricci scalar to be constant which leads to a substantial simplification of the field equations. We prove that a vacuum solution to quadratic gravity with traceless Ricci tensor of type N and aligned Weyl tensor of any Petrov type is necessarily a Kundt spacetime. This will considerably simplify the search for new non-Einstein solutions. Similarly, a vacuum solution to quadratic gravity with traceless Ricci type III and aligned Weyl tensor of Petrov type II or more special is again necessarily a Kundt spacetime. Then we study the general role of conformal transformations in constructing vacuum solutions to quadratic gravity. We find that such solutions can be obtained by solving one nonlinear partial differential equation for a conformal factor on any Einstein spacetime or, more generally, on any background with vanishing Bach tensor. In particular, we show that all geometries conformal to Kundt are either Kundt or Robinson-Trautman, and we provide some explicit Kundt and Robinson-Trautman solutions to quadratic gravity by solving the above mentioned equation on certain Kundt backgrounds.

The beaming of subhalo accretion

NASA Astrophysics Data System (ADS)

Libeskind, Noam I.

2016-10-01

We examine the infall pattern of subhaloes onto hosts in the context of the large-scale structure. We find that the infall pattern is essentially driven by the shear tensor of the ambient velocity field. Dark matter subhaloes are preferentially accreted along the principal axis of the shear tensor which corresponds to the direction of weakest collapse. We examine the dependence of this preferential infall on subhalo mass, host halo mass and redshift. Although strongest for the most massive hosts and the most massive subhaloes at high redshift, the preferential infall of subhaloes is effectively universal in the sense that its always aligned with the axis of weakest collapse of the velocity shear tensor. It is the same shear tensor that dictates the structure of the cosmic web and hence the shear field emerges as the key factor that governs the local anisotropic pattern of structure formation. Since the small (sub-Mpc) scale is strongly correlated with the mid-range (~ 10 Mpc) scale - a scale accessible by current surveys of peculiar velocities - it follows that findings presented here open a new window into the relation between the observed large scale structure unveiled by current surveys of peculiar velocities and the preferential infall direction of the Local Group. This may shed light on the unexpected alignments of dwarf galaxies seen in the Local Group.

The cosmic web and the orientation of angular momenta

NASA Astrophysics Data System (ADS)

Libeskind, Noam I.; Hoffman, Yehuda; Knebe, Alexander; Steinmetz, Matthias; Gottlöber, Stefan; Metuki, Ofer; Yepes, Gustavo

2012-03-01

We use a 64 h-1 Mpc dark-matter-only cosmological simulation to examine the large-scale orientation of haloes and substructures with respect to the cosmic web. A web classification scheme based on the velocity shear tensor is used to assign to each halo in the simulation a web type: knot, filament, sheet or void. Using ˜106 haloes that span ˜3 orders of magnitude in mass, the orientation of the halo's spin and the orbital angular momentum of subhaloes with respect to the eigenvectors of the shear tensor is examined. We find that the orbital angular momentum of subhaloes tends to align with the intermediate eigenvector of the velocity shear tensor for all haloes in knots, filaments and sheets. This result indicates that the kinematics of substructures located deep within the virialized regions of a halo is determined by its infall which in turn is determined by the large-scale velocity shear, a surprising result given the virialized nature of haloes. The non-random nature of subhalo accretion is thus imprinted on the angular momentum measured at z= 0. We also find that the haloes' spin axis is aligned with the third eigenvector of the velocity shear tensor in filaments and sheets: the halo spin axis points along filaments and lies in the plane of cosmic sheets.

Tensor Rank Preserving Discriminant Analysis for Facial Recognition.

PubMed

Tao, Dapeng; Guo, Yanan; Li, Yaotang; Gao, Xinbo

2017-10-12

Facial recognition, one of the basic topics in computer vision and pattern recognition, has received substantial attention in recent years. However, for those traditional facial recognition algorithms, the facial images are reshaped to a long vector, thereby losing part of the original spatial constraints of each pixel. In this paper, a new tensor-based feature extraction algorithm termed tensor rank preserving discriminant analysis (TRPDA) for facial image recognition is proposed; the proposed method involves two stages: in the first stage, the low-dimensional tensor subspace of the original input tensor samples was obtained; in the second stage, discriminative locality alignment was utilized to obtain the ultimate vector feature representation for subsequent facial recognition. On the one hand, the proposed TRPDA algorithm fully utilizes the natural structure of the input samples, and it applies an optimization criterion that can directly handle the tensor spectral analysis problem, thereby decreasing the computation cost compared those traditional tensor-based feature selection algorithms. On the other hand, the proposed TRPDA algorithm extracts feature by finding a tensor subspace that preserves most of the rank order information of the intra-class input samples. Experiments on the three facial databases are performed here to determine the effectiveness of the proposed TRPDA algorithm.

A Local Fast Marching-Based Diffusion Tensor Image Registration Algorithm by Simultaneously Considering Spatial Deformation and Tensor Orientation

PubMed Central

Xue, Zhong; Li, Hai; Guo, Lei; Wong, Stephen T.C.

2010-01-01

It is a key step to spatially align diffusion tensor images (DTI) to quantitatively compare neural images obtained from different subjects or the same subject at different timepoints. Different from traditional scalar or multi-channel image registration methods, tensor orientation should be considered in DTI registration. Recently, several DTI registration methods have been proposed in the literature, but deformation fields are purely dependent on the tensor features not the whole tensor information. Other methods, such as the piece-wise affine transformation and the diffeomorphic non-linear registration algorithms, use analytical gradients of the registration objective functions by simultaneously considering the reorientation and deformation of tensors during the registration. However, only relatively local tensor information such as voxel-wise tensor-similarity, is utilized. This paper proposes a new DTI image registration algorithm, called local fast marching (FM)-based simultaneous registration. The algorithm not only considers the orientation of tensors during registration but also utilizes the neighborhood tensor information of each voxel to drive the deformation, and such neighborhood tensor information is extracted from a local fast marching algorithm around the voxels of interest. These local fast marching-based tensor features efficiently reflect the diffusion patterns around each voxel within a spherical neighborhood and can capture relatively distinctive features of the anatomical structures. Using simulated and real DTI human brain data the experimental results show that the proposed algorithm is more accurate compared with the FA-based registration and is more efficient than its counterpart, the neighborhood tensor similarity-based registration. PMID:20382233

Measuring Alignments between Galaxies and the Cosmic Web at z ˜ 2-3 Using IGM Tomography

NASA Astrophysics Data System (ADS)

Krolewski, Alex; Lee, Khee-Gan; Lukić, Zarija; White, Martin

2017-03-01

Many galaxy formation models predict alignments between galaxy spin and the cosmic web (I.e., directions of filaments and sheets), leading to an intrinsic alignment between galaxies that creates a systematic error in weak-lensing measurements. These effects are often predicted to be stronger at high redshifts (z ≳ 1) that are inaccessible to massive galaxy surveys on foreseeable instrumentation, but IGM tomography of the Lyα forest from closely spaced quasars and galaxies is starting to measure the z ˜ 2-3 cosmic web with requisite fidelity. Using mock surveys from hydrodynamical simulations, we examine the utility of this technique, in conjunction with coeval galaxy samples, to measure alignment between galaxies and the cosmic web at z ˜ 2.5. We show that IGM tomography surveys with ≲5 h -1 Mpc sightline spacing can accurately recover the eigenvectors of the tidal tensor, which we use to define the directions of the cosmic web. For galaxy spins and shapes, we use a model parameterized by the alignment strength, {{Δ }}< \\cos θ > , with respect to the tidal tensor eigenvectors from the underlying density field, and also consider observational effects such as errors in the galaxy position angle, inclination, and redshift. Measurements using the upcoming ˜1 deg2 CLAMATO tomographic survey and 600 coeval zCOSMOS-Deep galaxies should place 3σ limits on extreme alignment models with {{Δ }}< \\cos θ > ˜ 0.1, but much larger surveys encompassing >10,000 galaxies, such as Subaru PFS, will be required to constrain models with {{Δ }}< \\cos θ > ˜ 0.03. These measurements will constrain models of galaxy-cosmic web alignment and test tidal torque theory at z ˜ 2, improving our understanding of the physics of intrinsic alignments.

Measuring Alignments between Galaxies and the Cosmic Web at z ~ 2–3 Using IGM Tomography

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

Krolewski, Alex; Lee, Khee-Gan; Luki?, Zarija

Many galaxy formation models predict alignments between galaxy spin and the cosmic web (i.e., directions of filaments and sheets), leading to an intrinsic alignment between galaxies that creates a systematic error in weak-lensing measurements. These effects are often predicted to be stronger at high redshifts (z ≳ 1) that are inaccessible to massive galaxy surveys on foreseeable instrumentation, but IGM tomography of the Lyα forest from closely spaced quasars and galaxies is starting to measure the z ~ 2-3 cosmic web with requisite fidelity. Using mock surveys from hydrodynamical simulations, we examine the utility of this technique, in conjunction withmore » coeval galaxy samples, to measure alignment between galaxies and the cosmic web at z ~ 2.5. We show that IGM tomography surveys with ≲ 5 h -1 Mpc sightline spacing can accurately recover the eigenvectors of the tidal tensor, which we use to define the directions of the cosmic web. For galaxy spins and shapes, we use a model parameterized by the alignment strength, Δ (cos θ), with respect to the tidal tensor eigenvectors from the underlying density field, and also consider observational effects such as errors in the galaxy position angle, inclination, and redshift. Measurements using the upcoming ~ 1 deg 2 CLAMATO tomographic survey and 600 coeval zCOSMOS-Deep galaxies should place 3σ limits on extreme alignment models with Δ (cos θ) ~ 0.1, but much larger surveys encompassing > 10,000 galaxies, such as Subaru PFS, will be required to constrain models with Δ (cos θ) ~ 0.3. These measurements will constrain models of galaxy-cosmic web alignment and test tidal torque theory at z ~ 2, improving our understanding of the physics of intrinsic alignments.« less

Measuring Alignments between Galaxies and the Cosmic Web at z ~ 2–3 Using IGM Tomography

DOE PAGES

Krolewski, Alex; Lee, Khee-Gan; Luki?, Zarija; ...

2017-02-28

Many galaxy formation models predict alignments between galaxy spin and the cosmic web (i.e., directions of filaments and sheets), leading to an intrinsic alignment between galaxies that creates a systematic error in weak-lensing measurements. These effects are often predicted to be stronger at high redshifts (z ≳ 1) that are inaccessible to massive galaxy surveys on foreseeable instrumentation, but IGM tomography of the Lyα forest from closely spaced quasars and galaxies is starting to measure the z ~ 2-3 cosmic web with requisite fidelity. Using mock surveys from hydrodynamical simulations, we examine the utility of this technique, in conjunction withmore » coeval galaxy samples, to measure alignment between galaxies and the cosmic web at z ~ 2.5. We show that IGM tomography surveys with ≲ 5 h -1 Mpc sightline spacing can accurately recover the eigenvectors of the tidal tensor, which we use to define the directions of the cosmic web. For galaxy spins and shapes, we use a model parameterized by the alignment strength, Δ (cos θ), with respect to the tidal tensor eigenvectors from the underlying density field, and also consider observational effects such as errors in the galaxy position angle, inclination, and redshift. Measurements using the upcoming ~ 1 deg 2 CLAMATO tomographic survey and 600 coeval zCOSMOS-Deep galaxies should place 3σ limits on extreme alignment models with Δ (cos θ) ~ 0.1, but much larger surveys encompassing > 10,000 galaxies, such as Subaru PFS, will be required to constrain models with Δ (cos θ) ~ 0.3. These measurements will constrain models of galaxy-cosmic web alignment and test tidal torque theory at z ~ 2, improving our understanding of the physics of intrinsic alignments.« less

Micro-beam Laue alignment of multi-reflection Bragg coherent diffraction imaging measurements

DOE PAGES

Hofmann, Felix; Phillips, Nicholas W.; Harder, Ross J.; ...

2017-08-08

Multi-reflection Bragg coherent diffraction imaging has the potential to allow three-dimensional (3D) resolved measurements of the full lattice strain tensor in specific micro-crystals. Until now such measurements were hampered by the need for laborious, time-intensive alignment procedures. Here, in this paper, a different approach is demonstrated, using micro-beam Laue X-ray diffraction to first determine the lattice orientation of the micro-crystal. This information is then used to rapidly align coherent diffraction measurements of three or more reflections from the crystal. Based on these, 3D strain and stress fields in the crystal are successfully determined. This approach is demonstrated on a focusedmore » ion beam milled micro-crystal from which six reflections could be measured. Since information from more than three independent reflections is available, the reliability of the phases retrieved from the coherent diffraction data can be assessed. Lastly, our results show that rapid, reliable 3D coherent diffraction measurements of the full lattice strain tensor in specific micro-crystals are now feasible and can be successfully carried out even in heavily distorted samples.« less

Micro-beam Laue alignment of multi-reflection Bragg coherent diffraction imaging measurements

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

Hofmann, Felix; Phillips, Nicholas W.; Harder, Ross J.

Multi-reflection Bragg coherent diffraction imaging has the potential to allow three-dimensional (3D) resolved measurements of the full lattice strain tensor in specific micro-crystals. Until now such measurements were hampered by the need for laborious, time-intensive alignment procedures. Here, in this paper, a different approach is demonstrated, using micro-beam Laue X-ray diffraction to first determine the lattice orientation of the micro-crystal. This information is then used to rapidly align coherent diffraction measurements of three or more reflections from the crystal. Based on these, 3D strain and stress fields in the crystal are successfully determined. This approach is demonstrated on a focusedmore » ion beam milled micro-crystal from which six reflections could be measured. Since information from more than three independent reflections is available, the reliability of the phases retrieved from the coherent diffraction data can be assessed. Lastly, our results show that rapid, reliable 3D coherent diffraction measurements of the full lattice strain tensor in specific micro-crystals are now feasible and can be successfully carried out even in heavily distorted samples.« less

Micro-beam Laue alignment of multi-reflection Bragg coherent diffraction imaging measurements.

PubMed

Hofmann, Felix; Phillips, Nicholas W; Harder, Ross J; Liu, Wenjun; Clark, Jesse N; Robinson, Ian K; Abbey, Brian

2017-09-01

Multi-reflection Bragg coherent diffraction imaging has the potential to allow three-dimensional (3D) resolved measurements of the full lattice strain tensor in specific micro-crystals. Until now such measurements were hampered by the need for laborious, time-intensive alignment procedures. Here a different approach is demonstrated, using micro-beam Laue X-ray diffraction to first determine the lattice orientation of the micro-crystal. This information is then used to rapidly align coherent diffraction measurements of three or more reflections from the crystal. Based on these, 3D strain and stress fields in the crystal are successfully determined. This approach is demonstrated on a focused ion beam milled micro-crystal from which six reflections could be measured. Since information from more than three independent reflections is available, the reliability of the phases retrieved from the coherent diffraction data can be assessed. Our results show that rapid, reliable 3D coherent diffraction measurements of the full lattice strain tensor in specific micro-crystals are now feasible and can be successfully carried out even in heavily distorted samples.

Micro-beam Laue Alignment of Multi-Reflection Bragg Coherent Diffraction Imaging Measurements

PubMed Central

Hofmann, Felix; Phillips, Nicholas W.; Harder, Ross J.; Liu, Wenjun; Clark, Jesse N.; Robinson, Ian K.; Abbey, Brian

2017-01-01

Multi-reflection Bragg coherent diffraction imaging has the potential to allow 3D resolved measurements of the full lattice strain tensor in specific micro-crystals. Until now such measurements were hampered by the need for laborious, time-intensive alignment procedures. Here we demonstrate a different approach, using micro-beam Laue X-ray diffraction to first determine the lattice orientation of the micro-crystal. This information is then used to rapidly align coherent diffraction measurements of three or more reflections from the crystal. Based on these, 3D strain and stress fields in the crystal are successfully determined. This approach is demonstrated on a focussed ion beam milled micro-crystal from which six reflections could be measured. Since information from more than three independent reflections is available, the reliability of the phases retrieved from the coherent diffraction data can be assessed. Our results show that rapid, reliable 3D coherent diffraction measurements of the full lattice strain tensor in specific micro-crystals are now feasible and can be successfully carried out even in heavily distorted samples. PMID:28862628

Effects of Orientation and Anisometry of Magnetic Resonance Imaging Acquisitions on Diffusion Tensor Imaging and Structural Connectomes.

PubMed

Tudela, Raúl; Muñoz-Moreno, Emma; López-Gil, Xavier; Soria, Guadalupe

2017-01-01

Diffusion-weighted imaging (DWI) quantifies water molecule diffusion within tissues and is becoming an increasingly used technique. However, it is very challenging as correct quantification depends on many different factors, ranging from acquisition parameters to a long pipeline of image processing. In this work, we investigated the influence of voxel geometry on diffusion analysis, comparing different acquisition orientations as well as isometric and anisometric voxels. Diffusion-weighted images of one rat brain were acquired with four different voxel geometries (one isometric and three anisometric in different directions) and three different encoding orientations (coronal, axial and sagittal). Diffusion tensor scalar measurements, tractography and the brain structural connectome were analyzed for each of the 12 acquisitions. The acquisition direction with respect to the main magnetic field orientation affected the diffusion results. When the acquisition slice-encoding direction was not aligned with the main magnetic field, there were more artifacts and a lower signal-to-noise ratio that led to less anisotropic tensors (lower fractional anisotropic values), producing poorer quality results. The use of anisometric voxels generated statistically significant differences in the values of diffusion metrics in specific regions. It also elicited differences in tract reconstruction and in different graph metric values describing the brain networks. Our results highlight the importance of taking into account the geometric aspects of acquisitions, especially when comparing diffusion data acquired using different geometries.

Anisotropic Mesoscale Eddy Transport in Ocean General Circulation Models

NASA Astrophysics Data System (ADS)

Reckinger, S. J.; Fox-Kemper, B.; Bachman, S.; Bryan, F.; Dennis, J.; Danabasoglu, G.

2014-12-01

Modern climate models are limited to coarse-resolution representations of large-scale ocean circulation that rely on parameterizations for mesoscale eddies. The effects of eddies are typically introduced by relating subgrid eddy fluxes to the resolved gradients of buoyancy or other tracers, where the proportionality is, in general, governed by an eddy transport tensor. The symmetric part of the tensor, which represents the diffusive effects of mesoscale eddies, is universally treated isotropically in general circulation models. Thus, only a single parameter, namely the eddy diffusivity, is used at each spatial and temporal location to impart the influence of mesoscale eddies on the resolved flow. However, the diffusive processes that the parameterization approximates, such as shear dispersion, potential vorticity barriers, oceanic turbulence, and instabilities, typically have strongly anisotropic characteristics. Generalizing the eddy diffusivity tensor for anisotropy extends the number of parameters to three: a major diffusivity, a minor diffusivity, and the principal axis of alignment. The Community Earth System Model (CESM) with the anisotropic eddy parameterization is used to test various choices for the newly introduced parameters, which are motivated by observations and the eddy transport tensor diagnosed from high resolution simulations. Simply setting the ratio of major to minor diffusivities to a value of five globally, while aligning the major axis along the flow direction, improves biogeochemical tracer ventilation and reduces global temperature and salinity biases. These effects can be improved even further by parameterizing the anisotropic transport mechanisms in the ocean.

Alignments of the galaxies in and around the Virgo cluster with the local velocity shear

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

Lee, Jounghun; Rey, Soo Chang; Kim, Suk, E-mail: jounghun@astro.snu.ac.kr

2014-08-10

Observational evidence is presented for the alignment between the cosmic sheet and the principal axis of the velocity shear field at the position of the Virgo cluster. The galaxies in and around the Virgo cluster from the Extended Virgo Cluster Catalog that was recently constructed by Kim et al. are used to determine the direction of the local sheet. The peculiar velocity field reconstructed from the Sloan Digital Sky Survey Data Release 7 is analyzed to estimate the local velocity shear tensor at the Virgo center. Showing first that the minor principal axis of the local velocity shear tensor ismore » almost parallel to the direction of the line of sight, we detect a clear signal of alignment between the positions of the Virgo satellites and the intermediate principal axis of the local velocity shear projected onto the plane of the sky. Furthermore, the dwarf satellites are found to appear more strongly aligned than their normal counterparts, which is interpreted as an indication of the following. (1) The normal satellites and the dwarf satellites fall in the Virgo cluster preferentially along the local filament and the local sheet, respectively. (2) The local filament is aligned with the minor principal axis of the local velocity shear while the local sheet is parallel to the plane spanned by the minor and intermediate principal axes. Our result is consistent with the recent numerical claim that the velocity shear is a good tracer of the cosmic web.« less

Spatial distribution of F-net moment tensors for the 2005 West Off Fukuoka Prefecture Earthquake determined by the extended method of the NIED F-net routine

NASA Astrophysics Data System (ADS)

Matsumoto, Takumi; Ito, Yoshihiro; Matsubayashi, Hirotoshi; Sekiguchi, Shoji

2006-01-01

The 2005 West Off Fukuoka Prefecture Earthquake with a Japan Meteorological Agency (JMA) magnitude (MJMA) of 7.0 occurred on March 20, 2005. We determined moment tensor solutions, using a surface wave with an extended method of the NIED F-net routine processing. The horizontal distance to the station is rounded to the nearest interval of 1 km, and the variance reduction approach is applied to a focal depth from 2 km with an interval of 1 km. We obtain the moment tensors of 101 events with (MJMA) exceeding 3.0 and spatial distribution of these moment tensors. The focal mechanism of aftershocks is mainly of the strike-slip type. The alignment of the epicenters in the rupture zone of the main-shock is oriented between N110°E and N130°E, which is close to the strike of the main-shock's moment tensor solutions (N122°E). These moment tensor solutions of intermediatesized aftershocks around the focal region represent basic and important information concerning earthquakes in investigating regional tectonic stress fields, source mechanisms and so on.

Tetrahedron deformation and alignment of perceived vorticity and strain in a turbulent flow

NASA Astrophysics Data System (ADS)

Pumir, Alain; Bodenschatz, Eberhard; Xu, Haitao

2013-03-01

We describe the structure and dynamics of turbulence by the scale-dependent perceived velocity gradient tensor as supported by following four tracers, i.e., fluid particles, that initially form a regular tetrahedron. We report results from experiments in a von Kármán swirling water flow and from numerical simulations of the incompressible Navier-Stokes equation. We analyze the statistics and the dynamics of the perceived rate of strain tensor and vorticity for initially regular tetrahedron of size r0 from the dissipative to the integral scale. Just as for the true velocity gradient, at any instant, the perceived vorticity is also preferentially aligned with the intermediate eigenvector of the perceived rate of strain. However, in the perceived rate of strain eigenframe fixed at a given time t = 0, the perceived vorticity evolves in time such as to align with the strongest eigendirection at t = 0. This also applies to the true velocity gradient. The experimental data at the higher Reynolds number suggests the existence of a self-similar regime in the inertial range. In particular, the dynamics of alignment of the perceived vorticity and strain can be rescaled by t0, the turbulence time scale of the flow when the scale r0 is in the inertial range. For smaller Reynolds numbers we found the dynamics to be scale dependent.

Intrinsic alignments of galaxies in the MassiveBlack-II simulation: Analysis of two-point statistics

DOE PAGES

Tenneti, Ananth; Singh, Sukhdeep; Mandelbaum, Rachel; ...

2015-03-11

The intrinsic alignment of galaxies with the large-scale density field in an important astrophysical contaminant in upcoming weak lensing surveys. We present detailed measurements of the galaxy intrinsic alignments and associated ellipticity-direction (ED) and projected shape (w g₊) correlation functions for galaxies in the cosmological hydrodynamic MassiveBlack-II (MB-II) simulation. We carefully assess the effects on galaxy shapes, misalignment of the stellar component with the dark matter shape and two-point statistics of iterative weighted (by mass and luminosity) definitions of the (reduced and unreduced) inertia tensor. We find that iterative procedures must be adopted for a reliable measurement of the reducedmore » tensor but that luminosity versus mass weighting has only negligible effects. Both ED and w g₊ correlations increase in amplitude with subhalo mass (in the range of 10¹⁰ – 6.0 X 10¹⁴h⁻¹ M ⊙), with a weak redshift dependence (from z = 1 to z = 0.06) at fixed mass. At z ~ 0.3, we predict a w g₊ that is in reasonable agreement with SDSS LRG measurements and that decreases in amplitude by a factor of ~ 5–18 for galaxies in the LSST survey. We also compared the intrinsic alignment of centrals and satellites, with clear detection of satellite radial alignments within the host halos. Finally, we show that w g₊ (using subhalos as tracers of density and w δ (using dark matter density) predictions from the simulations agree with that of non-linear alignment models (NLA) at scales where the 2-halo term dominates in the correlations (and tabulate associated NLA fitting parameters). The 1-halo term induces a scale dependent bias at small scales which is not modeled in the NLA model.« less

Intrinsic alignments of galaxies in the MassiveBlack-II simulation: analysis of two-point statistics

NASA Astrophysics Data System (ADS)

Tenneti, Ananth; Singh, Sukhdeep; Mandelbaum, Rachel; di Matteo, Tiziana; Feng, Yu; Khandai, Nishikanta

2015-04-01

The intrinsic alignment of galaxies with the large-scale density field is an important astrophysical contaminant in upcoming weak lensing surveys. We present detailed measurements of the galaxy intrinsic alignments and associated ellipticity-direction (ED) and projected shape (wg+) correlation functions for galaxies in the cosmological hydrodynamic MassiveBlack-II simulation. We carefully assess the effects on galaxy shapes, misalignment of the stellar component with the dark matter shape and two-point statistics of iterative weighted (by mass and luminosity) definitions of the (reduced and unreduced) inertia tensor. We find that iterative procedures must be adopted for a reliable measurement of the reduced tensor but that luminosity versus mass weighting has only negligible effects. Both ED and wg+ correlations increase in amplitude with subhalo mass (in the range of 1010-6.0 × 1014 h-1 M⊙), with a weak redshift dependence (from z = 1 to 0.06) at fixed mass. At z ˜ 0.3, we predict a wg+ that is in reasonable agreement with Sloan Digital Sky Survey luminous red galaxy measurements and that decreases in amplitude by a factor of ˜5-18 for galaxies in the Large Synoptic Survey Telescope survey. We also compared the intrinsic alignments of centrals and satellites, with clear detection of satellite radial alignments within their host haloes. Finally, we show that wg+ (using subhaloes as tracers of density) and wδ+ (using dark matter density) predictions from the simulations agree with that of non-linear alignment (NLA) models at scales where the two-halo term dominates in the correlations (and tabulate associated NLA fitting parameters). The one-halo term induces a scale-dependent bias at small scales which is not modelled in the NLA model.

Spacetime encodings. IV. The relationship between Weyl curvature and Killing tensors in stationary axisymmetric vacuum spacetimes

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

Brink, Jeandrew

The problem of obtaining an explicit representation for the fourth invariant of geodesic motion (generalized Carter constant) of an arbitrary stationary axisymmetric vacuum spacetime generated from an Ernst potential is considered. The coupling between the nonlocal curvature content of the spacetime as encoded in the Weyl tensor, and the existence of a Killing tensor is explored and a constructive, algebraic test for a fourth-order Killing tensor suggested. The approach used exploits the variables defined for the Baecklund transformations to clarify the relationship between Weyl curvature, constants of geodesic motion, expressed as Killing tensors, and the solution-generation techniques. A new symmetricmore » noncovariant formulation of the Killing equations is given. This formulation transforms the problem of looking for fourth-order Killing tensors in 4D into one of looking for four interlocking two-manifolds admitting fourth-order Killing tensors in 2D.« less

Geodesic-loxodromes for diffusion tensor interpolation and difference measurement.

PubMed

Kindlmann, Gordon; Estépar, Raúl San José; Niethammer, Marc; Haker, Steven; Westin, Carl-Fredrik

2007-01-01

In algorithms for processing diffusion tensor images, two common ingredients are interpolating tensors, and measuring the distance between them. We propose a new class of interpolation paths for tensors, termed geodesic-loxodromes, which explicitly preserve clinically important tensor attributes, such as mean diffusivity or fractional anisotropy, while using basic differential geometry to interpolate tensor orientation. This contrasts with previous Riemannian and Log-Euclidean methods that preserve the determinant. Path integrals of tangents of geodesic-loxodromes generate novel measures of over-all difference between two tensors, and of difference in shape and in orientation.

Integrability conditions for Killing-Yano tensors and conformal Killing-Yano tensors

NASA Astrophysics Data System (ADS)

Batista, Carlos

2015-01-01

The integrability conditions for the existence of a conformal Killing-Yano tensor of arbitrary order are worked out in all dimensions and expressed in terms of the Weyl tensor. As a consequence, the integrability conditions for the existence of a Killing-Yano tensor are also obtained. By means of such conditions, it is shown that in certain Einstein spaces one can use a conformal Killing-Yano tensor of order p to generate a Killing-Yano tensor of order (p -1 ) . Finally, it is proved that in maximally symmetric spaces the covariant derivative of a Killing-Yano tensor is a closed conformal Killing-Yano tensor and that every conformal Killing-Yano tensor is uniquely decomposed as the sum of a Killing-Yano tensor and a closed conformal Killing-Yano tensor.

Shear Wave Generation by Explosions in Anisotropic Crystalline Rock

NASA Astrophysics Data System (ADS)

Rogers-Martinez, M. A.; Sammis, C. G.; Stroujkova, A. F.

2015-12-01

The use of seismic waves to discriminate between earthquakes and underground explosions is complicated by the observation that explosions routinely radiate strong S waves. Whether these S waves are primarily generated by non-linear processes at the source, or by mode conversions and scattering along the path remains an open question. It has been demonstrated that S waves are generated at the source by any mechanism that breaks the spherical symmetry of the explosion. Examples of such mechanisms include tectonic shear stress, spall, and anisotropy in the emplacement medium. Many crystalline rock massifs are transversely isotropic because they contain aligned fractures over a range of scales from microfractures at the grain scale (called the rift) to regional sets of joints. In this study we use a micromechanical damage mechanics to model the fracture damage patterns and seismic radiation generated by explosions in a material in which the initial distribution of fractures has a preferred direction. Our simulations are compared with a set of field experiments in a granite quarry in Barre, VT conducted by New England Research and Weston Geophysical. Barre granite has a strong rift plane of aligned microfractures. Our model captures two important results of these field studies: 1) the spatial extent of rock fracture and generation of S waves depends on the burn-rate of the explosion and 2) the resultant damage is anisotropic with most damage occurring in the preferred direction of the microfractures (the rift plane in the granite). The physical reason damage is enhanced in the rift direction is that the mode I stress intensity factor is large for each fracture in the array of parallel fractures in the rift plane. Tensile opening on the rift plane plus sliding on the preexisting fractures make strong non-spherical contributions to the moment tensor in the far-field.

An anisotropic elastoplastic constitutive formulation generalised for orthotropic materials

NASA Astrophysics Data System (ADS)

Mohd Nor, M. K.; Ma'at, N.; Ho, C. S.

2018-03-01

This paper presents a finite strain constitutive model to predict a complex elastoplastic deformation behaviour that involves very high pressures and shockwaves in orthotropic materials using an anisotropic Hill's yield criterion by means of the evolving structural tensors. The yield surface of this hyperelastic-plastic constitutive model is aligned uniquely within the principal stress space due to the combination of Mandel stress tensor and a new generalised orthotropic pressure. The formulation is developed in the isoclinic configuration and allows for a unique treatment for elastic and plastic orthotropy. An isotropic hardening is adopted to define the evolution of plastic orthotropy. The important feature of the proposed hyperelastic-plastic constitutive model is the introduction of anisotropic effect in the Mie-Gruneisen equation of state (EOS). The formulation is further combined with Grady spall failure model to predict spall failure in the materials. The proposed constitutive model is implemented as a new material model in the Lawrence Livermore National Laboratory (LLNL)-DYNA3D code of UTHM's version, named Material Type 92 (Mat92). The combination of the proposed stress tensor decomposition and the Mie-Gruneisen EOS requires some modifications in the code to reflect the formulation of the generalised orthotropic pressure. The validation approach is also presented in this paper for guidance purpose. The \\varvec{ψ} tensor used to define the alignment of the adopted yield surface is first validated. This is continued with an internal validation related to elastic isotropic, elastic orthotropic and elastic-plastic orthotropic of the proposed formulation before a comparison against range of plate impact test data at 234, 450 and {895 ms}^{-1} impact velocities is performed. A good agreement is obtained in each test.

Reconstruction of interatomic vectors by principle component analysis of nuclear magnetic resonance data in multiple alignments

NASA Astrophysics Data System (ADS)

Hus, Jean-Christophe; Bruschweiler, Rafael

2002-07-01

A general method is presented for the reconstruction of interatomic vector orientations from nuclear magnetic resonance (NMR) spectroscopic data of tensor interactions of rank 2, such as dipolar coupling and chemical shielding anisotropy interactions, in solids and partially aligned liquid-state systems. The method, called PRIMA, is based on a principal component analysis of the covariance matrix of the NMR parameters collected for multiple alignments. The five nonzero eigenvalues and their eigenvectors efficiently allow the approximate reconstruction of the vector orientations of the underlying interactions. The method is demonstrated for an isotropic distribution of sample orientations as well as for finite sets of orientations and internuclear vectors encountered in protein systems.

A Hybrid Kinetic Model of Asymmetric Thin Current Sheets with Sheared Flows in a Collisionless Plasma

DTIC Science & Technology

2010-12-27

z are aligned with those of the usual Geocentric Sun - Earth (aSE) coordinates. In this frame, +x points from the Earth to the Sun , +y points out of...current sheet (box) in the solar wind. x, y, and z are aligned with the aSE coordinates, with +X pointing from the Earth toward the Sun , +y out of the...account the exact ion orbits and such properties as the anisotropic and nondiagonal pressure tensor and sheared ion flows. Figure 1a shows a schematic

Fine-scale features in the far-field of a turbulent jet

NASA Astrophysics Data System (ADS)

Buxton, Oliver; Ganapathisubramani, Bharathram

2008-11-01

The structure of a fully turbulent axisymmetric jet, at Reynolds number based on jet exit conditions of 5000, is investigated with cinematographic (1 kHz) stereoscopic PIV in a plane normal to the jet axis. Taylor's hypothesis is employed to calculate all three velocity gradients in the axial direction. The technique's resolution allows all terms of the velocity gradient tensor, hence strain rate tensor and kinetic energy dissipation, to be computed at each point within the plane. The data reveals that the vorticity field is dominated by high enstrophy tube-like structures. Conversely, the dissipation field appears to consist of sheet-like structures. Several criteria for isolating these strongly swirling vortical structures from the background turbulence were employed. One such technique involves isolating points in which the velocity gradient tensor has a real and a pair of complex conjugate eigenvectors. Once identified, the alignment of the various structures with relation to the vorticity vector and the real velocity gradient tensor eigenvector is investigated. The effect of the strain field on the geometry of the structures is also examined.

Dimension towers of SICs. I. Aligned SICs and embedded tight frames

NASA Astrophysics Data System (ADS)

Appleby, Marcus; Bengtsson, Ingemar; Dumitru, Irina; Flammia, Steven

2017-11-01

Algebraic number theory relates SIC-POVMs in dimension d > 3 to those in dimension d(d - 2). We define a SIC in dimension d(d - 2) to be aligned to a SIC in dimension d if and only if the squares of the overlap phases in dimension d appear as a subset of the overlap phases in dimension d(d - 2) in a specified way. We give 19 (mostly numerical) examples of aligned SICs. We conjecture that given any SIC in dimension d, there exists an aligned SIC in dimension d(d - 2). In all our examples, the aligned SIC has lower dimensional equiangular tight frames embedded in it. If d is odd so that a natural tensor product structure exists, we prove that the individual vectors in the aligned SIC have a very special entanglement structure, and the existence of the embedded tight frames follows as a theorem. If d - 2 is an odd prime number, we prove that a complete set of mutually unbiased bases can be obtained by reducing an aligned SIC to this dimension.

Ab initio elastic tensor of cubic Ti0.5Al0.5N alloys: Dependence of elastic constants on size and shape of the supercell model and their convergence

NASA Astrophysics Data System (ADS)

Tasnádi, Ferenc; Odén, M.; Abrikosov, Igor A.

2012-04-01

In this study we discuss the performance of the special quasirandom structure (SQS) method in predicting the elastic properties of B1 (rocksalt) Ti0.5Al0.5N alloy. We use a symmetry-based projection technique, which gives the closest cubic approximate of the elastic tensor and allows us to align the SQSs of different shapes and sizes for a comparison in modeling elastic tensors. We show that the derived closest cubic approximate of the elastic tensor converges faster with respect to SQS size than the elastic tensor itself. That establishes a less demanding computational strategy to achieve convergence for the elastic constants. We determine the cubic elastic constants (Cij) and Zener's type elastic anisotropy (A) of Ti0.5Al0.5N. Optimal supercells, which capture accurately both the configurational disorder and cubic symmetry of elastic tensor, result in C11=447 GPa, C12=158 GPa, and C44=203 GPa with 3% of error and A=1.40 with 6% of error. In addition, we establish the general importance of selecting proper SQS with symmetry arguments to reliably model elasticity of alloys. We suggest the calculation of nine elastic tensor elements: C11, C22, C33, C12, C13, C23, C44, C55, and C66, to analyze the performance of SQSs and predict elastic constants of cubic alloys. The described methodology is general enough to be extended for alloys with other symmetry at arbitrary composition.

The effect of longitudinal conductance variations on the ionospheric prompt penetration electric fields

NASA Astrophysics Data System (ADS)

Sazykin, S.; Wolf, R.; Spiro, R.; Fejer, B.

Ionospheric prompt penetration electric fields of magnetospheric origin, together with the atmospheric disturbance dynamo, represent the most important parameters controlling the storm-time dynamics of the low and mid-latitude ionosphere. These prompt penetration fields result from the disruption of region-2 field-aligned shielding currents during geomagnetically disturbed conditions. Penetration electric fields con- trol, to a large extent, the generation and development of equatorial spread-F plasma instabilities as well as other dynamic space weather phenomena in the ionosphere equatorward of the auroral zone. While modeling studies typically agree with average patterns of prompt penetration fields, experimental results suggest that longitudinal variations of the ionospheric con- ductivities play a non-negligible role in controlling spread-F phenomena, an effect that has not previously been modeled. We present first results of modeling prompt pene- tration electric fields using a version of the Rice Convection Model (RCM) that allows for longitudinal variations in the ionospheric conductance tensor. The RCM is a first- principles numerical ionosphere-magnetosphere coupling model that solves for the electric fields, field-aligned currents, and particle distributions in the ionosphere and inner/middle magnetosphere. We compare these new theoretical results with electric field observations.

Alignments of Dark Matter Halos with Large-scale Tidal Fields: Mass and Redshift Dependence

NASA Astrophysics Data System (ADS)

Chen, Sijie; Wang, Huiyuan; Mo, H. J.; Shi, Jingjing

2016-07-01

Large-scale tidal fields estimated directly from the distribution of dark matter halos are used to investigate how halo shapes and spin vectors are aligned with the cosmic web. The major, intermediate, and minor axes of halos are aligned with the corresponding tidal axes, and halo spin axes tend to be parallel with the intermediate axes and perpendicular to the major axes of the tidal field. The strengths of these alignments generally increase with halo mass and redshift, but the dependence is only on the peak height, ν \\equiv {δ }{{c}}/σ ({M}{{h}},z). The scaling relations of the alignment strengths with the value of ν indicate that the alignment strengths remain roughly constant when the structures within which the halos reside are still in a quasi-linear regime, but decreases as nonlinear evolution becomes more important. We also calculate the alignments in projection so that our results can be compared directly with observations. Finally, we investigate the alignments of tidal tensors on large scales, and use the results to understand alignments of halo pairs separated at various distances. Our results suggest that the coherent structure of the tidal field is the underlying reason for the alignments of halos and galaxies seen in numerical simulations and in observations.

Databases post-processing in Tensoral

NASA Technical Reports Server (NTRS)

Dresselhaus, Eliot

1994-01-01

The Center for Turbulent Research (CTR) post-processing effort aims to make turbulence simulations and data more readily and usefully available to the research and industrial communities. The Tensoral language, introduced in this document and currently existing in prototype form, is the foundation of this effort. Tensoral provides a convenient and powerful protocol to connect users who wish to analyze fluids databases with the authors who generate them. In this document we introduce Tensoral and its prototype implementation in the form of a user's guide. This guide focuses on use of Tensoral for post-processing turbulence databases. The corresponding document - the Tensoral 'author's guide' - which focuses on how authors can make databases available to users via the Tensoral system - is currently unwritten. Section 1 of this user's guide defines Tensoral's basic notions: we explain the class of problems at hand and how Tensoral abstracts them. Section 2 defines Tensoral syntax for mathematical expressions. Section 3 shows how these expressions make up Tensoral statements. Section 4 shows how Tensoral statements and expressions are embedded into other computer languages (such as C or Vectoral) to make Tensoral programs. We conclude with a complete example program.

Killing-Yano tensors of order n - 1

NASA Astrophysics Data System (ADS)

Batista, Carlos

2014-08-01

The properties of a Killing-Yano tensor of order n-1 in an n-dimensional manifold are investigated. The integrability conditions are worked out and all metrics admitting a Killing-Yano tensor of order n-1 are found. A connection between such tensors and a generalization of the concept of angular momentum is pointed out. A theorem on how to generate closed conformal Killing vectors using the symmetries of a manifold is proved and used to find all Killing-Yano tensors of order n-1 of a maximally symmetric space.

A Communication-Optimal Framework for Contracting Distributed Tensors

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

Rajbhandari, Samyam; NIkam, Akshay; Lai, Pai-Wei

Tensor contractions are extremely compute intensive generalized matrix multiplication operations encountered in many computational science fields, such as quantum chemistry and nuclear physics. Unlike distributed matrix multiplication, which has been extensively studied, limited work has been done in understanding distributed tensor contractions. In this paper, we characterize distributed tensor contraction algorithms on torus networks. We develop a framework with three fundamental communication operators to generate communication-efficient contraction algorithms for arbitrary tensor contractions. We show that for a given amount of memory per processor, our framework is communication optimal for all tensor contractions. We demonstrate performance and scalability of our frameworkmore » on up to 262,144 cores of BG/Q supercomputer using five tensor contraction examples.« less

Diffusion tensor analysis with invariant gradients and rotation tangents.

PubMed

Kindlmann, Gordon; Ennis, Daniel B; Whitaker, Ross T; Westin, Carl-Fredrik

2007-11-01

Guided by empirically established connections between clinically important tissue properties and diffusion tensor parameters, we introduce a framework for decomposing variations in diffusion tensors into changes in shape and orientation. Tensor shape and orientation both have three degrees-of-freedom, spanned by invariant gradients and rotation tangents, respectively. As an initial demonstration of the framework, we create a tunable measure of tensor difference that can selectively respond to shape and orientation. Second, to analyze the spatial gradient in a tensor volume (a third-order tensor), our framework generates edge strength measures that can discriminate between different neuroanatomical boundaries, as well as creating a novel detector of white matter tracts that are adjacent yet distinctly oriented. Finally, we apply the framework to decompose the fourth-order diffusion covariance tensor into individual and aggregate measures of shape and orientation covariance, including a direct approximation for the variance of tensor invariants such as fractional anisotropy.

Magnification effect of Kerr metric by configurations of collisionless particles in non-isotropic kinetic equilibria

NASA Astrophysics Data System (ADS)

Cremaschini, Claudio; Stuchlík, Zdeněk

2018-05-01

A test fluid composed of relativistic collisionless neutral particles in the background of Kerr metric is expected to generate non-isotropic equilibrium configurations in which the corresponding stress-energy tensor exhibits pressure and temperature anisotropies. This arises as a consequence of the constraints placed on single-particle dynamics by Killing tensor symmetries, leading to a peculiar non-Maxwellian functional form of the kinetic distribution function describing the continuum system. Based on this outcome, in this paper the generation of Kerr-like metric by collisionless N -body systems of neutral matter orbiting in the field of a rotating black hole is reported. The result is obtained in the framework of covariant kinetic theory by solving the Einstein equations in terms of an analytical perturbative treatment whereby the gravitational field is decomposed as a prescribed background metric tensor described by the Kerr solution plus a self-field correction. The latter one is generated by the uncharged fluid at equilibrium and satisfies the linearized Einstein equations having the non-isotropic stress-energy tensor as source term. It is shown that the resulting self-metric is again of Kerr type, providing a mechanism of magnification of the background metric tensor and its qualitative features.

Diffusion tensor optical coherence tomography

NASA Astrophysics Data System (ADS)

Marks, Daniel L.; Blackmon, Richard L.; Oldenburg, Amy L.

2018-01-01

In situ measurements of diffusive particle transport provide insight into tissue architecture, drug delivery, and cellular function. Analogous to diffusion-tensor magnetic resonance imaging (DT-MRI), where the anisotropic diffusion of water molecules is mapped on the millimeter scale to elucidate the fibrous structure of tissue, here we propose diffusion-tensor optical coherence tomography (DT-OCT) for measuring directional diffusivity and flow of optically scattering particles within tissue. Because DT-OCT is sensitive to the sub-resolution motion of Brownian particles as they are constrained by tissue macromolecules, it has the potential to quantify nanoporous anisotropic tissue structure at micrometer resolution as relevant to extracellular matrices, neurons, and capillaries. Here we derive the principles of DT-OCT, relating the detected optical signal from a minimum of six probe beams with the six unique diffusion tensor and three flow vector components. The optimal geometry of the probe beams is determined given a finite numerical aperture, and a high-speed hardware implementation is proposed. Finally, Monte Carlo simulations are employed to assess the ability of the proposed DT-OCT system to quantify anisotropic diffusion of nanoparticles in a collagen matrix, an extracellular constituent that is known to become highly aligned during tumor development.

Geometry of Lax pairs: Particle motion and Killing-Yano tensors

NASA Astrophysics Data System (ADS)

Cariglia, Marco; Frolov, Valeri P.; Krtouš, Pavel; Kubizňák, David

2013-01-01

A geometric formulation of the Lax pair equation on a curved manifold is studied using the phase-space formalism. The corresponding (covariantly conserved) Lax tensor is defined and the method of generation of constants of motion from it is discussed. It is shown that when the Hamilton equations of motion are used, the conservation of the Lax tensor translates directly to the well-known Lax pair equation, with one matrix identified with components of the Lax tensor and the other matrix constructed from the (metric) connection. A generalization to Clifford objects is also discussed. Nontrivial examples of Lax tensors for geodesic and charged particle motion are found in spacetimes admitting a hidden symmetry of Killing-Yano tensors.

Polarized two-photon photoselection in EGFP: Theory and experiment

NASA Astrophysics Data System (ADS)

Masters, T. A.; Marsh, R. J.; Blacker, T. S.; Armoogum, D. A.; Larijani, B.; Bain, A. J.

2018-04-01

In this work, we present a complete theoretical description of the excited state order created by two-photon photoselection from an isotropic ground state; this encompasses both the conventionally measured quadrupolar (K = 2) and the "hidden" degree of hexadecapolar (K = 4) transition dipole alignment, their dependence on the two-photon transition tensor and emission transition dipole moment orientation. Linearly and circularly polarized two-photon absorption (TPA) and time-resolved single- and two-photon fluorescence anisotropy measurements are used to determine the structure of the transition tensor in the deprotonated form of enhanced green fluorescent protein. For excitation wavelengths between 800 nm and 900 nm, TPA is best described by a single element, almost completely diagonal, two-dimensional (planar) transition tensor whose principal axis is collinear to that of the single-photon S0 → S1 transition moment. These observations are in accordance with assignments of the near-infrared two-photon absorption band in fluorescent proteins to a vibronically enhanced S0 → S1 transition.

Polarized two-photon photoselection in EGFP: Theory and experiment.

PubMed

Masters, T A; Marsh, R J; Blacker, T S; Armoogum, D A; Larijani, B; Bain, A J

2018-04-07

In this work, we present a complete theoretical description of the excited state order created by two-photon photoselection from an isotropic ground state; this encompasses both the conventionally measured quadrupolar (K = 2) and the "hidden" degree of hexadecapolar (K = 4) transition dipole alignment, their dependence on the two-photon transition tensor and emission transition dipole moment orientation. Linearly and circularly polarized two-photon absorption (TPA) and time-resolved single- and two-photon fluorescence anisotropy measurements are used to determine the structure of the transition tensor in the deprotonated form of enhanced green fluorescent protein. For excitation wavelengths between 800 nm and 900 nm, TPA is best described by a single element, almost completely diagonal, two-dimensional (planar) transition tensor whose principal axis is collinear to that of the single-photon S 0 → S 1 transition moment. These observations are in accordance with assignments of the near-infrared two-photon absorption band in fluorescent proteins to a vibronically enhanced S 0 → S 1 transition.

Gravitational body forces focus North American intraplate earthquakes

USGS Publications Warehouse

Levandowski, William Brower; Zellman, Mark; Briggs, Richard

2017-01-01

Earthquakes far from tectonic plate boundaries generally exploit ancient faults, but not all intraplate faults are equally active. The North American Great Plains exemplify such intraplate earthquake localization, with both natural and induced seismicity generally clustered in discrete zones. Here we use seismic velocity, gravity and topography to generate a 3D lithospheric density model of the region; subsequent finite-element modelling shows that seismicity focuses in regions of high-gravity-derived deviatoric stress. Furthermore, predicted principal stress directions generally align with those observed independently in earthquake moment tensors and borehole breakouts. Body forces therefore appear to control the state of stress and thus the location and style of intraplate earthquakes in the central United States with no influence from mantle convection or crustal weakness necessary. These results show that mapping where gravitational body forces encourage seismicity is crucial to understanding and appraising intraplate seismic hazard.

Gravitational body forces focus North American intraplate earthquakes

PubMed Central

Levandowski, Will; Zellman, Mark; Briggs, Rich

2017-01-01

Earthquakes far from tectonic plate boundaries generally exploit ancient faults, but not all intraplate faults are equally active. The North American Great Plains exemplify such intraplate earthquake localization, with both natural and induced seismicity generally clustered in discrete zones. Here we use seismic velocity, gravity and topography to generate a 3D lithospheric density model of the region; subsequent finite-element modelling shows that seismicity focuses in regions of high-gravity-derived deviatoric stress. Furthermore, predicted principal stress directions generally align with those observed independently in earthquake moment tensors and borehole breakouts. Body forces therefore appear to control the state of stress and thus the location and style of intraplate earthquakes in the central United States with no influence from mantle convection or crustal weakness necessary. These results show that mapping where gravitational body forces encourage seismicity is crucial to understanding and appraising intraplate seismic hazard. PMID:28211459

Planes of satellite galaxies and the cosmic web

NASA Astrophysics Data System (ADS)

Libeskind, Noam I.; Hoffman, Yehuda; Tully, R. Brent; Courtois, Helene M.; Pomarède, Daniel; Gottlöber, Stefan; Steinmetz, Matthias

2015-09-01

Recent observational studies have demonstrated that the majority of satellite galaxies tend to orbit their hosts on highly flattened, vast, possibly corotating planes. Two nearly parallel planes of satellites have been confirmed around the M31 galaxy and around the Centaurus A galaxy, while the Milky Way also sports a plane of satellites. It has been argued that such an alignment of satellites on vast planes is unexpected in the standard Λ cold dark matter (ΛCDM) model of cosmology if not even in contradiction to its generic predictions. Guided by ΛCDM numerical simulations, which suggest that satellites are channelled towards hosts along the axis of the slowest collapse as dictated by the ambient velocity shear tensor, we re-examine the planes of local satellites systems within the framework of the local shear tensor derived from the Cosmicflows-2 data set. The analysis reveals that the Local Group and Centaurus A reside in a filament stretched by the Virgo cluster and compressed by the expansion of the Local Void. Four out of five thin planes of satellite galaxies are indeed closely aligned with the axis of compression induced by the Local Void. Being the less massive system, the moderate misalignment of the Milky Way's satellite plane can likely be ascribed to its greater susceptibility to tidal torques, as suggested by numerical simulations. The alignment of satellite systems in the local Universe with the ambient shear field is thus in general agreement with predictions of the ΛCDM model.

Aspects of the Antisymmetric Tensor Field

NASA Astrophysics Data System (ADS)

Lahiri, Amitabha

1991-02-01

With the possible exception of gravitation, fundamental interactions are generally described by theories of point particles interacting via massless gauge fields. Since the advent of string theories the picture of physical interaction has changed to accommodate one in which extended objects interact with each other. The generalization of the gauge theories to extended objects leads to theories of antisymmetric tensor fields. At scales corresponding to present-day laboratory experiments one expects to see only point particles, their interactions modified by the presence of antisymmetric tensor fields in the theory. Therefore, in order to establish the validity of any theory with antisymmetric tensor fields one needs to look for manifestations of these fields at low energies. The principal problem of gauge theories is the failure to provide a suitable explanation for the generation of masses for the fields in the theory. While there is a known mechanism (spontaneous symmetry breaking) for generating masses for both the matter fields and the gauge fields, the lack of experimental evidence in support of an elementary scalar field suggests that one look for alternative ways of generating masses for the fields. The interaction of gauge fields with an antisymmetric tensor field seems to be an attractive way of doing so, especially since all indications point to the possibility that there will be no remnant degrees of freedom. On the other hand the interaction of such a field with black holes suggest an independent way of verifying the existence of such fields. In this dissertation the origins of the antisymmetric tensor field are discussed in terms of string theory. The interaction of black holes with such a field is discussed next. The last chapter discusses the effects of an antisymmetric tensor field on quantum electrodynamics when the fields are minimally coupled.

The spectral element method (SEM) on variable-resolution grids: evaluating grid sensitivity and resolution-aware numerical viscosity

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

Guba, O.; Taylor, M. A.; Ullrich, P. A.

2014-11-27

We evaluate the performance of the Community Atmosphere Model's (CAM) spectral element method on variable-resolution grids using the shallow-water equations in spherical geometry. We configure the method as it is used in CAM, with dissipation of grid scale variance, implemented using hyperviscosity. Hyperviscosity is highly scale selective and grid independent, but does require a resolution-dependent coefficient. For the spectral element method with variable-resolution grids and highly distorted elements, we obtain the best results if we introduce a tensor-based hyperviscosity with tensor coefficients tied to the eigenvalues of the local element metric tensor. The tensor hyperviscosity is constructed so that, formore » regions of uniform resolution, it matches the traditional constant-coefficient hyperviscosity. With the tensor hyperviscosity, the large-scale solution is almost completely unaffected by the presence of grid refinement. This later point is important for climate applications in which long term climatological averages can be imprinted by stationary inhomogeneities in the truncation error. We also evaluate the robustness of the approach with respect to grid quality by considering unstructured conforming quadrilateral grids generated with a well-known grid-generating toolkit and grids generated by SQuadGen, a new open source alternative which produces lower valence nodes.« less

The spectral element method on variable resolution grids: evaluating grid sensitivity and resolution-aware numerical viscosity

DOE PAGES

Guba, O.; Taylor, M. A.; Ullrich, P. A.; ...

2014-06-25

We evaluate the performance of the Community Atmosphere Model's (CAM) spectral element method on variable resolution grids using the shallow water equations in spherical geometry. We configure the method as it is used in CAM, with dissipation of grid scale variance implemented using hyperviscosity. Hyperviscosity is highly scale selective and grid independent, but does require a resolution dependent coefficient. For the spectral element method with variable resolution grids and highly distorted elements, we obtain the best results if we introduce a tensor-based hyperviscosity with tensor coefficients tied to the eigenvalues of the local element metric tensor. The tensor hyperviscosity ismore » constructed so that for regions of uniform resolution it matches the traditional constant coefficient hyperviscsosity. With the tensor hyperviscosity the large scale solution is almost completely unaffected by the presence of grid refinement. This later point is important for climate applications where long term climatological averages can be imprinted by stationary inhomogeneities in the truncation error. We also evaluate the robustness of the approach with respect to grid quality by considering unstructured conforming quadrilateral grids generated with a well-known grid-generating toolkit and grids generated by SQuadGen, a new open source alternative which produces lower valence nodes.« less

Chapter 5. Hidden Symmetry and Exact Solutions in Einstein Gravity

NASA Astrophysics Data System (ADS)

Yasui, Y.; Houri, T.

Conformal Killing-Yano tensors are introduced as ageneralization of Killing vectors. They describe symmetries of higher-dimensional rotating black holes. In particular, a rank-2 closed conformal Killing-Yano tensor generates the tower of both hidden symmetries and isometries. We review a classification of higher-dimensional spacetimes admitting such a tensor, and present exact solutions to the Einstein equations for these spacetimes.

Optimizing Tensor Contraction Expressions for Hybrid CPU-GPU Execution

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

Ma, Wenjing; Krishnamoorthy, Sriram; Villa, Oreste

2013-03-01

Tensor contractions are generalized multidimensional matrix multiplication operations that widely occur in quantum chemistry. Efficient execution of tensor contractions on Graphics Processing Units (GPUs) requires several challenges to be addressed, including index permutation and small dimension-sizes reducing thread block utilization. Moreover, to apply the same optimizations to various expressions, we need a code generation tool. In this paper, we present our approach to automatically generate CUDA code to execute tensor contractions on GPUs, including management of data movement between CPU and GPU. To evaluate our tool, GPU-enabled code is generated for the most expensive contractions in CCSD(T), a key coupledmore » cluster method, and incorporated into NWChem, a popular computational chemistry suite. For this method, we demonstrate speedup over a factor of 8.4 using one GPU (instead of one core per node) and over 2.6 when utilizing the entire system using hybrid CPU+GPU solution with 2 GPUs and 5 cores (instead of 7 cores per node). Finally, we analyze the implementation behavior on future GPU systems.« less

Three-dimensional model-based object recognition and segmentation in cluttered scenes.

PubMed

Mian, Ajmal S; Bennamoun, Mohammed; Owens, Robyn

2006-10-01

Viewpoint independent recognition of free-form objects and their segmentation in the presence of clutter and occlusions is a challenging task. We present a novel 3D model-based algorithm which performs this task automatically and efficiently. A 3D model of an object is automatically constructed offline from its multiple unordered range images (views). These views are converted into multidimensional table representations (which we refer to as tensors). Correspondences are automatically established between these views by simultaneously matching the tensors of a view with those of the remaining views using a hash table-based voting scheme. This results in a graph of relative transformations used to register the views before they are integrated into a seamless 3D model. These models and their tensor representations constitute the model library. During online recognition, a tensor from the scene is simultaneously matched with those in the library by casting votes. Similarity measures are calculated for the model tensors which receive the most votes. The model with the highest similarity is transformed to the scene and, if it aligns accurately with an object in the scene, that object is declared as recognized and is segmented. This process is repeated until the scene is completely segmented. Experiments were performed on real and synthetic data comprised of 55 models and 610 scenes and an overall recognition rate of 95 percent was achieved. Comparison with the spin images revealed that our algorithm is superior in terms of recognition rate and efficiency.

Synchrotron X-ray microbeam diffraction measurements of full elastic long range internal strain and stress tensors in commercial-purity aluminum processed by multiple passes of equal-channel angular pressing

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

Phan, Thien Q.; Levine, Lyle E.; Lee, I-Fang

Synchrotron X-ray microbeam diffraction was used to measure the full elastic long range internal strain and stress tensors of low dislocation density regions within the submicrometer grain/subgrain structure of equal-channel angular pressed (ECAP) aluminum alloy AA1050 after 1, 2, and 8 passes using route B C. This is the first time that full tensors were measured in plastically deformed metals at this length scale. The maximum (most tensile or least compressive) principal elastic strain directions for the unloaded 1 pass sample for the grain/subgrain interiors align well with the pressing direction, and are more random for the 2 and 8more » pass samples. The measurements reported here indicate that the local stresses and strains become increasingly isotropic (homogenized) with increasing ECAP passes using route BC. The average maximum (in magnitude) LRISs are -0.43 σ a for 1 pass, -0.44 σ a for 2 pass, and 0.14 σ a for the 8 pass sample. Furthermore, these LRISs are larger than those reported previously because those earlier measurements were unable to measure the full stress tensor. Significantly, the measured stresses are inconsistent with the two-component composite model.« less

Modelling Dynamic Behaviour and Spall Failure of Aluminium Alloy AA7010

NASA Astrophysics Data System (ADS)

Ma'at, N.; Nor, M. K. Mohd; Ismail, A. E.; Kamarudin, K. A.; Jamian, S.; Ibrahim, M. N.; Awang, M. K.

2017-10-01

A finite strain constitutive model to predict the dynamic deformation behaviour of Aluminium Alloy 7010 including shockwaves and spall failure is developed in this work. The important feature of this newly hyperelastic-plastic constitutive formulation is a new Mandel stress tensor formulated using new generalized orthotropic pressure. This tensor is combined with a shock equation of state (EOS) and Grady spall failure. The Hill’s yield criterion is adopted to characterize plastic orthotropy by means of the evolving structural tensors that is defined in the isoclinic configuration. This material model was developed and integration into elastic and plastic parts. The elastic anisotropy is taken into account through the newly stress tensor decomposition of a generalized orthotropic pressure. Plastic anisotropy is considered through yield surface and an isotropic hardening defined in a unique alignment of deviatoric plane within the stress space. To test its ability to describe shockwave propagation and spall failure, the new material model was implemented into the LLNL-DYNA3D code of UTHM’s. The capability of this newly constitutive model were compared against published experimental data of Plate Impact Test at 234m/s, 450m/s and 895m/s impact velocities. A good agreement is obtained between experimental and simulation in each test.

Synchrotron X-ray microbeam diffraction measurements of full elastic long range internal strain and stress tensors in commercial-purity aluminum processed by multiple passes of equal-channel angular pressing

DOE PAGES

Phan, Thien Q.; Levine, Lyle E.; Lee, I-Fang; ...

2016-04-23

Synchrotron X-ray microbeam diffraction was used to measure the full elastic long range internal strain and stress tensors of low dislocation density regions within the submicrometer grain/subgrain structure of equal-channel angular pressed (ECAP) aluminum alloy AA1050 after 1, 2, and 8 passes using route B C. This is the first time that full tensors were measured in plastically deformed metals at this length scale. The maximum (most tensile or least compressive) principal elastic strain directions for the unloaded 1 pass sample for the grain/subgrain interiors align well with the pressing direction, and are more random for the 2 and 8more » pass samples. The measurements reported here indicate that the local stresses and strains become increasingly isotropic (homogenized) with increasing ECAP passes using route BC. The average maximum (in magnitude) LRISs are -0.43 σ a for 1 pass, -0.44 σ a for 2 pass, and 0.14 σ a for the 8 pass sample. Furthermore, these LRISs are larger than those reported previously because those earlier measurements were unable to measure the full stress tensor. Significantly, the measured stresses are inconsistent with the two-component composite model.« less

Computational modeling for prediction of the shear stress of three-dimensional isotropic and aligned fiber networks.

PubMed

Park, Seungman

2017-09-01

Interstitial flow (IF) is a creeping flow through the interstitial space of the extracellular matrix (ECM). IF plays a key role in diverse biological functions, such as tissue homeostasis, cell function and behavior. Currently, most studies that have characterized IF have focused on the permeability of ECM or shear stress distribution on the cells, but less is known about the prediction of shear stress on the individual fibers or fiber networks despite its significance in the alignment of matrix fibers and cells observed in fibrotic or wound tissues. In this study, I developed a computational model to predict shear stress for different structured fibrous networks. To generate isotropic models, a random growth algorithm and a second-order orientation tensor were employed. Then, a three-dimensional (3D) solid model was created using computer-aided design (CAD) software for the aligned models (i.e., parallel, perpendicular and cubic models). Subsequently, a tetrahedral unstructured mesh was generated and flow solutions were calculated by solving equations for mass and momentum conservation for all models. Through the flow solutions, I estimated permeability using Darcy's law. Average shear stress (ASS) on the fibers was calculated by averaging the wall shear stress of the fibers. By using nonlinear surface fitting of permeability, viscosity, velocity, porosity and ASS, I devised new computational models. Overall, the developed models showed that higher porosity induced higher permeability, as previous empirical and theoretical models have shown. For comparison of the permeability, the present computational models were matched well with previous models, which justify our computational approach. ASS tended to increase linearly with respect to inlet velocity and dynamic viscosity, whereas permeability was almost the same. Finally, the developed model nicely predicted the ASS values that had been directly estimated from computational fluid dynamics (CFD). The present computational models will provide new tools for predicting accurate functional properties and designing fibrous porous materials, thereby significantly advancing tissue engineering. Copyright © 2017 Elsevier B.V. All rights reserved.

Mesoscopic model for the viscosities of nematic liquid crystals.

PubMed

Chrzanowska, A; Kröger, M; Sellers, S

1999-10-01

Based on the definition of the mesoscopic concept by Blenk et al. [Physica A 174, 119 (1991); J. Noneq. Therm. 16, 67 (1991); Mol. Cryst. Liq. Cryst. 204, 133 (1991)] an approach to calculate the Leslie viscosity coefficients for nematic liquid crystals is presented. The approach rests upon the mesoscopic stress tensor, whose structure is assumed similar to the macroscopic Leslie viscous stress. The proposed form is also the main dissipation part of the mesoscopic Navier-Stokes equation. On the basis of the correspondence between microscopic and mesoscopic scales a mean-field mesoscopic potential is introduced. It allows us to obtain the stress tensor angular velocity of the free rotating molecules with the help of the orientational Fokker-Planck equation. The macroscopic stress tensor is calculated as an average of the mesoscopic counterpart. Appropriate relations among mesoscopic viscosities have been found. The mesoscopic analysis results are shown to be consistent with the diffusional model of Kuzuu-Doi and Osipov-Terentjev with the exception of the shear viscosity alpha(4). In the nematic phase alpha(4) is shown to have two contributions: isotropic and nematic. There exists an indication that the influence of the isotropic part is dominant over the nematic part. The so-called microscopic stress tensor used in the microscopic theories is shown to be the mean-field potential-dependent representation of the mesoscopic stress tensor. In the limiting case of total alignment the Leslie coefficients are estimated for the diffusional and mesoscopic models. They are compared to the results of the affine transformation model of the perfectly ordered systems. This comparison shows disagreement concerning the rotational viscosity, whereas the coefficients characteristic for the symmetric part of the viscous stress tensor remain the same. The difference is caused by the hindered diffusion in the affine model case.

Metal alkyls programmed to generate metal alkylidenes by α-H abstraction: prognosis from NMR chemical shift† †Electronic supplementary information (ESI) available: Experimental and computational details, NMR spectra, results of NMR calculations and NCS analysis, graphical representation of shielding tensors, molecular orbital diagrams of selected compounds, optimized structures for all calculated species. See DOI: 10.1039/c7sc05039a

PubMed Central

Gordon, Christopher P.; Yamamoto, Keishi; Searles, Keith; Shirase, Satoru

2018-01-01

Metal alkylidenes, which are key organometallic intermediates in reactions such as olefination or alkene and alkane metathesis, are typically generated from metal dialkyl compounds [M](CH2R)2 that show distinctively deshielded chemical shifts for their α-carbons. Experimental solid-state NMR measurements combined with DFT/ZORA calculations and a chemical shift tensor analysis reveal that this remarkable deshielding originates from an empty metal d-orbital oriented in the M–Cα–Cα′ plane, interacting with the Cα p-orbital lying in the same plane. This π-type interaction inscribes some alkylidene character into Cα that favors alkylidene generation via α-H abstraction. The extent of the deshielding and the anisotropy of the alkyl chemical shift tensors distinguishes [M](CH2R)2 compounds that form alkylidenes from those that do not, relating the reactivity to molecular orbitals of the respective molecules. The α-carbon chemical shifts and tensor orientations thus predict the reactivity of metal alkyl compounds towards alkylidene generation. PMID:29675237

The place of the Local Group in the cosmic web

NASA Astrophysics Data System (ADS)

Forero-Romero, Jaime E.; González, Roberto

2016-10-01

We use the Bolshoi Simulation to find the most probable location of the Local Group (LG) in the cosmic web. Our LG simulacra are pairs of halos with isolation and kinematic properties consistent with observations. The cosmic web is defined using a tidal tensor approach. We find that the LG's preferred location is regions with a dark matter overdensity close to the cosmic average. This makes filaments and sheets the preferred environment. We also find a strong alignment between the LG and the cosmic web. The orbital angular momentum is preferentially perpendicular to the smallest tidal eigenvector, while the vector connecting the two halos is strongly aligned along the the smallest tidal eigenvector and perpendicular to the largest tidal eigenvector; the pair lies and moves along filaments and sheets. We do not find any evidence for an alignment between the spin of each halo in the pair and the cosmic web.

Tensoral for post-processing users and simulation authors

NASA Technical Reports Server (NTRS)

Dresselhaus, Eliot

1993-01-01

The CTR post-processing effort aims to make turbulence simulations and data more readily and usefully available to the research and industrial communities. The Tensoral language, which provides the foundation for this effort, is introduced here in the form of a user's guide. The Tensoral user's guide is presented in two main sections. Section one acts as a general introduction and guides database users who wish to post-process simulation databases. Section two gives a brief description of how database authors and other advanced users can make simulation codes and/or the databases they generate available to the user community via Tensoral database back ends. The two-part structure of this document conforms to the two-level design structure of the Tensoral language. Tensoral has been designed to be a general computer language for performing tensor calculus and statistics on numerical data. Tensoral's generality allows it to be used for stand-alone native coding of high-level post-processing tasks (as described in section one of this guide). At the same time, Tensoral's specialization to a minute task (namely, to numerical tensor calculus and statistics) allows it to be easily embedded into applications written partly in Tensoral and partly in other computer languages (here, C and Vectoral). Embedded Tensoral, aimed at advanced users for more general coding (e.g. of efficient simulations, for interfacing with pre-existing software, for visualization, etc.), is described in section two of this guide.

Quantitative characterization of collagen in the fibrotic capsule surrounding implanted polymeric microparticles through second harmonic generation imaging

DOE PAGES

Akilbekova, Dana; Bratlie, Kaitlin M.; Abraham, Thomas

2015-06-30

The collagenous capsule formed around an implant will ultimately determine the nature of its in vivo fate. To provide a better understanding of how surface modifications can alter the collagen orientation and composition in the fibrotic capsule, we used second harmonic generation (SHG) microscopy to evaluate collagen organization and structure generated in mice subcutaneously injected with chemically functionalized polystyrene particles. SHG is sensitive to the orientation of a molecule, making it a powerful tool for measuring the alignment of collagen fibers. Additionally, SHG arises from the second order susceptibility of the interrogated molecule in response to the electric field. Variationmore » in these tensor components distinguishes different molecular sources of SHG, providing collagen type specificity. Here, we demonstrated the ability of SHG to differentiate collagen type I and type III quantitatively and used this method to examine fibrous capsules of implanted polystyrene particles. Data presented in this work shows a wide range of collagen fiber orientations and collagen compositions in response to surface functionalized polystyrene particles. Dimethylamino functionalized particles were able to form a thin collagenous matrix resembling healthy skin. These findings have the potential to improve the fundamental understanding of how material properties influence collagen organization and composition quantitatively.« less

Quantitative Characterization of Collagen in the Fibrotic Capsule Surrounding Implanted Polymeric Microparticles through Second Harmonic Generation Imaging.

PubMed

Akilbekova, Dana; Bratlie, Kaitlin M

2015-01-01

The collagenous capsule formed around an implant will ultimately determine the nature of its in vivo fate. To provide a better understanding of how surface modifications can alter the collagen orientation and composition in the fibrotic capsule, we used second harmonic generation (SHG) microscopy to evaluate collagen organization and structure generated in mice subcutaneously injected with chemically functionalized polystyrene particles. SHG is sensitive to the orientation of a molecule, making it a powerful tool for measuring the alignment of collagen fibers. Additionally, SHG arises from the second order susceptibility of the interrogated molecule in response to the electric field. Variation in these tensor components distinguishes different molecular sources of SHG, providing collagen type specificity. Here, we demonstrated the ability of SHG to differentiate collagen type I and type III quantitatively and used this method to examine fibrous capsules of implanted polystyrene particles. Data presented in this work shows a wide range of collagen fiber orientations and collagen compositions in response to surface functionalized polystyrene particles. Dimethylamino functionalized particles were able to form a thin collagenous matrix resembling healthy skin. These findings have the potential to improve the fundamental understanding of how material properties influence collagen organization and composition quantitatively.

Quantitative Characterization of Collagen in the Fibrotic Capsule Surrounding Implanted Polymeric Microparticles through Second Harmonic Generation Imaging

PubMed Central

Akilbekova, Dana; Bratlie, Kaitlin M.

2015-01-01

The collagenous capsule formed around an implant will ultimately determine the nature of its in vivo fate. To provide a better understanding of how surface modifications can alter the collagen orientation and composition in the fibrotic capsule, we used second harmonic generation (SHG) microscopy to evaluate collagen organization and structure generated in mice subcutaneously injected with chemically functionalized polystyrene particles. SHG is sensitive to the orientation of a molecule, making it a powerful tool for measuring the alignment of collagen fibers. Additionally, SHG arises from the second order susceptibility of the interrogated molecule in response to the electric field. Variation in these tensor components distinguishes different molecular sources of SHG, providing collagen type specificity. Here, we demonstrated the ability of SHG to differentiate collagen type I and type III quantitatively and used this method to examine fibrous capsules of implanted polystyrene particles. Data presented in this work shows a wide range of collagen fiber orientations and collagen compositions in response to surface functionalized polystyrene particles. Dimethylamino functionalized particles were able to form a thin collagenous matrix resembling healthy skin. These findings have the potential to improve the fundamental understanding of how material properties influence collagen organization and composition quantitatively. PMID:26125551

Quantitative characterization of collagen in the fibrotic capsule surrounding implanted polymeric microparticles through second harmonic generation imaging

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

Akilbekova, Dana; Bratlie, Kaitlin M.; Abraham, Thomas

The collagenous capsule formed around an implant will ultimately determine the nature of its in vivo fate. To provide a better understanding of how surface modifications can alter the collagen orientation and composition in the fibrotic capsule, we used second harmonic generation (SHG) microscopy to evaluate collagen organization and structure generated in mice subcutaneously injected with chemically functionalized polystyrene particles. SHG is sensitive to the orientation of a molecule, making it a powerful tool for measuring the alignment of collagen fibers. Additionally, SHG arises from the second order susceptibility of the interrogated molecule in response to the electric field. Variationmore » in these tensor components distinguishes different molecular sources of SHG, providing collagen type specificity. Here, we demonstrated the ability of SHG to differentiate collagen type I and type III quantitatively and used this method to examine fibrous capsules of implanted polystyrene particles. Data presented in this work shows a wide range of collagen fiber orientations and collagen compositions in response to surface functionalized polystyrene particles. Dimethylamino functionalized particles were able to form a thin collagenous matrix resembling healthy skin. These findings have the potential to improve the fundamental understanding of how material properties influence collagen organization and composition quantitatively.« less

Matrix product density operators: Renormalization fixed points and boundary theories

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

Cirac, J.I.; Pérez-García, D., E-mail: dperezga@ucm.es; ICMAT, Nicolas Cabrera, Campus de Cantoblanco, 28049 Madrid

We consider the tensors generating matrix product states and density operators in a spin chain. For pure states, we revise the renormalization procedure introduced in (Verstraete et al., 2005) and characterize the tensors corresponding to the fixed points. We relate them to the states possessing zero correlation length, saturation of the area law, as well as to those which generate ground states of local and commuting Hamiltonians. For mixed states, we introduce the concept of renormalization fixed points and characterize the corresponding tensors. We also relate them to concepts like finite correlation length, saturation of the area law, as well asmore » to those which generate Gibbs states of local and commuting Hamiltonians. One of the main result of this work is that the resulting fixed points can be associated to the boundary theories of two-dimensional topological states, through the bulk-boundary correspondence introduced in (Cirac et al., 2011).« less

Inference of segmented color and texture description by tensor voting.

PubMed

Jia, Jiaya; Tang, Chi-Keung

2004-06-01

A robust synthesis method is proposed to automatically infer missing color and texture information from a damaged 2D image by (N)D tensor voting (N > 3). The same approach is generalized to range and 3D data in the presence of occlusion, missing data and noise. Our method translates texture information into an adaptive (N)D tensor, followed by a voting process that infers noniteratively the optimal color values in the (N)D texture space. A two-step method is proposed. First, we perform segmentation based on insufficient geometry, color, and texture information in the input, and extrapolate partitioning boundaries by either 2D or 3D tensor voting to generate a complete segmentation for the input. Missing colors are synthesized using (N)D tensor voting in each segment. Different feature scales in the input are automatically adapted by our tensor scale analysis. Results on a variety of difficult inputs demonstrate the effectiveness of our tensor voting approach.

Progressive Stereo Locking (PSL): A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and Other Small Molecules.

PubMed

Cornilescu, Gabriel; Ramos Alvarenga, René F; Wyche, Thomas P; Bugni, Tim S; Gil, Roberto R; Cornilescu, Claudia C; Westler, William M; Markley, John L; Schwieters, Charles D

2017-08-18

Establishing the relative configuration of a bioactive natural product represents the most challenging part in determining its structure. Residual dipolar couplings (RDCs) are sensitive probes of the relative spatial orientation of internuclear vectors. We adapted a force field structure calculation methodology to allow free sampling of both R and S configurations of the stereocenters of interest. The algorithm uses a floating alignment tensor in a simulated annealing protocol to identify the conformations and configurations that best fit experimental RDC and distance restraints (from NOE and J-coupling data). A unique configuration (for rigid molecules) or a very small number of configurations (for less rigid molecules) of the structural models having the lowest chiral angle energies and reasonable magnitudes of the alignment tensor are provided as the best predictions of the unknown configuration. For highly flexible molecules, the progressive locking of their stereocenters into their statistically dominant R or S state dramatically reduces the number of possible relative configurations. The result is verified by checking that the same configuration is obtained by initiating the locking from different regions of the molecule. For all molecules tested having known configurations (with conformations ranging from mostly rigid to highly flexible), the method accurately determined the correct configuration.

Randomized interpolative decomposition of separated representations

NASA Astrophysics Data System (ADS)

Biagioni, David J.; Beylkin, Daniel; Beylkin, Gregory

2015-01-01

We introduce an algorithm to compute tensor interpolative decomposition (dubbed CTD-ID) for the reduction of the separation rank of Canonical Tensor Decompositions (CTDs). Tensor ID selects, for a user-defined accuracy ɛ, a near optimal subset of terms of a CTD to represent the remaining terms via a linear combination of the selected terms. CTD-ID can be used as an alternative to or in combination with the Alternating Least Squares (ALS) algorithm. We present examples of its use within a convergent iteration to compute inverse operators in high dimensions. We also briefly discuss the spectral norm as a computational alternative to the Frobenius norm in estimating approximation errors of tensor ID. We reduce the problem of finding tensor IDs to that of constructing interpolative decompositions of certain matrices. These matrices are generated via randomized projection of the terms of the given tensor. We provide cost estimates and several examples of the new approach to the reduction of separation rank.

Propagation of threading dislocations in heteroepitaxial diamond films with (111) orientation and their role in the formation of intrinsic stress

NASA Astrophysics Data System (ADS)

Gallheber, B.-C.; Klein, O.; Fischer, M.; Schreck, M.

2017-06-01

In the present study, systematic correlations were revealed between the propagation direction of threading dislocations, the off-axis growth conditions, and the stress state of heteroepitaxial diamond on Ir/YSZ/Si(111). Measurements of the strain tensor ɛ ⃡ by X-ray diffraction and the subsequent calculation of the tensor of intrinsic stress σ ⃡ showed stress-free samples as well as symmetric biaxial stress states for on-axis samples. Transmission electron microscopy (TEM) lamellas were prepared for plan-view studies along the [ 1 ¯ 1 ¯ 1 ¯ ] direction and for cross-section investigations along the [11 2 ¯ ] and [1 1 ¯ 0] zone axes. For samples grown on-axis with parameters which avoid the formation of intrinsic stress, the majority of dislocations have line vectors clearly aligned along [111]. A sudden change to conditions that promote stress formation is correlated with an abrupt bending of the dislocations away from [111]. This behaviour is in nice agreement with the predictions of a model that attributes formation of intrinsic stress to an effective climb of dislocations. Further growth experiments under off-axis conditions revealed the generation of stress states with pronounced in-plane anisotropy of several Gigapascal. Their formation is attributed to the combined action of two basic processes, i.e., the step flow driven dislocation tilting and the temperature dependent effective climb of dislocations. Again, our interpretation is supported by the dislocation propagation derived from TEM observations.

Method and apparatus for second-rank tensor generation

NASA Technical Reports Server (NTRS)

Liu, Hua-Kuang (Inventor)

1991-01-01

A method and apparatus are disclosed for generation of second-rank tensors using a photorefractive crystal to perform the outer-product between two vectors via four-wave mixing, thereby taking 2n input data to a control n squared output data points. Two orthogonal amplitude modulated coherent vector beams x and y are expanded and then parallel sides of the photorefractive crystal in exact opposition. A beamsplitter is used to direct a coherent pumping beam onto the crystal at an appropriate angle so as to produce a conjugate beam that is the matrix product of the vector beam that propagates in the exact opposite direction from the pumping beam. The conjugate beam thus separated is the tensor output xy (sup T).

Microwave and Millimeter Wave Properties of Vertically-Aligned Single Wall Carbon Nanotubes Films

NASA Astrophysics Data System (ADS)

Haddadi, K.; Tripon-Canseliet, C.; Hivin, Q.; Ducournau, G.; Teo, E.; Coquet, P.; Tay, B. K.; Lepilliet, S.; Avramovic, V.; Chazelas, J.; Decoster, D.

2016-05-01

We present the experimental determination of the complex permittivity of vertically aligned single wall carbon nanotubes (SWCNTs) films grown on quartz substrates in the microwave regime from 10 MHz up to 67 GHz, with the electrical field perpendicular to the main axis of the carbon nanotubes (CNTs), based on coplanar waveguide transmission line approach together with the measurement of the microwave impedance of top metalized vertically—aligned SWCNTs grown on conductive silicon substrates up to 26 GHz. From coplanar waveguide measurements, we obtain a real part of the permittivity almost equal to unity, which is interpreted in terms of low carbon atom density (3 × 1019 at/cm3) associated with a very low imaginary part of permittivity (<10-3) in the frequency range considered due to a very small perpendicular conductivity. The microwave impedance of a vertically aligned CNTs bundle equivalent to a low resistance reveals a good conductivity (3 S/cm) parallel to the CNTs axis. From these two kinds of data, we experimentally demonstrate the tensor nature of the vertically grown CNTs bundles.

Depth inpainting by tensor voting.

PubMed

Kulkarni, Mandar; Rajagopalan, Ambasamudram N

2013-06-01

Depth maps captured by range scanning devices or by using optical cameras often suffer from missing regions due to occlusions, reflectivity, limited scanning area, sensor imperfections, etc. In this paper, we propose a fast and reliable algorithm for depth map inpainting using the tensor voting (TV) framework. For less complex missing regions, local edge and depth information is utilized for synthesizing missing values. The depth variations are modeled by local planes using 3D TV, and missing values are estimated using plane equations. For large and complex missing regions, we collect and evaluate depth estimates from self-similar (training) datasets. We align the depth maps of the training set with the target (defective) depth map and evaluate the goodness of depth estimates among candidate values using 3D TV. We demonstrate the effectiveness of the proposed approaches on real as well as synthetic data.

Scale dependence of the alignment between strain rate and rotation in turbulent shear flow

NASA Astrophysics Data System (ADS)

Fiscaletti, D.; Elsinga, G. E.; Attili, A.; Bisetti, F.; Buxton, O. R. H.

2016-10-01

The scale dependence of the statistical alignment tendencies of the eigenvectors of the strain-rate tensor ei, with the vorticity vector ω , is examined in the self-preserving region of a planar turbulent mixing layer. Data from a direct numerical simulation are filtered at various length scales and the probability density functions of the magnitude of the alignment cosines between the two unit vectors | ei.ω ̂| are examined. It is observed that the alignment tendencies are insensitive to the concurrent large-scale velocity fluctuations, but are quantitatively affected by the nature of the concurrent large-scale velocity-gradient fluctuations. It is confirmed that the small-scale (local) vorticity vector is preferentially aligned in parallel with the large-scale (background) extensive strain-rate eigenvector e1, in contrast to the global tendency for ω to be aligned in parallel with the intermediate strain-rate eigenvector [Hamlington et al., Phys. Fluids 20, 111703 (2008), 10.1063/1.3021055]. When only data from regions of the flow that exhibit strong swirling are included, the so-called high-enstrophy worms, the alignment tendencies are exaggerated with respect to the global picture. These findings support the notion that the production of enstrophy, responsible for a net cascade of turbulent kinetic energy from large scales to small scales, is driven by vorticity stretching due to the preferential parallel alignment between ω and nonlocal e1 and that the strongly swirling worms are kinematically significant to this process.

Kronecker-Basis-Representation Based Tensor Sparsity and Its Applications to Tensor Recovery.

PubMed

Xie, Qi; Zhao, Qian; Meng, Deyu; Xu, Zongben

2017-08-02

It is well known that the sparsity/low-rank of a vector/matrix can be rationally measured by nonzero-entries-number ($l_0$ norm)/nonzero- singular-values-number (rank), respectively. However, data from real applications are often generated by the interaction of multiple factors, which obviously cannot be sufficiently represented by a vector/matrix, while a high order tensor is expected to provide more faithful representation to deliver the intrinsic structure underlying such data ensembles. Unlike the vector/matrix case, constructing a rational high order sparsity measure for tensor is a relatively harder task. To this aim, in this paper we propose a measure for tensor sparsity, called Kronecker-basis-representation based tensor sparsity measure (KBR briefly), which encodes both sparsity insights delivered by Tucker and CANDECOMP/PARAFAC (CP) low-rank decompositions for a general tensor. Then we study the KBR regularization minimization (KBRM) problem, and design an effective ADMM algorithm for solving it, where each involved parameter can be updated with closed-form equations. Such an efficient solver makes it possible to extend KBR to various tasks like tensor completion and tensor robust principal component analysis. A series of experiments, including multispectral image (MSI) denoising, MSI completion and background subtraction, substantiate the superiority of the proposed methods beyond state-of-the-arts.

Active tensor magnetic gradiometer system final report for Project MM–1514

USGS Publications Warehouse

Smith, David V.; Phillips, Jeffrey D.; Hutton, S. Raymond

2014-01-01

An interactive computer simulation program, based on physical models of system sensors, platform geometry, Earth environment, and spheroidal magnetically-permeable targets, was developed to generate synthetic magnetic field data from a conceptual tensor magnetic gradiometer system equipped with an active primary field generator. The system sensors emulate the prototype tensor magnetic gradiometer system (TMGS) developed under a separate contract for unexploded ordnance (UXO) detection and classification. Time-series data from different simulation scenarios were analyzed to recover physical dimensions of the target source. Helbig-Euler simulations were run with rectangular and rod-like source bodies to determine whether such a system could separate the induced component of the magnetization from the remanent component for each target. This report concludes with an engineering assessment of a practical system design.

Introduction of a computer-based method for automated planning of reduction paths under consideration of simulated muscular forces.

PubMed

Buschbaum, Jan; Fremd, Rainer; Pohlemann, Tim; Kristen, Alexander

2017-08-01

Reduction is a crucial step in the surgical treatment of bone fractures. Finding an optimal path for restoring anatomical alignment is considered technically demanding because collisions as well as high forces caused by surrounding soft tissues can avoid desired reduction movements. The repetition of reduction movements leads to a trial-and-error process which causes a prolonged duration of surgery. By planning an appropriate reduction path-an optimal sequence of target-directed movements-these problems should be overcome. For this purpose, a computer-based method has been developed. Using the example of simple femoral shaft fractures, 3D models are generated out of CT images. A reposition algorithm aligns both fragments by reconstructing their broken edges. According to the criteria of a deduced planning strategy, a modified A*-algorithm searches collision-free route of minimal force from the dislocated into the computed target position. Muscular forces are considered using a musculoskeletal reduction model (OpenSim model), and bone collisions are detected by an appropriate method. Five femoral SYNBONE models were broken into different fracture classification types and were automatically reduced from ten randomly selected displaced positions. Highest mean translational and rotational error for achieving target alignment is [Formula: see text] and [Formula: see text]. Mean value and standard deviation of occurring forces are [Formula: see text] for M. tensor fasciae latae and [Formula: see text] for M. semitendinosus over all trials. These pathways are precise, collision-free, required forces are minimized, and thus regarded as optimal paths. A novel method for planning reduction paths under consideration of collisions and muscular forces is introduced. The results deliver additional knowledge for an appropriate tactical reduction procedure and can provide a basis for further navigated or robotic-assisted developments.

Octupolar tensors for liquid crystals

NASA Astrophysics Data System (ADS)

Chen, Yannan; Qi, Liqun; Virga, Epifanio G.

2018-01-01

A third-rank three-dimensional symmetric traceless tensor, called the octupolar tensor, has been introduced to study tetrahedratic nematic phases in liquid crystals. The octupolar potential, a scalar-valued function generated on the unit sphere by that tensor, should ideally have four maxima (on the vertices of a tetrahedron), but it was recently found to possess an equally generic variant with three maxima instead of four. It was also shown that the irreducible admissible region for the octupolar tensor in a three-dimensional parameter space is bounded by a dome-shaped surface, beneath which is a separatrix surface connecting the two generic octupolar states. The latter surface, which was obtained through numerical continuation, may be physically interpreted as marking a possible intra-octupolar transition. In this paper, by using the resultant theory of algebraic geometry and the E-characteristic polynomial of spectral theory of tensors, we give a closed-form, algebraic expression for both the dome-shaped surface and the separatrix surface. This turns the envisaged intra-octupolar transition into a quantitative, possibly observable prediction.

Estimation of full moment tensors, including uncertainties, for earthquakes, volcanic events, and nuclear explosions

NASA Astrophysics Data System (ADS)

Alvizuri, Celso R.

We present a catalog of full seismic moment tensors for 63 events from Uturuncu volcano in Bolivia. The events were recorded during 2011-2012 in the PLUTONS seismic array of 24 broadband stations. Most events had magnitudes between 0.5 and 2.0 and did not generate discernible surface waves; the largest event was Mw 2.8. For each event we computed the misfit between observed and synthetic waveforms, and we used first-motion polarity measurements to reduce the number of possible solutions. Each moment tensor solution was obtained using a grid search over the six-dimensional space of moment tensors. For each event we show the misfit function in eigenvalue space, represented by a lune. We identify three subsets of the catalog: (1) 6 isotropic events, (2) 5 tensional crack events, and (3) a swarm of 14 events southeast of the volcanic center that appear to be double couples. The occurrence of positively isotropic events is consistent with other published results from volcanic and geothermal regions. Several of these previous results, as well as our results, cannot be interpreted within the context of either an oblique opening crack or a crack-plus-double-couple model. Proper characterization of uncertainties for full moment tensors is critical for distinguishing among physical models of source processes. A seismic moment tensor is a 3x3 symmetric matrix that provides a compact representation of a seismic source. We develop an algorithm to estimate moment tensors and their uncertainties from observed seismic data. For a given event, the algorithm performs a grid search over the six-dimensional space of moment tensors by generating synthetic waveforms for each moment tensor and then evaluating a misfit function between the observed and synthetic waveforms. 'The' moment tensor M0 for the event is then the moment tensor with minimum misfit. To describe the uncertainty associated with M0, we first convert the misfit function to a probability function. The uncertainty, or rather the confidence, is then given by the 'confidence curve' P( V), where P(V) is the probability that the true moment tensor for the event lies within the neighborhood of M that has fractional volume V. The area under the confidence curve provides a single, abbreviated 'confidence parameter' for M0. We apply the method to data from events in different regions and tectonic settings: 63 small (M w 4) earthquakes in the southern Alaska subduction zone, and 12 earthquakes and 17 nuclear explosions at the Nevada Test Site. Characterization of moment tensor uncertainties puts us in better position to discriminate among moment tensor source types and to assign physical processes to the events.

Tensor hypercontraction. II. Least-squares renormalization

NASA Astrophysics Data System (ADS)

Parrish, Robert M.; Hohenstein, Edward G.; Martínez, Todd J.; Sherrill, C. David

2012-12-01

The least-squares tensor hypercontraction (LS-THC) representation for the electron repulsion integral (ERI) tensor is presented. Recently, we developed the generic tensor hypercontraction (THC) ansatz, which represents the fourth-order ERI tensor as a product of five second-order tensors [E. G. Hohenstein, R. M. Parrish, and T. J. Martínez, J. Chem. Phys. 137, 044103 (2012)], 10.1063/1.4732310. Our initial algorithm for the generation of the THC factors involved a two-sided invocation of overlap-metric density fitting, followed by a PARAFAC decomposition, and is denoted PARAFAC tensor hypercontraction (PF-THC). LS-THC supersedes PF-THC by producing the THC factors through a least-squares renormalization of a spatial quadrature over the otherwise singular 1/r12 operator. Remarkably, an analytical and simple formula for the LS-THC factors exists. Using this formula, the factors may be generated with O(N^5) effort if exact integrals are decomposed, or O(N^4) effort if the decomposition is applied to density-fitted integrals, using any choice of density fitting metric. The accuracy of LS-THC is explored for a range of systems using both conventional and density-fitted integrals in the context of MP2. The grid fitting error is found to be negligible even for extremely sparse spatial quadrature grids. For the case of density-fitted integrals, the additional error incurred by the grid fitting step is generally markedly smaller than the underlying Coulomb-metric density fitting error. The present results, coupled with our previously published factorizations of MP2 and MP3, provide an efficient, robust O(N^4) approach to both methods. Moreover, LS-THC is generally applicable to many other methods in quantum chemistry.

Tensor hypercontraction. II. Least-squares renormalization.

PubMed

Parrish, Robert M; Hohenstein, Edward G; Martínez, Todd J; Sherrill, C David

2012-12-14

The least-squares tensor hypercontraction (LS-THC) representation for the electron repulsion integral (ERI) tensor is presented. Recently, we developed the generic tensor hypercontraction (THC) ansatz, which represents the fourth-order ERI tensor as a product of five second-order tensors [E. G. Hohenstein, R. M. Parrish, and T. J. Martínez, J. Chem. Phys. 137, 044103 (2012)]. Our initial algorithm for the generation of the THC factors involved a two-sided invocation of overlap-metric density fitting, followed by a PARAFAC decomposition, and is denoted PARAFAC tensor hypercontraction (PF-THC). LS-THC supersedes PF-THC by producing the THC factors through a least-squares renormalization of a spatial quadrature over the otherwise singular 1∕r(12) operator. Remarkably, an analytical and simple formula for the LS-THC factors exists. Using this formula, the factors may be generated with O(N(5)) effort if exact integrals are decomposed, or O(N(4)) effort if the decomposition is applied to density-fitted integrals, using any choice of density fitting metric. The accuracy of LS-THC is explored for a range of systems using both conventional and density-fitted integrals in the context of MP2. The grid fitting error is found to be negligible even for extremely sparse spatial quadrature grids. For the case of density-fitted integrals, the additional error incurred by the grid fitting step is generally markedly smaller than the underlying Coulomb-metric density fitting error. The present results, coupled with our previously published factorizations of MP2 and MP3, provide an efficient, robust O(N(4)) approach to both methods. Moreover, LS-THC is generally applicable to many other methods in quantum chemistry.

On the Alignment of Strain, Vorticity and Scalar Gradient in Turbulent, Buoyant, Nonpremixed Flames

NASA Technical Reports Server (NTRS)

Boratav, O. N.; Elghobashi, S. E.; Zhong, R.

1999-01-01

The alignment of vorticity and scalar gradient with the eigendirections of the rate of strain tensor is investigated in turbulent buoyant nonpremixed horizontal and vertical flames. The uniqueness of a buoyant nonpremixed flame is that it contains regions with distinct alignment characteristics. The strain-enstrophy angle Psi is used to identify these regions. Examination of the vorticity field and the vorticity production in these different regions indicates that Psi and consequently the alignment properties near the flame surface identified by the mixture fraction band F approximately equals F(sub st) differ from those in the fuel region, F > F(sub st) and the oxidizer region, F < F(sub st). The F approximately equals F(sub st) band shows strain-dominance resulting in vorticity/alpha alignment while F > F(sub st) (and F < F(sub st) for the vertical flame) band(s) show(s) vorticity/beta alignment. The implication of this result is that the scalar dissipation, epsilon(sub F), attains its maximum value always near F approximately equals F(sub st). These results are also discussed within the framework of recent dynamical results [Galanti et al., Nonlinearity 10, 1675 (1997)] suggesting that the Navier-Stokes equations evolved towards an attracting solution. It is shown that the properties of such an attracting solution are also consistent with our results of buoyant turbulent nonpremixed flames.

Strain distributions and their influence on electronic structures of WSe2-MoS2 laterally strained heterojunctions

NASA Astrophysics Data System (ADS)

Zhang, Chendong; Li, Ming-Yang; Tersoff, Jerry; Han, Yimo; Su, Yushan; Li, Lain-Jong; Muller, David A.; Shih, Chih-Kang

2018-02-01

Monolayer transition metal dichalcogenide heterojunctions, including vertical and lateral p-n junctions, have attracted considerable attention due to their potential applications in electronics and optoelectronics. Lattice-misfit strain in atomically abrupt lateral heterojunctions, such as WSe2-MoS2, offers a new band-engineering strategy for tailoring their electronic properties. However, this approach requires an understanding of the strain distribution and its effect on band alignment. Here, we study a WSe2-MoS2 lateral heterojunction using scanning tunnelling microscopy and image its moiré pattern to map the full two-dimensional strain tensor with high spatial resolution. Using scanning tunnelling spectroscopy, we measure both the strain and the band alignment of the WSe2-MoS2 lateral heterojunction. We find that the misfit strain induces type II to type I band alignment transformation. Scanning transmission electron microscopy reveals the dislocations at the interface that partially relieve the strain. Finally, we observe a distinctive electronic structure at the interface due to hetero-bonding.

Hyperbolic and Plasmonic Properties of Silicon/Ag Aligned Nanowire Arrays

DTIC Science & Technology

2013-06-17

Cleveland, J. D. Caldwell, E. Foos, J. Niinistö, and M. Ritala, “Spoof-like plasmonic behavior of plasma enhanced atomic layer deposition grown Ag thin...M. Leskela, “ Plasma -enhanced atomic layer deposition of silver thin films,” Chem. Mater. 23(11), 2901–2907 (2011). 52. O. J. Glembocki, S. M. Prokes...all principal components of the dielectric permittivity tensor are positive, the iso-frequency surface is “closed” and forms a spheroid or ellipsoid

Linear dichroism of DNA: Characterization of the orientation distribution function caused by hydrodynamic shear

DOE PAGES

Sutherland, John C.

2017-04-15

Linear dichroism provides information on the orientation of chromophores part of, or bound to, an orientable molecule such as DNA. For molecular alignment induced by hydrodynamic shear, the principal axes orthogonal to the direction of alignment are not equivalent. Thus, the magnitude of the flow-induced change in absorption for light polarized parallel to the direction of flow can be more than a factor of two greater than the corresponding change for light polarized perpendicular to both that direction and the shear axis. The ratio of the two flow-induced changes in absorption, the dichroic increment ratio, is characterized using the orthogonalmore » orientation model, which assumes that each absorbing unit is aligned parallel to one of the principal axes of the apparatus. The absorption of the alienable molecules is characterized by components parallel and perpendicular to the orientable axis of the molecule. The dichroic increment ratio indicates that for the alignment of DNA in rectangular flow cells, average alignment is not uniaxial, but for higher shear, as produced in a Couette cell, it can be. The results from the simple model are identical to tensor models for typical experimental configuration. Approaches for measuring the dichroic increment ratio with modern dichrometers are further discussed.« less

Linear dichroism of DNA: Characterization of the orientation distribution function caused by hydrodynamic shear

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

Sutherland, John C.

Linear dichroism provides information on the orientation of chromophores part of, or bound to, an orientable molecule such as DNA. For molecular alignment induced by hydrodynamic shear, the principal axes orthogonal to the direction of alignment are not equivalent. Thus, the magnitude of the flow-induced change in absorption for light polarized parallel to the direction of flow can be more than a factor of two greater than the corresponding change for light polarized perpendicular to both that direction and the shear axis. The ratio of the two flow-induced changes in absorption, the dichroic increment ratio, is characterized using the orthogonalmore » orientation model, which assumes that each absorbing unit is aligned parallel to one of the principal axes of the apparatus. The absorption of the alienable molecules is characterized by components parallel and perpendicular to the orientable axis of the molecule. The dichroic increment ratio indicates that for the alignment of DNA in rectangular flow cells, average alignment is not uniaxial, but for higher shear, as produced in a Couette cell, it can be. The results from the simple model are identical to tensor models for typical experimental configuration. Approaches for measuring the dichroic increment ratio with modern dichrometers are further discussed.« less

Linear dichroism of DNA: Characterization of the orientation distribution function caused by hydrodynamic shear.

PubMed

Sutherland, John C

2017-04-15

Linear dichroism provides information on the orientation of chromophores part of, or bound to, an orientable molecule such as DNA. For molecular alignment induced by hydrodynamic shear, the principal axes orthogonal to the direction of alignment are not equivalent. Thus, the magnitude of the flow-induced change in absorption for light polarized parallel to the direction of flow can be more than a factor of two greater than the corresponding change for light polarized perpendicular to both that direction and the shear axis. The ratio of the two flow-induced changes in absorption, the dichroic increment ratio, is characterized using the orthogonal orientation model, which assumes that each absorbing unit is aligned parallel to one of the principal axes of the apparatus. The absorption of the alienable molecules is characterized by components parallel and perpendicular to the orientable axis of the molecule. The dichroic increment ratio indicates that for the alignment of DNA in rectangular flow cells, average alignment is not uniaxial, but for higher shear, as produced in a Couette cell, it can be. The results from the simple model are identical to tensor models for typical experimental configurations. Approaches for measuring the dichroic increment ratio with modern dichrometers are discussed. Copyright © 2017. Published by Elsevier Inc.

A continuous tensor field approximation of discrete DT-MRI data for extracting microstructural and architectural features of tissue.

PubMed

Pajevic, Sinisa; Aldroubi, Akram; Basser, Peter J

2002-01-01

The effective diffusion tensor of water, D, measured by diffusion tensor MRI (DT-MRI), is inherently a discrete, noisy, voxel-averaged sample of an underlying macroscopic effective diffusion tensor field, D(x). Within fibrous tissues this field is presumed to be continuous and smooth at a gross anatomical length scale. Here a new, general mathematical framework is proposed that uses measured DT-MRI data to produce a continuous approximation to D(x). One essential finding is that the continuous tensor field representation can be constructed by repeatedly performing one-dimensional B-spline transforms of the DT-MRI data. The fidelity and noise-immunity of this approximation are tested using a set of synthetically generated tensor fields to which background noise is added via Monte Carlo methods. Generally, these tensor field templates are reproduced faithfully except at boundaries where diffusion properties change discontinuously or where the tensor field is not microscopically homogeneous. Away from such regions, the tensor field approximation does not introduce bias in useful DT-MRI parameters, such as Trace(D(x)). It also facilitates the calculation of several new parameters, particularly differential quantities obtained from the tensor of spatial gradients of D(x). As an example, we show that they can identify tissue boundaries across which diffusion properties change rapidly using in vivo human brain data. One important application of this methodology is to improve the reliability and robustness of DT-MRI fiber tractography.

Estimation of full moment tensors, including uncertainties, for earthquakes, volcanic events, and nuclear explosions

NASA Astrophysics Data System (ADS)

Alvizuri, Celso; Silwal, Vipul; Krischer, Lion; Tape, Carl

2017-04-01

A seismic moment tensor is a 3 × 3 symmetric matrix that provides a compact representation of seismic events within Earth's crust. We develop an algorithm to estimate moment tensors and their uncertainties from observed seismic data. For a given event, the algorithm performs a grid search over the six-dimensional space of moment tensors by generating synthetic waveforms at each grid point and then evaluating a misfit function between the observed and synthetic waveforms. 'The' moment tensor M for the event is then the moment tensor with minimum misfit. To describe the uncertainty associated with M, we first convert the misfit function to a probability function. The uncertainty, or rather the confidence, is then given by the 'confidence curve' P(V ), where P(V ) is the probability that the true moment tensor for the event lies within the neighborhood of M that has fractional volume V . The area under the confidence curve provides a single, abbreviated 'confidence parameter' for M. We apply the method to data from events in different regions and tectonic settings: small (Mw < 2.5) events at Uturuncu volcano in Bolivia, moderate (Mw > 4) earthquakes in the southern Alaska subduction zone, and natural and man-made events at the Nevada Test Site. Moment tensor uncertainties allow us to better discriminate among moment tensor source types and to assign physical processes to the events.

APPROXIMATING SYMMETRIC POSITIVE SEMIDEFINITE TENSORS OF EVEN ORDER*

PubMed Central

BARMPOUTIS, ANGELOS; JEFFREY, HO; VEMURI, BABA C.

2012-01-01

Tensors of various orders can be used for modeling physical quantities such as strain and diffusion as well as curvature and other quantities of geometric origin. Depending on the physical properties of the modeled quantity, the estimated tensors are often required to satisfy the positivity constraint, which can be satisfied only with tensors of even order. Although the space P02m of 2mth-order symmetric positive semi-definite tensors is known to be a convex cone, enforcing positivity constraint directly on P02m is usually not straightforward computationally because there is no known analytic description of P02m for m > 1. In this paper, we propose a novel approach for enforcing the positivity constraint on even-order tensors by approximating the cone P02m for the cases 0 < m < 3, and presenting an explicit characterization of the approximation Σ2m ⊂ Ω2m for m ≥ 1, using the subset Ω2m⊂P02m of semi-definite tensors that can be written as a sum of squares of tensors of order m. Furthermore, we show that this approximation leads to a non-negative linear least-squares (NNLS) optimization problem with the complexity that equals the number of generators in Σ2m. Finally, we experimentally validate the proposed approach and we present an application for computing 2mth-order diffusion tensors from Diffusion Weighted Magnetic Resonance Images. PMID:23285313

Full Tensor Diffusion Imaging Is Not Required To Assess the White-Matter Integrity in Mouse Contusion Spinal Cord Injury

PubMed Central

Tu, Tsang-Wei; Kim, Joong H.; Wang, Jian

2010-01-01

Abstract In vivo diffusion tensor imaging (DTI) derived indices have been demonstrated to quantify accurately white-matter injury after contusion spinal cord injury (SCI) in rodents. In general, a full diffusion tensor analysis requires the acquisition of diffusion-weighted images (DWI) along at least six independent directions of diffusion-sensitizing gradients. Thus, DTI measurements of the rodent central nervous system are time consuming. In this study, diffusion indices derived using the two-direction DWI (parallel and perpendicular to axonal tracts) were compared with those obtained using six-direction DTI in a mouse model of SCI. It was hypothesized that the mouse spinal cord ventral-lateral white-matter (VLWM) tracts, T8–T10 in this study, aligned with the main magnet axis (z) allowing the apparent diffusion coefficient parallel and perpendicular to the axis of the spine to be derived with diffusion-weighting gradients in the z and y axes of the magnet coordinate respectively. Compared with six-direction full tensor DTI, two-direction DWI provided comparable diffusion indices in mouse spinal cords. The measured extent of spared white matter after injury, estimated by anisotropy indices, using both six-direction DTI and two-direction DWI were in close agreement and correlated well with histological staining and behavioral assessment. The results suggest that the two-direction DWI derived indices may be used, with significantly reduced imaging time, to estimate accurately spared white matter in mouse SCI. PMID:19715399

Conservation laws and stress-energy-momentum tensors for systems with background fields

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

Gratus, Jonathan, E-mail: j.gratus@lancaster.ac.uk; The Cockcroft Institute, Daresbury Laboratory, Warrington WA4 4AD; Obukhov, Yuri N., E-mail: yo@thp.uni-koeln.de

2012-10-15

This article attempts to delineate the roles played by non-dynamical background structures and Killing symmetries in the construction of stress-energy-momentum tensors generated from a diffeomorphism invariant action density. An intrinsic coordinate independent approach puts into perspective a number of spurious arguments that have historically lead to the main contenders, viz the Belinfante-Rosenfeld stress-energy-momentum tensor derived from a Noether current and the Einstein-Hilbert stress-energy-momentum tensor derived in the context of Einstein's theory of general relativity. Emphasis is placed on the role played by non-dynamical background (phenomenological) structures that discriminate between properties of these tensors particularly in the context of electrodynamics inmore » media. These tensors are used to construct conservation laws in the presence of Killing Lie-symmetric background fields. - Highlights: Black-Right-Pointing-Pointer The role of background fields in diffeomorphism invariant actions is demonstrated. Black-Right-Pointing-Pointer Interrelations between different stress-energy-momentum tensors are emphasised. Black-Right-Pointing-Pointer The Abraham and Minkowski electromagnetic tensors are discussed in this context. Black-Right-Pointing-Pointer Conservation laws in the presence of nondynamic background fields are formulated. Black-Right-Pointing-Pointer The discussion is facilitated by the development of a new variational calculus.« less

Using Perturbation Theory to Reduce Noise in Diffusion Tensor Fields

PubMed Central

Bansal, Ravi; Staib, Lawrence H.; Xu, Dongrong; Laine, Andrew F.; Liu, Jun; Peterson, Bradley S.

2009-01-01

We propose the use of Perturbation theory to reduce noise in Diffusion Tensor (DT) fields. Diffusion Tensor Imaging (DTI) encodes the diffusion of water molecules along different spatial directions in a positive-definite, 3 × 3 symmetric tensor. Eigenvectors and eigenvalues of DTs allow the in vivo visualization and quantitative analysis of white matter fiber bundles across the brain. The validity and reliability of these analyses are limited, however, by the low spatial resolution and low Signal-to-Noise Ratio (SNR) in DTI datasets. Our procedures can be applied to improve the validity and reliability of these quantitative analyses by reducing noise in the tensor fields. We model a tensor field as a three-dimensional Markov Random Field and then compute the likelihood and the prior terms of this model using Perturbation theory. The prior term constrains the tensor field to be smooth, whereas the likelihood term constrains the smoothed tensor field to be similar to the original field. Thus, the proposed method generates a smoothed field that is close in structure to the original tensor field. We evaluate the performance of our method both visually and quantitatively using synthetic and real-world datasets. We quantitatively assess the performance of our method by computing the SNR for eigenvalues and the coherence measures for eigenvectors of DTs across tensor fields. In addition, we quantitatively compare the performance of our procedures with the performance of one method that uses a Riemannian distance to compute the similarity between two tensors, and with another method that reduces noise in tensor fields by anisotropically filtering the diffusion weighted images that are used to estimate diffusion tensors. These experiments demonstrate that our method significantly increases the coherence of the eigenvectors and the SNR of the eigenvalues, while simultaneously preserving the fine structure and boundaries between homogeneous regions, in the smoothed tensor field. PMID:19540791

Improved object optimal synthetic description, modeling, learning, and discrimination by GEOGINE computational kernel

NASA Astrophysics Data System (ADS)

Fiorini, Rodolfo A.; Dacquino, Gianfranco

2005-03-01

GEOGINE (GEOmetrical enGINE), a state-of-the-art OMG (Ontological Model Generator) based on n-D Tensor Invariants for n-Dimensional shape/texture optimal synthetic representation, description and learning, was presented in previous conferences elsewhere recently. Improved computational algorithms based on the computational invariant theory of finite groups in Euclidean space and a demo application is presented. Progressive model automatic generation is discussed. GEOGINE can be used as an efficient computational kernel for fast reliable application development and delivery in advanced biomedical engineering, biometric, intelligent computing, target recognition, content image retrieval, data mining technological areas mainly. Ontology can be regarded as a logical theory accounting for the intended meaning of a formal dictionary, i.e., its ontological commitment to a particular conceptualization of the world object. According to this approach, "n-D Tensor Calculus" can be considered a "Formal Language" to reliably compute optimized "n-Dimensional Tensor Invariants" as specific object "invariant parameter and attribute words" for automated n-Dimensional shape/texture optimal synthetic object description by incremental model generation. The class of those "invariant parameter and attribute words" can be thought as a specific "Formal Vocabulary" learned from a "Generalized Formal Dictionary" of the "Computational Tensor Invariants" language. Even object chromatic attributes can be effectively and reliably computed from object geometric parameters into robust colour shape invariant characteristics. As a matter of fact, any highly sophisticated application needing effective, robust object geometric/colour invariant attribute capture and parameterization features, for reliable automated object learning and discrimination can deeply benefit from GEOGINE progressive automated model generation computational kernel performance. Main operational advantages over previous, similar approaches are: 1) Progressive Automated Invariant Model Generation, 2) Invariant Minimal Complete Description Set for computational efficiency, 3) Arbitrary Model Precision for robust object description and identification.

Multiscale analysis of the invariants of the velocity gradient tensor in isotropic turbulence

NASA Astrophysics Data System (ADS)

Danish, Mohammad; Meneveau, Charles

2018-04-01

Knowledge of local flow-topology, the patterns of streamlines around a moving fluid element as described by the velocity-gradient tensor, is useful for developing insights into turbulence processes, such as energy cascade, material element deformation, or scalar mixing. Much has been learned in the recent past about flow topology at the smallest (viscous) scales of turbulence. However, less is known at larger scales, for instance, at the inertial scales of turbulence. In this work, we present a detailed study on the scale dependence of various quantities of interest, such as the population fraction of different types of flow-topologies, the joint probability distribution of the second and third invariants of the velocity gradient tensor, and the geometrical alignment of vorticity with strain-rate eigenvectors. We perform the analysis on a simulation dataset of isotropic turbulence at Reλ=433 . While quantities appear close to scale invariant in the inertial range, we observe a "bump" in several quantities at length scales between the inertial and viscous ranges. For instance, the population fraction of unstable node-saddle-saddle flow topology shows an increase when reducing the scale from the inertial entering the viscous range. A similar bump is observed for the vorticity-strain-rate alignment. In order to document possible dynamical causes for the different trends in the viscous and inertial ranges, we examine the probability fluxes appearing in the Fokker-Plank equation governing the velocity gradient invariants. Specifically, we aim to understand whether the differences observed between the viscous and inertial range statistics are due to effects caused by pressure, subgrid-scale, or viscous stresses or various combinations of these terms. To decompose the flow into small and large scales, we mainly use a spectrally compact non-negative filter with good spatial localization properties (Eyink-Aluie filter). The analysis shows that when going from the inertial range into the viscous range, the subgrid-stress effect decreases more rapidly as a function of scale than the viscous effects increase. To make up for the difference, the pressure Hessian also behaves somewhat differently in the viscous than in the inertial range. The results have implications for models for the velocity gradient tensor showing that the effects of subgrid scales may not be simply modeled via a constant eddy viscosity in the inertial range if one wishes to reproduce the observed trends.

Conformal Collineations of the Ricci and Energy-Momentum Tensors in Static Plane Symmetric Space-Times

NASA Astrophysics Data System (ADS)

Akhtar, S. S.; Hussain, T.; Bokhari, A. H.; Khan, F.

2018-04-01

We provide a complete classification of static plane symmetric space-times according to conformal Ricci collineations (CRCs) and conformal matter collineations (CMCs) in both the degenerate and nondegenerate cases. In the case of a nondegenerate Ricci tensor, we find a general form of the vector field generating CRCs in terms of unknown functions of t and x subject to some integrability conditions. We then solve the integrability conditions in different cases depending upon the nature of the Ricci tensor and conclude that the static plane symmetric space-times have a 7-, 10- or 15-dimensional Lie algebra of CRCs. Moreover, we find that these space-times admit an infinite number of CRCs if the Ricci tensor is degenerate. We use a similar procedure to study CMCs in the case of a degenerate or nondegenerate matter tensor. We obtain the exact form of some static plane symmetric space-time metrics that admit nontrivial CRCs and CMCs. Finally, we present some physical applications of our obtained results by considering a perfect fluid as a source of the energy-momentum tensor.

Single-shot measurement of ultrafast time-varying phase modulation induced by femtosecond laser pulses with arbitrary polarization

NASA Astrophysics Data System (ADS)

Hartinger, Klaus; Bartels, Randy A.

2008-01-01

We demonstrate a single-shot measurement of the transient phase modulation due to field free molecular alignment at the revival times of a rotational wave packet. The wave packet is excited by an arbitrarily polarized ultrashort laser pulse in CO2 at room temperature. With this technique the time dependence along the eigenpolarization directions of the linear susceptibility tensor, i.e., the time dependence of its principle components, can be directly observed with high sensitivity.

Second Harmonic Generation of Unpolarized Light

NASA Astrophysics Data System (ADS)

Ding, Changqin; Ulcickas, James R. W.; Deng, Fengyuan; Simpson, Garth J.

2017-11-01

A Mueller tensor mathematical framework was applied for predicting and interpreting the second harmonic generation (SHG) produced with an unpolarized fundamental beam. In deep tissue imaging through SHG and multiphoton fluorescence, partial or complete depolarization of the incident light complicates polarization analysis. The proposed framework has the distinct advantage of seamlessly merging the purely polarized theory based on the Jones or Cartesian susceptibility tensors with a more general Mueller tensor framework capable of handling partial depolarized fundamental and/or SHG produced. The predictions of the model are in excellent agreement with experimental measurements of z -cut quartz and mouse tail tendon obtained with polarized and depolarized incident light. The polarization-dependent SHG produced with unpolarized fundamental allowed determination of collagen fiber orientation in agreement with orthogonal methods based on image analysis. This method has the distinct advantage of being immune to birefringence or depolarization of the fundamental beam for structural analysis of tissues.

PREFACE: 1st Tensor Polarized Solid Target Workshop

NASA Astrophysics Data System (ADS)

2014-10-01

These are the proceedings of the first Tensor Spin Observables Workshop that was held in March 2014 at the Thomas Jefferson National Accelerator Facility in Newport News, Virginia. The conference was convened to study the physics that can be done with the recently approved E12-13-011 polarized target. A tensor polarized target holds the potential of initiating a new generation of tensor spin physics at Jefferson Lab. Experiments which utilize tensor polarized targets can help clarify how nuclear properties arise from partonic degrees of freedom, provide unique insight into short-range correlations and quark angular momentum, and also help pin down the polarization of the quark sea with a future Electron Ion Collider. This three day workshop was focused on tensor spin observables and the associated tensor target development. The workshop goals were to stimulate progress in the theoretical treatment of polarized spin-1 systems, foster the development of new proposals, and to reach a consensus on the optimal polarized target configuration for the tensor spin program. The workshop was sponsored by the University of New Hampshire, the Jefferson Science Associates, Florida International University, and Jefferson Lab. It was organized by Karl Slifer (chair), Patricia Solvignon, and Elena Long of the University of New Hampshire, Douglas Higinbotham and Christopher Keith of Jefferson Lab, and Misak Sargsian of the Florida International University. These proceedings represent the effort put forth by the community to begin exploring the possibilities that a high-luminosity, high-tensor polarized solid target can offer.

Newton-based optimization for Kullback-Leibler nonnegative tensor factorizations

DOE PAGES

Plantenga, Todd; Kolda, Tamara G.; Hansen, Samantha

2015-04-30

Tensor factorizations with nonnegativity constraints have found application in analysing data from cyber traffic, social networks, and other areas. We consider application data best described as being generated by a Poisson process (e.g. count data), which leads to sparse tensors that can be modelled by sparse factor matrices. In this paper, we investigate efficient techniques for computing an appropriate canonical polyadic tensor factorization based on the Kullback–Leibler divergence function. We propose novel subproblem solvers within the standard alternating block variable approach. Our new methods exploit structure and reformulate the optimization problem as small independent subproblems. We employ bound-constrained Newton andmore » quasi-Newton methods. Finally, we compare our algorithms against other codes, demonstrating superior speed for high accuracy results and the ability to quickly find sparse solutions.« less

Fixture for aligning motor assembly

DOEpatents

Shervington, Roger M.; Vaghani, Vallabh V.; Vanek, Laurence D.; Christensen, Scott A.

2009-12-08

An alignment fixture includes a rotor fixture, a stator fixture and a sensor system which measures a rotational displacement therebetween. The fixture precisely measures rotation of a generator stator assembly away from a NULL position referenced by a unique reference spline on the rotor shaft. By providing an adjustable location of the stator assembly within the housing, the magnetic axes within each generator shall be aligned to a predetermined and controlled tolerance between the generator interface mounting pin and the reference spline on the rotor shaft. Once magnetically aligned, each generator is essentially a line replaceable unit which may be readily mounted to any input of a multi-generator gearbox assembly with the assurance that the magnetic alignment will be within a predetermined tolerance.

Constructively determining the MBL spectrum using Tensor Networks

NASA Astrophysics Data System (ADS)

Clark, Bryan; Yu, Xiongjie; Pekker, David

All the eigenstates of a many-body localized phase can be compactly represented in the tensor-network language. Current algorithms to find these states often only target single states and/or require difficult optimization to find. In this talk we will show how to generate every eigenstate in the spectrum constructively and discuss its implication for the properties of the MBL phase.

Estimation of relative order tensors, and reconstruction of vectors in space using unassigned RDC data and its application

NASA Astrophysics Data System (ADS)

Miao, Xijiang; Mukhopadhyay, Rishi; Valafar, Homayoun

2008-10-01

Advances in NMR instrumentation and pulse sequence design have resulted in easier acquisition of Residual Dipolar Coupling (RDC) data. However, computational and theoretical analysis of this type of data has continued to challenge the international community of investigators because of their complexity and rich information content. Contemporary use of RDC data has required a-priori assignment, which significantly increases the overall cost of structural analysis. This article introduces a novel algorithm that utilizes unassigned RDC data acquired from multiple alignment media ( nD-RDC, n ⩾ 3) for simultaneous extraction of the relative order tensor matrices and reconstruction of the interacting vectors in space. Estimation of the relative order tensors and reconstruction of the interacting vectors can be invaluable in a number of endeavors. An example application has been presented where the reconstructed vectors have been used to quantify the fitness of a template protein structure to the unknown protein structure. This work has other important direct applications such as verification of the novelty of an unknown protein and validation of the accuracy of an available protein structure model in drug design. More importantly, the presented work has the potential to bridge the gap between experimental and computational methods of structure determination.

Steps to reconcile inflationary tensor and scalar spectra

NASA Astrophysics Data System (ADS)

Miranda, Vinícius; Hu, Wayne; Adshead, Peter

2014-05-01

The recent BICEP2 B-mode polarization determination of an inflationary tensor-scalar ratio r=0.2-0.05+0.07 is in tension with simple scale-free models of inflation due to a lack of a corresponding low multipole excess in the temperature power spectrum which places a limit of r0.002<0.11 (95% C.L.) on such models. Single-field inflationary models that reconcile these two observations, even those where the tilt runs substantially, introduce a scale into the scalar power spectrum. To cancel the tensor excess, and simultaneously remove the excess already present without tensors, ideally the model should introduce this scale as a relatively sharp transition in the tensor-scalar ratio around the horizon at recombination. We consider models which generate such a step in this quantity and find that they can improve the joint fit to the temperature and polarization data by up to 2ΔlnL≈-14 without changing cosmological parameters. Precision E-mode polarization measurements should be able to test this explanation.

Hollow elliptical Gaussian beam and its propagation through aligned and misaligned paraxial optical systems.

PubMed

Cai, Yangjian; Lin, Qiang

2004-06-01

A new mathematical model called hollow elliptical Gaussian beam (HEGB) is proposed to describe a dark-hollow laser beam with noncircular symmetry in terms of a tensor method. The HEGB can be expressed as a superposition of a series of elliptical Hermite-Gaussian modes. By using the generalized diffraction integral formulas for light passing through paraxial optical systems, analytical propagation formulas for HEGBs passing through paraxial aligned and misaligned optical systems are obtained through vector integration. As examples of applications, evolution properties of the intensity distribution of HEGBs in free-space propagation were studied. Propagation properties of HEGBs through a misaligned thin lens were also studied. The HEGB provides a convenient way to describe elliptical dark-hollow laser beams and can be used conveniently to study the motion of atoms in a dark-hollow laser beam.

Hollow elliptical Gaussian beam and its propagation through aligned and misaligned paraxial optical systems

NASA Astrophysics Data System (ADS)

Cai, Yangjian; Lin, Qiang

2004-06-01

A new mathematical model called hollow elliptical Gaussian beam (HEGB) is proposed to describe a dark-hollow laser beam with noncircular symmetry in terms of a tensor method. The HEGB can be expressed as a superposition of a series of elliptical Hermite-Gaussian modes. By using the generalized diffraction integral formulas for light passing through paraxial optical systems, analytical propagation formulas for HEGBs passing through paraxial aligned and misaligned optical systems are obtained through vector integration. As examples of applications, evolution properties of the intensity distribution of HEGBs in free-space propagation were studied. Propagation properties of HEGBs through a misaligned thin lens were also studied. The HEGB provides a convenient way to describe elliptical dark-hollow laser beams and can be used conveniently to study the motion of atoms in a dark-hollow laser beam.

Polynomial interpretation of multipole vectors

NASA Astrophysics Data System (ADS)

Katz, Gabriel; Weeks, Jeff

2004-09-01

Copi, Huterer, Starkman, and Schwarz introduced multipole vectors in a tensor context and used them to demonstrate that the first-year Wilkinson microwave anisotropy probe (WMAP) quadrupole and octopole planes align at roughly the 99.9% confidence level. In the present article, the language of polynomials provides a new and independent derivation of the multipole vector concept. Bézout’s theorem supports an elementary proof that the multipole vectors exist and are unique (up to rescaling). The constructive nature of the proof leads to a fast, practical algorithm for computing multipole vectors. We illustrate the algorithm by finding exact solutions for some simple toy examples and numerical solutions for the first-year WMAP quadrupole and octopole. We then apply our algorithm to Monte Carlo skies to independently reconfirm the estimate that the WMAP quadrupole and octopole planes align at the 99.9% level.

Inversion of calcite twin data for paleostress (1) : improved Etchecopar technique tested on numerically-generated and natural data

NASA Astrophysics Data System (ADS)

Parlangeau, Camille; Lacombe, Olivier; Daniel, Jean-Marc; Schueller, Sylvie

2015-04-01

Inversion of calcite twin data are known to be a powerful tool to reconstruct the past-state of stress in carbonate rocks of the crust, especially in fold-and-thrust belts and sedimentary basins. This is of key importance to constrain results of geomechanical modelling. Without proposing a new inversion scheme, this contribution reports some recent improvements of the most efficient stress inversion technique to date (Etchecopar, 1984) that allows to reconstruct the 5 parameters of the deviatoric paleostress tensors (principal stress orientations and differential stress magnitudes) from monophase and polyphase twin data sets. The improvements consist in the search of the possible tensors that account for the twin data (twinned and untwinned planes) and the aid to the user to define the best stress tensor solution, among others. We perform a systematic exploration of an hypersphere in 4 dimensions by varying different parameters, Euler's angles and the stress ratio. We first record all tensors with a minimum penalization function accounting for 20% of the twinned planes. We then define clusters of tensors following a dissimilarity criterion based on the stress distance between the 4 parameters of the reduced stress tensors and a degree of disjunction of the related sets of twinned planes. The percentage of twinned data to be explained by each tensor is then progressively increased and tested using the standard Etchecopar procedure until the best solution that explains the maximum number of twinned planes and the whole set of untwinned planes is reached. This new inversion procedure is tested on monophase and polyphase numerically-generated as well as natural calcite twin data in order to more accurately define the ability of the technique to separate more or less similar deviatoric stress tensors applied in sequence on the samples, to test the impact of strain hardening through the change of the critical resolved shear stress for twinning as well as to evaluate the possible bias due to measurement uncertainties or clustering of grain optical axes in the samples.

Creating a medical dictionary using word alignment: the influence of sources and resources.

PubMed

Nyström, Mikael; Merkel, Magnus; Petersson, Håkan; Ahlfeldt, Hans

2007-11-23

Automatic word alignment of parallel texts with the same content in different languages is among other things used to generate dictionaries for new translations. The quality of the generated word alignment depends on the quality of the input resources. In this paper we report on automatic word alignment of the English and Swedish versions of the medical terminology systems ICD-10, ICF, NCSP, KSH97-P and parts of MeSH and how the terminology systems and type of resources influence the quality. We automatically word aligned the terminology systems using static resources, like dictionaries, statistical resources, like statistically derived dictionaries, and training resources, which were generated from manual word alignment. We varied which part of the terminology systems that we used to generate the resources, which parts that we word aligned and which types of resources we used in the alignment process to explore the influence the different terminology systems and resources have on the recall and precision. After the analysis, we used the best configuration of the automatic word alignment for generation of candidate term pairs. We then manually verified the candidate term pairs and included the correct pairs in an English-Swedish dictionary. The results indicate that more resources and resource types give better results but the size of the parts used to generate the resources only partly affects the quality. The most generally useful resources were generated from ICD-10 and resources generated from MeSH were not as general as other resources. Systematic inter-language differences in the structure of the terminology system rubrics make the rubrics harder to align. Manually created training resources give nearly as good results as a union of static resources, statistical resources and training resources and noticeably better results than a union of static resources and statistical resources. The verified English-Swedish dictionary contains 24,000 term pairs in base forms. More resources give better results in the automatic word alignment, but some resources only give small improvements. The most important type of resource is training and the most general resources were generated from ICD-10.

Creating a medical dictionary using word alignment: The influence of sources and resources

PubMed Central

Nyström, Mikael; Merkel, Magnus; Petersson, Håkan; Åhlfeldt, Hans

2007-01-01

Background Automatic word alignment of parallel texts with the same content in different languages is among other things used to generate dictionaries for new translations. The quality of the generated word alignment depends on the quality of the input resources. In this paper we report on automatic word alignment of the English and Swedish versions of the medical terminology systems ICD-10, ICF, NCSP, KSH97-P and parts of MeSH and how the terminology systems and type of resources influence the quality. Methods We automatically word aligned the terminology systems using static resources, like dictionaries, statistical resources, like statistically derived dictionaries, and training resources, which were generated from manual word alignment. We varied which part of the terminology systems that we used to generate the resources, which parts that we word aligned and which types of resources we used in the alignment process to explore the influence the different terminology systems and resources have on the recall and precision. After the analysis, we used the best configuration of the automatic word alignment for generation of candidate term pairs. We then manually verified the candidate term pairs and included the correct pairs in an English-Swedish dictionary. Results The results indicate that more resources and resource types give better results but the size of the parts used to generate the resources only partly affects the quality. The most generally useful resources were generated from ICD-10 and resources generated from MeSH were not as general as other resources. Systematic inter-language differences in the structure of the terminology system rubrics make the rubrics harder to align. Manually created training resources give nearly as good results as a union of static resources, statistical resources and training resources and noticeably better results than a union of static resources and statistical resources. The verified English-Swedish dictionary contains 24,000 term pairs in base forms. Conclusion More resources give better results in the automatic word alignment, but some resources only give small improvements. The most important type of resource is training and the most general resources were generated from ICD-10. PMID:18036221

Relating cell shape and mechanical stress in a spatially disordered epithelium using a vertex-based model

PubMed Central

Nestor-Bergmann, Alexander; Goddard, Georgina; Woolner, Sarah; Jensen, Oliver E

2018-01-01

Abstract Using a popular vertex-based model to describe a spatially disordered planar epithelial monolayer, we examine the relationship between cell shape and mechanical stress at the cell and tissue level. Deriving expressions for stress tensors starting from an energetic formulation of the model, we show that the principal axes of stress for an individual cell align with the principal axes of shape, and we determine the bulk effective tissue pressure when the monolayer is isotropic at the tissue level. Using simulations for a monolayer that is not under peripheral stress, we fit parameters of the model to experimental data for Xenopus embryonic tissue. The model predicts that mechanical interactions can generate mesoscopic patterns within the monolayer that exhibit long-range correlations in cell shape. The model also suggests that the orientation of mechanical and geometric cues for processes such as cell division are likely to be strongly correlated in real epithelia. Some limitations of the model in capturing geometric features of Xenopus epithelial cells are highlighted. PMID:28992197

Shielded beam delivery apparatus and method

DOEpatents

Hershcovitch, Ady; Montano, Rory Dominick

2006-07-11

An apparatus includes a plasma generator aligned with a beam generator for producing a plasma to shield an energized beam. An electrode is coaxially aligned with the plasma generator and followed in turn by a vortex generator coaxially aligned with the electrode. A target is spaced from the vortex generator inside a fluid environment. The electrode is electrically biased relative to the electrically grounded target for driving the plasma toward the target inside a vortex shield.

Using structure to explore the sequence alignment space of remote homologs.

PubMed

Kuziemko, Andrew; Honig, Barry; Petrey, Donald

2011-10-01

Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

Structural re-alignment in an immunologic surface region of ricin A chain

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

Zemla, A T; Zhou, C E

2007-07-24

We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connectingmore » the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.« less

Virtual viewpoint generation for three-dimensional display based on the compressive light field

NASA Astrophysics Data System (ADS)

Meng, Qiao; Sang, Xinzhu; Chen, Duo; Guo, Nan; Yan, Binbin; Yu, Chongxiu; Dou, Wenhua; Xiao, Liquan

2016-10-01

Virtual view-point generation is one of the key technologies the three-dimensional (3D) display, which renders the new scene image perspective with the existing viewpoints. The three-dimensional scene information can be effectively recovered at different viewing angles to allow users to switch between different views. However, in the process of multiple viewpoints matching, when N free viewpoints are received, we need to match N viewpoints each other, namely matching C 2N = N(N-1)/2 times, and even in the process of matching different baselines errors can occur. To address the problem of great complexity of the traditional virtual view point generation process, a novel and rapid virtual view point generation algorithm is presented in this paper, and actual light field information is used rather than the geometric information. Moreover, for better making the data actual meaning, we mainly use nonnegative tensor factorization(NTF). A tensor representation is introduced for virtual multilayer displays. The light field emitted by an N-layer, M-frame display is represented by a sparse set of non-zero elements restricted to a plane within an Nth-order, rank-M tensor. The tensor representation allows for optimal decomposition of a light field into time-multiplexed, light-attenuating layers using NTF. Finally, the compressive light field of multilayer displays information synthesis is used to obtain virtual view-point by multiple multiplication. Experimental results show that the approach not only the original light field is restored with the high image quality, whose PSNR is 25.6dB, but also the deficiency of traditional matching is made up and any viewpoint can obtained from N free viewpoints.

On squares of representations of compact Lie algebras

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

Zeier, Robert, E-mail: robert.zeier@ch.tum.de; Zimborás, Zoltán, E-mail: zimboras@gmail.com

We study how tensor products of representations decompose when restricted from a compact Lie algebra to one of its subalgebras. In particular, we are interested in tensor squares which are tensor products of a representation with itself. We show in a classification-free manner that the sum of multiplicities and the sum of squares of multiplicities in the corresponding decomposition of a tensor square into irreducible representations has to strictly grow when restricted from a compact semisimple Lie algebra to a proper subalgebra. For this purpose, relevant details on tensor products of representations are compiled from the literature. Since the summore » of squares of multiplicities is equal to the dimension of the commutant of the tensor-square representation, it can be determined by linear-algebra computations in a scenario where an a priori unknown Lie algebra is given by a set of generators which might not be a linear basis. Hence, our results offer a test to decide if a subalgebra of a compact semisimple Lie algebra is a proper one without calculating the relevant Lie closures, which can be naturally applied in the field of controlled quantum systems.« less

Extended mimetic gravity: Hamiltonian analysis and gradient instabilities

NASA Astrophysics Data System (ADS)

Takahashi, Kazufumi; Kobayashi, Tsutomu

2017-11-01

We propose a novel class of degenerate higher-order scalar-tensor theories as an extension of mimetic gravity. By performing a noninvertible conformal transformation on "seed" scalar-tensor theories which may be nondegenerate, we can generate a large class of theories with at most three physical degrees of freedom. We identify a general seed theory for which this is possible. Cosmological perturbations in these extended mimetic theories are also studied. It is shown that either of tensor or scalar perturbations is plagued with gradient instabilities, except for a special case where the scalar perturbations are presumably strongly coupled, or otherwise there appear ghost instabilities.

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

Spatial Mapping of Translational Diffusion Coefficients Using Diffusion Tensor Imaging: A Mathematical Description

PubMed Central

SHETTY, ANIL N.; CHIANG, SHARON; MALETIC-SAVATIC, MIRJANA; KASPRIAN, GREGOR; VANNUCCI, MARINA; LEE, WESLEY

2016-01-01

In this article, we discuss the theoretical background for diffusion weighted imaging and diffusion tensor imaging. Molecular diffusion is a random process involving thermal Brownian motion. In biological tissues, the underlying microstructures restrict the diffusion of water molecules, making diffusion directionally dependent. Water diffusion in tissue is mathematically characterized by the diffusion tensor, the elements of which contain information about the magnitude and direction of diffusion and is a function of the coordinate system. Thus, it is possible to generate contrast in tissue based primarily on diffusion effects. Expressing diffusion in terms of the measured diffusion coefficient (eigenvalue) in any one direction can lead to errors. Nowhere is this more evident than in white matter, due to the preferential orientation of myelin fibers. The directional dependency is removed by diagonalization of the diffusion tensor, which then yields a set of three eigenvalues and eigenvectors, representing the magnitude and direction of the three orthogonal axes of the diffusion ellipsoid, respectively. For example, the eigenvalue corresponding to the eigenvector along the long axis of the fiber corresponds qualitatively to diffusion with least restriction. Determination of the principal values of the diffusion tensor and various anisotropic indices provides structural information. We review the use of diffusion measurements using the modified Stejskal–Tanner diffusion equation. The anisotropy is analyzed by decomposing the diffusion tensor based on symmetrical properties describing the geometry of diffusion tensor. We further describe diffusion tensor properties in visualizing fiber tract organization of the human brain. PMID:27441031

Longitudinal stability of MRI for mapping brain change using tensor-based morphometry.

PubMed

Leow, Alex D; Klunder, Andrea D; Jack, Clifford R; Toga, Arthur W; Dale, Anders M; Bernstein, Matt A; Britson, Paula J; Gunter, Jeffrey L; Ward, Chadwick P; Whitwell, Jennifer L; Borowski, Bret J; Fleisher, Adam S; Fox, Nick C; Harvey, Danielle; Kornak, John; Schuff, Norbert; Studholme, Colin; Alexander, Gene E; Weiner, Michael W; Thompson, Paul M

2006-06-01

Measures of brain change can be computed from sequential MRI scans, providing valuable information on disease progression, e.g., for patient monitoring and drug trials. Tensor-based morphometry (TBM) creates maps of these brain changes, visualizing the 3D profile and rates of tissue growth or atrophy, but its sensitivity depends on the contrast and geometric stability of the images. As part of the Alzheimer's Disease Neuroimaging Initiative (ADNI), 17 normal elderly subjects were scanned twice (at a 2-week interval) with several 3D 1.5 T MRI pulse sequences: high and low flip angle SPGR/FLASH (from which Synthetic T1 images were generated), MP-RAGE, IR-SPGR (N = 10) and MEDIC (N = 7) scans. For each subject and scan type, a 3D deformation map aligned baseline and follow-up scans, computed with a nonlinear, inverse-consistent elastic registration algorithm. Voxelwise statistics, in ICBM stereotaxic space, visualized the profile of mean absolute change and its cross-subject variance; these maps were then compared using permutation testing. Image stability depended on: (1) the pulse sequence; (2) the transmit/receive coil type (birdcage versus phased array); (3) spatial distortion corrections (using MEDIC sequence information); (4) B1-field intensity inhomogeneity correction (using N3). SPGR/FLASH images acquired using a birdcage coil had least overall deviation. N3 correction reduced coil type and pulse sequence differences and improved scan reproducibility, except for Synthetic T1 images (which were intrinsically corrected for B1-inhomogeneity). No strong evidence favored B0 correction. Although SPGR/FLASH images showed least deviation here, pulse sequence selection for the ADNI project was based on multiple additional image analyses, to be reported elsewhere.

Longitudinal stability of MRI for mapping brain change using tensor-based morphometry

PubMed Central

Leow, Alex D.; Klunder, Andrea D.; Jack, Clifford R.; Toga, Arthur W.; Dale, Anders M.; Bernstein, Matt A.; Britson, Paula J.; Gunter, Jeffrey L.; Ward, Chadwick P.; Whitwell, Jennifer L.; Borowski, Bret J.; Fleisher, Adam S.; Fox, Nick C.; Harvey, Danielle; Kornak, John; Schuff, Norbert; Studholme, Colin; Alexander, Gene E.; Weiner, Michael W.; Thompson, Paul M.

2007-01-01

Measures of brain change can be computed from sequential MRI scans, providing valuable information on disease progression, e.g., for patient monitoring and drug trials. Tensor-based morphometry (TBM) creates maps of these brain changes, visualizing the 3D profile and rates of tissue growth or atrophy, but its sensitivity depends on the contrast and geometric stability of the images. A s part of the Alzheimer’s Disease Neuroimaging Initiative (ADNI), 17 normal elderly subjects were scanned twice (at a 2-week interval) with several 3D 1.5 T MRI pulse sequences: high and low flip angle SPGR/FLASH (from which Synthetic T1 images were generated), MP-RAGE, IR-SPGR (N = 10) and MEDIC (N = 7) scans. For each subject and scan type, a 3D deformation map aligned baseline and follow-up scans, computed with a nonlinear, inverse-consistent elastic registration algorithm. Voxelwise statistics, in ICBM stereotaxic space, visualized the profile of mean absolute change and its cross-subject variance; these maps were then compared using permutation testing. Image stability depended on: (1) the pulse sequence; (2) the transmit/receive coil type (birdcage versus phased array); (3) spatial distortion corrections (using MEDIC sequence information); (4) B1-field intensity inhomogeneity correction (using N3). SPGR/FLASH images acquired using a birdcage coil had least overall deviation. N3 correction reduced coil type and pulse sequence differences and improved scan reproducibility, except for Synthetic T1 images (which were intrinsically corrected for B1-inhomogeneity). No strong evidence favored B0 correction. Although SPGR/FLASH images showed least deviation here, pulse sequence selection for the ADNI project was based on multiple additional image analyses, to be reported elsewhere. PMID:16480900

Influence of N-H...O and C-H...O hydrogen bonds on the 17O NMR tensors in crystalline uracil: computational study.

PubMed

Ida, Ramsey; De Clerk, Maurice; Wu, Gang

2006-01-26

We report a computational study for the 17O NMR tensors (electric field gradient and chemical shielding tensors) in crystalline uracil. We found that N-H...O and C-H...O hydrogen bonds around the uracil molecule in the crystal lattice have quite different influences on the 17O NMR tensors for the two C=O groups. The computed 17O NMR tensors on O4, which is involved in two strong N-H...O hydrogen bonds, show remarkable sensitivity toward the choice of cluster model, whereas the 17O NMR tensors on O2, which is involved in two weak C-H...O hydrogen bonds, show much smaller improvement when the cluster model includes the C-H...O hydrogen bonds. Our results demonstrate that it is important to have accurate hydrogen atom positions in the molecular models used for 17O NMR tensor calculations. In the absence of low-temperature neutron diffraction data, an effective way to generate reliable hydrogen atom positions in the molecular cluster model is to employ partial geometry optimization for hydrogen atom positions using a cluster model that includes all neighboring hydrogen-bonded molecules. Using an optimized seven-molecule model (a total of 84 atoms), we were able to reproduce the experimental 17O NMR tensors to a reasonably good degree of accuracy. However, we also found that the accuracy for the calculated 17O NMR tensors at O2 is not as good as that found for the corresponding tensors at O4. In particular, at the B3LYP/6-311++G(d,p) level of theory, the individual 17O chemical shielding tensor components differ by less than 10 and 30 ppm from the experimental values for O4 and O2, respectively. For the 17O quadrupole coupling constant, the calculated values differ by 0.30 and 0.87 MHz from the experimental values for O4 and O2, respectively.

Full moment tensors with uncertainties for the 2017 North Korea declared nuclear test and for a collocated, subsequent event

NASA Astrophysics Data System (ADS)

Alvizuri, C. R.; Tape, C.

2017-12-01

A seismic moment tensor is a 3×3 symmetric matrix that characterizes the far-field seismic radiation from a source, whether it be an earthquake, volcanic event, explosion. We estimate full moment tensors and their uncertainties for the North Korea declared nuclear test and for a collocated event that occurred eight minutes later. The nuclear test and the subsequent event occurred on September 3, 2017 at around 03:30 and 03:38 UTC time. We perform a grid search over the six-dimensional space of moment tensors, generating synthetic waveforms at each moment tensor grid point and then evaluating a misfit function between the observed and synthetic waveforms. The synthetic waveforms are computed using a 1-D structure model for the region; this approximation requires careful assessment of time shifts between data and synthetics, as well as careful choice of the bandpass for filtering. For each moment tensor we characterize its uncertainty in terms of waveform misfit, a probability function, and a confidence curve for the probability that the true moment tensor lies within the neighborhood of the optimal moment tensor. For each event we estimate its moment tensor using observed waveforms from all available seismic stations within a 2000-km radius. We use as much of the waveform as possible, including surface waves for all stations, and body waves above 1 Hz for some of the closest stations. Our preliminary magnitude estimates are Mw 5.1-5.3 for the first event and Mw 4.7 for the second event. Our results show a dominantly positive isotropic moment tensor for the first event, and a dominantly negative isotropic moment tensor for the subsequent event. As expected, the details of the probability density, waveform fit, and confidence curves are influenced by the structural model, the choice of filter frequencies, and the selection of stations.

Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129Xe NMR Spectroscopy

PubMed Central

Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J.; Laitinen, Risto; Jokisaari, Jukka

2017-01-01

Abstract An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o‐ and m‐fluorophenol, whose previously unknown clathrate structures have been studied by 129Xe NMR spectroscopy. The high sensitivity of the 129Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures. PMID:28111848

Shape-from-focus by tensor voting.

PubMed

Hariharan, R; Rajagopalan, A N

2012-07-01

In this correspondence, we address the task of recovering shape-from-focus (SFF) as a perceptual organization problem in 3-D. Using tensor voting, depth hypotheses from different focus operators are validated based on their likelihood to be part of a coherent 3-D surface, thereby exploiting scene geometry and focus information to generate reliable depth estimates. The proposed method is fast and yields significantly better results compared with existing SFF methods.

On scalar and vector fields coupled to the energy-momentum tensor

NASA Astrophysics Data System (ADS)

Jiménez, Jose Beltrán; Cembranos, Jose A. R.; Sánchez Velázquez, Jose M.

2018-05-01

We consider theories for scalar and vector fields coupled to the energy-momentum tensor. Since these fields also carry a non-trivial energy-momentum tensor, the coupling prescription generates self-interactions. In analogy with gravity theories, we build the action by means of an iterative process that leads to an infinite series, which can be resumed as the solution of a set of differential equations. We show that, in some particular cases, the equations become algebraic and that is also possible to find solutions in the form of polynomials. We briefly review the case of the scalar field that has already been studied in the literature and extend the analysis to the case of derivative (disformal) couplings. We then explore theories with vector fields, distinguishing between gauge-and non-gauge-invariant couplings. Interactions with matter are also considered, taking a scalar field as a proxy for the matter sector. We also discuss the ambiguity introduced by superpotential (boundary) terms in the definition of the energy-momentum tensor and use them to show that it is also possible to generate Galileon-like interactions with this procedure. We finally use collider and astrophysical observations to set constraints on the dimensionful coupling which characterises the phenomenology of these models.

SPHERE: SPherical Harmonic Elastic REgistration of HARDI Data

PubMed Central

Yap, Pew-Thian; Chen, Yasheng; An, Hongyu; Yang, Yang; Gilmore, John H.; Lin, Weili

2010-01-01

In contrast to the more common Diffusion Tensor Imaging (DTI), High Angular Resolution Diffusion Imaging (HARDI) allows superior delineation of angular microstructures of brain white matter, and makes possible multiple-fiber modeling of each voxel for better characterization of brain connectivity. However, the complex orientation information afforded by HARDI makes registration of HARDI images more complicated than scalar images. In particular, the question of how much orientation information is needed for satisfactory alignment has not been sufficiently addressed. Low order orientation representation is generally more robust than high order representation, although the latter provides more information for correct alignment of fiber pathways. However, high order representation, when naïvely utilized, might not necessarily be conducive to improving registration accuracy since similar structures with significant orientation differences prior to proper alignment might be mistakenly taken as non-matching structures. We present in this paper a HARDI registration algorithm, called SPherical Harmonic Elastic REgistration (SPHERE), which in a principled means hierarchically extracts orientation information from HARDI data for structural alignment. The image volumes are first registered using robust, relatively direction invariant features derived from the Orientation Distribution Function (ODF), and the alignment is then further refined using spherical harmonic (SH) representation with gradually increasing orders. This progression from non-directional, single-directional to multi-directional representation provides a systematic means of extracting directional information given by diffusion-weighted imaging. Coupled with a template-subject-consistent soft-correspondence-matching scheme, this approach allows robust and accurate alignment of HARDI data. Experimental results show marked increase in accuracy over a state-of-the-art DTI registration algorithm. PMID:21147231

Federated Tensor Factorization for Computational Phenotyping

PubMed Central

Kim, Yejin; Sun, Jimeng; Yu, Hwanjo; Jiang, Xiaoqian

2017-01-01

Tensor factorization models offer an effective approach to convert massive electronic health records into meaningful clinical concepts (phenotypes) for data analysis. These models need a large amount of diverse samples to avoid population bias. An open challenge is how to derive phenotypes jointly across multiple hospitals, in which direct patient-level data sharing is not possible (e.g., due to institutional policies). In this paper, we developed a novel solution to enable federated tensor factorization for computational phenotyping without sharing patient-level data. We developed secure data harmonization and federated computation procedures based on alternating direction method of multipliers (ADMM). Using this method, the multiple hospitals iteratively update tensors and transfer secure summarized information to a central server, and the server aggregates the information to generate phenotypes. We demonstrated with real medical datasets that our method resembles the centralized training model (based on combined datasets) in terms of accuracy and phenotypes discovery while respecting privacy. PMID:29071165

Tensor non-Gaussianity from axion-gauge-fields dynamics: parameter search

NASA Astrophysics Data System (ADS)

Agrawal, Aniket; Fujita, Tomohiro; Komatsu, Eiichiro

2018-06-01

We calculate the bispectrum of scale-invariant tensor modes sourced by spectator SU(2) gauge fields during inflation in a model containing a scalar inflaton, a pseudoscalar axion and SU(2) gauge fields. A large bispectrum is generated in this model at tree-level as the gauge fields contain a tensor degree of freedom, and its production is dominated by self-coupling of the gauge fields. This is a unique feature of non-Abelian gauge theory. The shape of the tensor bispectrum is approximately an equilateral shape for 3lesssim mQlesssim 4, where mQ is an effective dimensionless mass of the SU(2) field normalised by the Hubble expansion rate during inflation. The amplitude of non-Gaussianity of the tensor modes, characterised by the ratio Bh/P2h, is inversely proportional to the energy density fraction of the gauge field. This ratio can be much greater than unity, whereas the ratio from the vacuum fluctuation of the metric is of order unity. The bispectrum is effective at constraining large mQ regions of the parameter space, whereas the power spectrum constrains small mQ regions.

Bimodule structure of the mixed tensor product over Uq sℓ (2 | 1) and quantum walled Brauer algebra

NASA Astrophysics Data System (ADS)

Bulgakova, D. V.; Kiselev, A. M.; Tipunin, I. Yu.

2018-03-01

We study a mixed tensor product 3⊗m ⊗3 ‾ ⊗ n of the three-dimensional fundamental representations of the Hopf algebra Uq sℓ (2 | 1), whenever q is not a root of unity. Formulas for the decomposition of tensor products of any simple and projective Uq sℓ (2 | 1)-module with the generating modules 3 and 3 ‾ are obtained. The centralizer of Uq sℓ (2 | 1) on the mixed tensor product is calculated. It is shown to be the quotient Xm,n of the quantum walled Brauer algebra qw Bm,n. The structure of projective modules over Xm,n is written down explicitly. It is known that the walled Brauer algebras form an infinite tower. We have calculated the corresponding restriction functors on simple and projective modules over Xm,n. This result forms a crucial step in decomposition of the mixed tensor product as a bimodule over Xm,n ⊠Uq sℓ (2 | 1). We give an explicit bimodule structure for all m , n.

Spherical tensor analysis of polar liquid crystals with biaxial and chiral molecules

NASA Astrophysics Data System (ADS)

Iwamoto, Mitsumasa; Zhong-can, Ou-Yang

2012-11-01

With the help of spherical tensor expression, an irreducible calculus of a Lth-rank macroscopic susceptibility χ for a polar liquid crystal (PLC) of biaxial and chiral molecules written as the average of molecular hyperpolarizability tensor β associated with their spherical orientational order parameters (0⩽l⩽L) is presented. Comprehensive formulas of L=1,2 have been obtained and the latter explains the optical activity and spontaneous splay texture observed in bent-core PLC. The expression of L=3 specifies for the molecules with D2 symmetry which can be applied to analyze the nonlinear optical second harmonic generation (SHG) observed in proteins, peptides, and double-stranded DNA at interfaces.

Effective field theory of statistical anisotropies for primordial bispectrum and gravitational waves

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

Rostami, Tahereh; Karami, Asieh; Firouzjahi, Hassan, E-mail: t.rostami@ipm.ir, E-mail: karami@ipm.ir, E-mail: firouz@ipm.ir

2017-06-01

We present the effective field theory studies of primordial statistical anisotropies in models of anisotropic inflation. The general action in unitary gauge is presented to calculate the leading interactions between the gauge field fluctuations, the curvature perturbations and the tensor perturbations. The anisotropies in scalar power spectrum and bispectrum are calculated and the dependence of these anisotropies to EFT couplings are presented. In addition, we calculate the statistical anisotropy in tensor power spectrum and the scalar-tensor cross correlation. Our EFT approach incorporates anisotropies generated in models with non-trivial speed for the gauge field fluctuations and sound speed for scalar perturbationsmore » such as in DBI inflation.« less

Director Field Analysis (DFA): Exploring Local White Matter Geometric Structure in Diffusion MRI.

PubMed

Cheng, Jian; Basser, Peter J

2018-01-01

In Diffusion Tensor Imaging (DTI) or High Angular Resolution Diffusion Imaging (HARDI), a tensor field or a spherical function field (e.g., an orientation distribution function field), can be estimated from measured diffusion weighted images. In this paper, inspired by the microscopic theoretical treatment of phases in liquid crystals, we introduce a novel mathematical framework, called Director Field Analysis (DFA), to study local geometric structural information of white matter based on the reconstructed tensor field or spherical function field: (1) We propose a set of mathematical tools to process general director data, which consists of dyadic tensors that have orientations but no direction. (2) We propose Orientational Order (OO) and Orientational Dispersion (OD) indices to describe the degree of alignment and dispersion of a spherical function in a single voxel or in a region, respectively; (3) We also show how to construct a local orthogonal coordinate frame in each voxel exhibiting anisotropic diffusion; (4) Finally, we define three indices to describe three types of orientational distortion (splay, bend, and twist) in a local spatial neighborhood, and a total distortion index to describe distortions of all three types. To our knowledge, this is the first work to quantitatively describe orientational distortion (splay, bend, and twist) in general spherical function fields from DTI or HARDI data. The proposed DFA and its related mathematical tools can be used to process not only diffusion MRI data but also general director field data, and the proposed scalar indices are useful for detecting local geometric changes of white matter for voxel-based or tract-based analysis in both DTI and HARDI acquisitions. The related codes and a tutorial for DFA will be released in DMRITool. Copyright © 2017 Elsevier B.V. All rights reserved.

Linear Tidal Vestige Found in the WM Sheet

NASA Astrophysics Data System (ADS)

Lee, Jounghun; Kim, Suk; Rey, Soo-Chang

2018-06-01

We present a vestige of the linear tidal influence on the spin orientations of the constituent galaxies of the WM sheet discovered in the vicinity of the Virgo Cluster and the Local Void. The WM sheet is chosen as an optimal target since it has a rectangular parallelepiped-like shape whose three sides are in parallel with the supergalactic Cartesian axes. Determining three probability density functions of the absolute values of the supergalactic Cartesian components of the spin vectors of the WM sheet galaxies, we investigate their alignments with the principal directions of the surrounding large-scale tidal field. When the WM sheet galaxies located in the central region within the distance of 2 h ‑1 Mpc are excluded, the spin vectors of the remaining WM sheet galaxies are found to be weakly aligned, strongly aligned, and strongly anti-aligned with the minor, intermediate, and major principal directions of the surrounding large-scale tidal field, respectively. To examine whether or not the origin of the observed alignment tendency from the WM sheet is the linear tidal effect, we infer the eigenvalues of the linear tidal tensor from the axial ratios of the WM sheet with the help of the Zeldovich approximation and conduct a full analytic evaluation of the prediction of the linear tidal torque model for the three probability density functions. A detailed comparison between the analytical and the observational results reveals a good quantitative agreement not only in the behaviors but also in the amplitudes of the three probability density functions.

Diffusion tensor imaging with tract-based spatial statistics reveals local white matter abnormalities in preterm infants.

PubMed

Anjari, Mustafa; Srinivasan, Latha; Allsop, Joanna M; Hajnal, Joseph V; Rutherford, Mary A; Edwards, A David; Counsell, Serena J

2007-04-15

Infants born preterm have a high incidence of neurodevelopmental impairment in later childhood, often associated with poorly defined cerebral white matter abnormalities. Diffusion tensor imaging quantifies the diffusion of water within tissues and can assess microstructural abnormalities in the developing preterm brain. Tract-based spatial statistics (TBSS) is an automated observer-independent method of aligning fractional anisotropy (FA) images from multiple subjects to allow groupwise comparisons of diffusion tensor imaging data. We applied TBSS to test the hypothesis that preterm infants have reduced fractional anisotropy in specific regions of white matter compared to term-born controls. We studied 26 preterm infants with no evidence of focal lesions on conventional magnetic resonance imaging (MRI) at term equivalent age and 6 healthy term-born control infants. We found that the centrum semiovale, frontal white matter and the genu of the corpus callosum showed significantly lower FA in the preterm group. Infants born at less than or equal to 28 weeks gestational age (n=11) displayed additional reductions in FA in the external capsule, the posterior aspect of the posterior limb of the internal capsule and the isthmus and middle portion of the body of the corpus callosum. This study demonstrates that TBSS provides an observer-independent method of identifying white matter abnormalities in the preterm brain at term equivalent age in the absence of focal lesions.

H?, D? and HD adsorption upon the metal-organic framework [Cu?Zn?(btc)?]? studied by pulsed ENDOR and HYSCORE spectroscopy

NASA Astrophysics Data System (ADS)

Jee, Bettina; Hartmann, Martin; Pöppl, Andreas

2013-10-01

The adsorption of hydrogen has become interesting in terms of gas separation as well as safe and reversible storage of hydrogen as an energy carrier. In this regard, metal-organic framework compounds are potential candidates. The metal-organic framework [Cu?Zn?(btc)?]? as a partially Zn-substituted analogue of the well known compound HKUST-1 is well suited for studying adsorption geometries at cupric ions by electron paramagnetic resonance (EPR) methods due to the formation of few mixed Cu/Zn paddle wheel units with isolated S = 1/2 electron spins. The adsorption of hydrogen (H2) as well as the deuterium (D2) and HD molecules were investigated by continuous wave EPR and pulsed ENDOR and HYSCORE spectroscopy. The principal values of the proton and deuterium hyperfine coupling tensors ? and ? were determined by spectral simulations as well as of the deuterium nuclear quadrupole tensor ? for adsorbed HD and D2. The results show a side-on coordination of HD and D2 with identical Cu-H and Cu-D distances rCuX = 2.8 Å with the tensors ? and ? aligned parallel to the C4 symmetry axis of the paddle wheel unit. A thermodynamic non-equilibrium state with J = 1, mJ = ±1 is indicated by the experimental data with ? and ? averaged by rotation around C4.

Simultaneous Tensor Decomposition and Completion Using Factor Priors.

PubMed

Chen, Yi-Lei; Hsu, Chiou-Ting Candy; Liao, Hong-Yuan Mark

2013-08-27

Tensor completion, which is a high-order extension of matrix completion, has generated a great deal of research interest in recent years. Given a tensor with incomplete entries, existing methods use either factorization or completion schemes to recover the missing parts. However, as the number of missing entries increases, factorization schemes may overfit the model because of incorrectly predefined ranks, while completion schemes may fail to interpret the model factors. In this paper, we introduce a novel concept: complete the missing entries and simultaneously capture the underlying model structure. To this end, we propose a method called Simultaneous Tensor Decomposition and Completion (STDC) that combines a rank minimization technique with Tucker model decomposition. Moreover, as the model structure is implicitly included in the Tucker model, we use factor priors, which are usually known a priori in real-world tensor objects, to characterize the underlying joint-manifold drawn from the model factors. We conducted experiments to empirically verify the convergence of our algorithm on synthetic data, and evaluate its effectiveness on various kinds of real-world data. The results demonstrate the efficacy of the proposed method and its potential usage in tensor-based applications. It also outperforms state-of-the-art methods on multilinear model analysis and visual data completion tasks.

Expression of Lithospheric Shear Zones in Rock Elasticity Tensors and in Anisotropic Receiver Functions and Inferences on the Roots of Faults and Lower Crustal Deformation

NASA Astrophysics Data System (ADS)

Schulte-Pelkum, V.; Condit, C.; Brownlee, S. J.; Mahan, K. H.; Raju, A.

2016-12-01

We investigate shear zone-related deformation fabric from field samples, its dependence on conditions during fabric formation, and its detection in situ using seismic data. We present a compilation of published rock elasticity tensors measured in the lab or calculated from middle and deep crustal samples and compare the strength and symmetry of seismic anisotropy as a function of location within a shear zone, pressure-temperature conditions during formation, and composition. Common strengths of seismic anisotropy range from a few to 10 percent. Apart from the typically considered fabric in mica, amphibole and quartz also display fabrics that induce seismic anisotropy, although the interaction between different minerals can result in destructive interference in the total measured anisotropy. The availability of full elasticity tensors enables us to predict the seismic signal from rock fabric at depth. A method particularly sensitive to anisotropy of a few percent in localized zones of strain at depth is the analysis of azimuthally dependent amplitude and polarity variations in teleseismic receiver functions. We present seismic results from California and Colorado. In California, strikes of seismically detected fabric show a strong alignment with current strike-slip motion between the Pacific and North American plates, with high signal strength near faults and from depths below the brittle-ductile transition. These results suggest that the faults have roots in the ductile crust; determining the degree of localization, i.e., the width of the fault-associated shear zones, would require an analysis with denser station coverage, which now exists in some areas. In Colorado, strikes of seismically detected fabric show a broad NW-SE to NNW-SSE alignment that may be related to Proterozoic fabric developed at high temperatures, but locally may also show isotropic dipping contrasts associated with Laramide faulting. The broad trend is punctuated with NE-SW-trending strikes parallel to exhumed and highly localized structures such as the Idaho Springs-Ralston and Black Canyon shear zones. In either case, denser seismic studies should elucidate the width of the deep seismic expression of the shear zones.

New constraints on micro-seismicity and stress state in the western part of the North Anatolian Fault Zone: Observations from a dense seismic array

NASA Astrophysics Data System (ADS)

Altuncu Poyraz, Selda; Teoman, M. Uğur; Türkelli, Niyazi; Kahraman, Metin; Cambaz, Didem; Mutlu, Ahu; Rost, Sebastian; Houseman, Gregory A.; Thompson, David A.; Cornwell, David; Utkucu, Murat; Gülen, Levent

2015-08-01

With the aim of extensively investigating the crustal structure beneath the western segment of the North Anatolian Fault Zone where it splays into northern and southern branches, a temporary seismic network (dense array for North Anatolia-DANA) consisting of 70 stations was deployed in early May 2012 and operated for 18 months in the Sakarya region during the FaultLab experiment. Out of 2437 events contaminated by explosions, we extracted 1371 well located earthquakes. The enhanced station coverage having a nominal station spacing of 7 km, lead to a minimum magnitude calculation of 0.1. Horizontal and vertical location uncertainties within the array do not exceed 0.8 km and 0.9 km, respectively. We observe considerable seismic activity along both branches of the fault where the depth of the seismogenic zone was mostly confined to 15 km. Using our current earthquake catalog we obtained a b-value of 1. We also mapped the b-value variation with depth and observed a gradual decrease. Furthermore, we determined the source parameters of 41 earthquakes with magnitudes greater than 1.8 using P-wave first motion polarity method. Regional Moment Tensor Inversion method was also applied to earthquakes with magnitudes greater than 3.0. Focal mechanism solutions confirm that Sakarya and its vicinity is stressed by a compressional regime showing a primarily oblique-slip motion character. Stress tensor analysis indicates that the maximum principal stress is aligned in WNW-ESE direction and the tensional axis is aligned in NNE-SSW direction.

Large deformation analysis of axisymmetric inhomogeneities including coupled elastic and plastic anisotropy

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

Brannon, R.M.

1996-12-31

A mathematical framework is developed for the study of materials containing axisymmetric inclusions or flaws such as ellipsoidal voids, penny-shaped cracks, or fibers of circular cross-section. The general case of nonuniform statistical distributions of such heterogeneities is attacked by first considering a spatially uniform distribution of flaws that are all oriented in the same direction. Assuming an isotropic substrate, the macroscopic material properties of this simpler microstructure naturally should be transversely isotropic. An orthogonal basis for the linear subspace consisting of all double-symmetric transversely-isotropic fourth-order tensors associated with a given material vector is applied to deduce the explicit functional dependencemore » of the material properties of these aligned materials on the shared symmetry axis. The aligned and uniform microstructure seems geometrically simple enough that the macroscopic transversely isotropic properties could be derived in closed form. Since the resulting properties are transversely isotropic, the analyst must therefore be able to identify the appropriate coefficients of the transverse basis. Once these functions are identified, a principle of superposition of strain rates ay be applied to define an expectation integral for the composite properties of a material containing arbitrary anisotropic distributions of axisymmetric inhomogeneities. A proposal for coupling plastic anisotropy to the elastic anisotropy is presented in which the composite yield surface is interpreted as a distortion of the isotropic substrate yield surface; the distortion directions are coupled to the elastic anisotropy directions. Finally, some commonly assumed properties (such as major symmetry) of the Cauchy tangent stiffness tensor are shown to be inappropriate for large distortions of anisotropic materials.« less

Strong second harmonic generation in two-dimensional ferroelectric IV-monochalcogenides

NASA Astrophysics Data System (ADS)

Panday, Suman Raj; Fregoso, Benjamin M.

2017-11-01

The two-dimensional ferroelectrics GeS, GeSe, SnS and SnSe are expected to have large spontaneous in-plane electric polarization and enhanced shift-current response. Using density functional methods, we show that these materials also exhibit the largest effective second harmonic generation reported so far. It can reach magnitudes up to 10~nm~V-1 which is about an order of magnitude larger than that of prototypical GaAs. To rationalize this result we model the optical response with a simple one-dimensional two-band model along the spontaneous polarization direction. Within this model the second-harmonic generation tensor is proportional to the shift-current response tensor. The large shift current and second harmonic responses of GeS, GeSe, SnS and SnSe make them promising non-linear materials for optoelectronic applications.

Obtaining orthotropic elasticity tensor using entries zeroing method.

NASA Astrophysics Data System (ADS)

Gierlach, Bartosz; Danek, Tomasz

2017-04-01

A generally anisotropic elasticity tensor obtained from measurements can be represented by a tensor belonging to one of eight material symmetry classes. Knowledge of symmetry class and orientation is helpful for describing physical properties of a medium. For each non-trivial symmetry class except isotropic this problem is nonlinear. A common method of obtaining effective tensor is a choosing its non-trivial symmetry class and minimizing Frobenius norm between measured and effective tensor in the same coordinate system. Global optimization algorithm has to be used to determine the best rotation of a tensor. In this contribution, we propose a new approach to obtain optimal tensor, with the assumption that it is orthotropic (or at least has a similar shape to the orthotropic one). In orthotropic form tensor 24 out of 36 entries are zeros. The idea is to minimize the sum of squared entries which are supposed to be equal to zero through rotation calculated with optimization algorithm - in this case Particle Swarm Optimization (PSO) algorithm. Quaternions were used to parametrize rotations in 3D space to improve computational efficiency. In order to avoid a choice of local minima we apply PSO several times and only if we obtain similar results for the third time we consider it as a correct value and finish computations. To analyze obtained results Monte-Carlo method was used. After thousands of single runs of PSO optimization, we obtained values of quaternion parts and plot them. Points concentrate in several points of the graph following the regular pattern. It suggests the existence of more complex symmetry in the analyzed tensor. Then thousands of realizations of generally anisotropic tensor were generated - each tensor entry was replaced with a random value drawn from normal distribution having a mean equal to measured tensor entry and standard deviation of the measurement. Each of these tensors was subject of PSO based optimization delivering quaternion for optimal rotation. Computations were parallelized with OpenMP to decrease computational time what enables different tensors to be processed by different threads. As a result the distributions of rotated tensor entries values were obtained. For the entries which were to be zeroed we can observe almost normal distributions having mean equal to zero or sum of two normal distributions having inverse means. Non-zero entries represent different distributions with two or three maxima. Analysis of obtained results shows that described method produces consistent values of quaternions used to rotate tensors. Despite of less complex target function in a process of optimization in comparison to common approach, entries zeroing method provides results which can be applied to obtain an orthotropic tensor with good reliability. Modification of the method can produce also a tool for obtaining effective tensors belonging to another symmetry classes. This research was supported by the Polish National Science Center under contract No. DEC-2013/11/B/ST10/0472.

Tensors and Differential Geometry Applied to Analytic and Numerical Coordinate Generation

DTIC Science & Technology

1981-01-01

or surfaces. Since the writing of the first memoir on the subject of tensor analysis by Ricci and Levi - Civita [11 in 1901 some very significant...available in the standard texts, such as, Levi - Civita [2], Weatherburn [3), McConnell [41, Eisenhart [51, [6], Tolman [7], Graustein [8], Synge and...Equations (216) have been used in Ref. [29] to compute the coordinates for arbitrary shaped two -dimensional bodies . §7. Miscellaneous Derivations. In this

The Riemann-Lanczos equations in general relativity and their integrability

NASA Astrophysics Data System (ADS)

Dolan, P.; Gerber, A.

2008-06-01

The aim of this paper is to examine the Riemann-Lanczos equations and how they can be made integrable. They consist of a system of linear first-order partial differential equations that arise in general relativity, whereby the Riemann curvature tensor is generated by an unknown third-order tensor potential field called the Lanczos tensor. Our approach is based on the theory of jet bundles, where all field variables and all their partial derivatives of all relevant orders are treated as independent variables alongside the local manifold coordinates (xa) on the given space-time manifold M. This approach is adopted in (a) Cartan's method of exterior differential systems, (b) Vessiot's dual method using vector field systems, and (c) the Janet-Riquier theory of systems of partial differential equations. All three methods allow for the most general situations under which integrability conditions can be found. They give equivalent results, namely, that involutivity is always achieved at all generic points of the jet manifold M after a finite number of prolongations. Two alternative methods that appear in the general relativity literature to find integrability conditions for the Riemann-Lanczos equations generate new partial differential equations for the Lanczos potential that introduce a source term, which is nonlinear in the components of the Riemann tensor. We show that such sources do not occur when either of method (a), (b), or (c) are used.

Machine Learning Interface for Medical Image Analysis.

PubMed

Zhang, Yi C; Kagen, Alexander C

2017-10-01

TensorFlow is a second-generation open-source machine learning software library with a built-in framework for implementing neural networks in wide variety of perceptual tasks. Although TensorFlow usage is well established with computer vision datasets, the TensorFlow interface with DICOM formats for medical imaging remains to be established. Our goal is to extend the TensorFlow API to accept raw DICOM images as input; 1513 DaTscan DICOM images were obtained from the Parkinson's Progression Markers Initiative (PPMI) database. DICOM pixel intensities were extracted and shaped into tensors, or n-dimensional arrays, to populate the training, validation, and test input datasets for machine learning. A simple neural network was constructed in TensorFlow to classify images into normal or Parkinson's disease groups. Training was executed over 1000 iterations for each cross-validation set. The gradient descent optimization and Adagrad optimization algorithms were used to minimize cross-entropy between the predicted and ground-truth labels. Cross-validation was performed ten times to produce a mean accuracy of 0.938 ± 0.047 (95 % CI 0.908-0.967). The mean sensitivity was 0.974 ± 0.043 (95 % CI 0.947-1.00) and mean specificity was 0.822 ± 0.207 (95 % CI 0.694-0.950). We extended the TensorFlow API to enable DICOM compatibility in the context of DaTscan image analysis. We implemented a neural network classifier that produces diagnostic accuracies on par with excellent results from previous machine learning models. These results indicate the potential role of TensorFlow as a useful adjunct diagnostic tool in the clinical setting.

Moment tensor clustering: a tool to monitor mining induced seismicity

NASA Astrophysics Data System (ADS)

Cesca, Simone; Dahm, Torsten; Tolga Sen, Ali

2013-04-01

Automated moment tensor inversion routines have been setup in the last decades for the analysis of global and regional seismicity. Recent developments could be used to analyse smaller events and larger datasets. In particular, applications to microseismicity, e.g. in mining environments, have then led to the generation of large moment tensor catalogues. Moment tensor catalogues provide a valuable information about the earthquake source and details of rupturing processes taking place in the seismogenic region. Earthquake focal mechanisms can be used to discuss the local stress field, possible orientations of the fault system or to evaluate the presence of shear and/or tensile cracks. Focal mechanism and moment tensor solutions are typically analysed for selected events, and quick and robust tools for the automated analysis of larger catalogues are needed. We propose here a method to perform cluster analysis for large moment tensor catalogues and identify families of events which characterize the studied microseismicity. Clusters include events with similar focal mechanisms, first requiring the definition of distance between focal mechanisms. Different metrics are here proposed, both for the case of pure double couple, constrained moment tensor and full moment tensor catalogues. Different clustering approaches are implemented and discussed. The method is here applied to synthetic and real datasets from mining environments to demonstrate its potential: the proposed cluserting techniques prove to be able to automatically recognise major clusters. An important application for mining monitoring concerns the early identification of anomalous rupture processes, which is relevant for the hazard assessment. This study is funded by the project MINE, which is part of the R&D-Programme GEOTECHNOLOGIEN. The project MINE is funded by the German Ministry of Education and Research (BMBF), Grant of project BMBF03G0737.

Forces and moments generated by removable thermoplastic aligners: incisor torque, premolar derotation, and molar distalization.

PubMed

Simon, Mareike; Keilig, Ludger; Schwarze, Jörg; Jung, Britta A; Bourauel, Christoph

2014-06-01

The exact force systems as well as their progressions generated by removable thermoplastic appliances have not been investigated. Thus, the purposes of this experimental study were to quantify the forces and moments delivered by a single aligner and a series of aligners (Invisalign; Align Technology, Santa Clara, Calif) and to investigate the influence of attachments and power ridges on the force transfer. We studied 970 aligners of the Invisalign system (60 series of aligners). The aligners came from 30 consecutive patients, of which 3 tooth movements (incisor torque, premolar derotation, molar distalization) with 20 movements each were analyzed. The 3 movement groups were subdivided so that 10 movements were supported with an attachment and 10 were not. The patients' ClinCheck (Align Technology, Santa Clara, Calif) was planned so that the movements to be investigated were performed in isolation in the respective quadrant. Resin replicas of the patients' intraoral situation before the start of the investigated movement were taken and mounted in a biomechanical measurement system. An aligner was put on the model, the force systems were measured, and the calculated movements were experimentally performed until no further forces or moments were generated. Subsequently, the next aligners were installed, and the measurements were repeated. The initial mean moments were about 7.3 N·mm for maxillary incisor torque and about 1.0 N for distalization. Significant differences in the generated moments were measured in the premolar derotation group, whether they were supported with an attachment (8.8 N·mm) or not (1.2 N·mm). All measurements showed an exponential force change. Apart from a few maximal initial force systems, the forces and moments generated by aligners of the Invisalign system are within the range of orthodontic forces. The force change is exponential while a patient is wearing removable thermoplastic appliances. Copyright © 2014 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

LiDAR point classification based on sparse representation

NASA Astrophysics Data System (ADS)

Li, Nan; Pfeifer, Norbert; Liu, Chun

2017-04-01

In order to combine the initial spatial structure and features of LiDAR data for accurate classification. The LiDAR data is represented as a 4-order tensor. Sparse representation for classification(SRC) method is used for LiDAR tensor classification. It turns out SRC need only a few of training samples from each class, meanwhile can achieve good classification result. Multiple features are extracted from raw LiDAR points to generate a high-dimensional vector at each point. Then the LiDAR tensor is built by the spatial distribution and feature vectors of the point neighborhood. The entries of LiDAR tensor are accessed via four indexes. Each index is called mode: three spatial modes in direction X ,Y ,Z and one feature mode. Sparse representation for classification(SRC) method is proposed in this paper. The sparsity algorithm is to find the best represent the test sample by sparse linear combination of training samples from a dictionary. To explore the sparsity of LiDAR tensor, the tucker decomposition is used. It decomposes a tensor into a core tensor multiplied by a matrix along each mode. Those matrices could be considered as the principal components in each mode. The entries of core tensor show the level of interaction between the different components. Therefore, the LiDAR tensor can be approximately represented by a sparse tensor multiplied by a matrix selected from a dictionary along each mode. The matrices decomposed from training samples are arranged as initial elements in the dictionary. By dictionary learning, a reconstructive and discriminative structure dictionary along each mode is built. The overall structure dictionary composes of class-specified sub-dictionaries. Then the sparse core tensor is calculated by tensor OMP(Orthogonal Matching Pursuit) method based on dictionaries along each mode. It is expected that original tensor should be well recovered by sub-dictionary associated with relevant class, while entries in the sparse tensor associated with other classed should be nearly zero. Therefore, SRC use the reconstruction error associated with each class to do data classification. A section of airborne LiDAR points of Vienna city is used and classified into 6classes: ground, roofs, vegetation, covered ground, walls and other points. Only 6 training samples from each class are taken. For the final classification result, ground and covered ground are merged into one same class(ground). The classification accuracy for ground is 94.60%, roof is 95.47%, vegetation is 85.55%, wall is 76.17%, other object is 20.39%.

Adaptive local thresholding for robust nucleus segmentation utilizing shape priors

NASA Astrophysics Data System (ADS)

Wang, Xiuzhong; Srinivas, Chukka

2016-03-01

This paper describes a novel local thresholding method for foreground detection. First, a Canny edge detection method is used for initial edge detection. Then, tensor voting is applied on the initial edge pixels, using a nonsymmetric tensor field tailored to encode prior information about nucleus size, shape, and intensity spatial distribution. Tensor analysis is then performed to generate the saliency image and, based on that, the refined edge. Next, the image domain is divided into blocks. In each block, at least one foreground and one background pixel are sampled for each refined edge pixel. The saliency weighted foreground histogram and background histogram are then created. These two histograms are used to calculate a threshold by minimizing the background and foreground pixel classification error. The block-wise thresholds are then used to generate the threshold for each pixel via interpolation. Finally, the foreground is obtained by comparing the original image with the threshold image. The effective use of prior information, combined with robust techniques, results in far more reliable foreground detection, which leads to robust nucleus segmentation.

Fusion 2.0: The Next Generation of Fusion in California: Aligning State and Regional Fusion Centers

DTIC Science & Technology

2010-03-01

bible ” for fusion center management, as evidenced by the theme of the 2009 National Fusion Center Conference; appropriately called “Achieving Baseline...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS FUSION 2.0: THE NEXT GENERATION OF FUSION IN CALIFORNIA: ALIGNING STATE AND...Master’s Thesis 4. TITLE AND SUBTITLE Fusion 2.0: The Next Generation of Fusion in California: Aligning State and Regional Fusion

What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual

USDA-ARS?s Scientific Manuscript database

BACKGROUND: Next-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain u...

Mueller tensor approach for nonlinear optics in turbid media

NASA Astrophysics Data System (ADS)

Ulcickas, James R. W.; Deng, Fengyuan; Ding, Changqin; Simpson, Garth J.

2018-02-01

As plane-polarized light propagates through a turbid medium, scattering alters the phase and polarization differently in different locations. The corresponding depolarization of the beam complicates recovery of the rich information content contained within the polarization-dependence of second harmonic generation (SHG) microscopy. A theoretical framework connecting Jones and Stokes formalisms for describing optical polarization allows prediction of the polarization-dependent SHG produced from "ballistic", but depolarized incident light. Measurements with collagen-rich tissue sections support the predictions of the framework. Partially polarized SHG produced from a depolarized source enabled recovery of local orientation distribution for collagen and local tensor information. Bridging the gap between SHG instigated by fully depolarized light and partially polarized light more common to practical turbid systems, a method for predicting local nonlinear optical susceptibility tensor elements was developed and applied to collagen in thick sections. Recovered values for the tensor element ratio ρ are in good agreement with previous results for thin tissue and literature reports.

Killing vector fields in three dimensions: a method to solve massive gravity field equations

NASA Astrophysics Data System (ADS)

Gürses, Metin

2010-10-01

Killing vector fields in three dimensions play an important role in the construction of the related spacetime geometry. In this work we show that when a three-dimensional geometry admits a Killing vector field then the Ricci tensor of the geometry is determined in terms of the Killing vector field and its scalars. In this way we can generate all products and covariant derivatives at any order of the Ricci tensor. Using this property we give ways to solve the field equations of topologically massive gravity (TMG) and new massive gravity (NMG) introduced recently. In particular when the scalars of the Killing vector field (timelike, spacelike and null cases) are constants then all three-dimensional symmetric tensors of the geometry, the Ricci and Einstein tensors, their covariant derivatives at all orders, and their products of all orders are completely determined by the Killing vector field and the metric. Hence, the corresponding three-dimensional metrics are strong candidates for solving all higher derivative gravitational field equations in three dimensions.

A Tensor Product Formulation of Strassen's Matrix Multiplication Algorithm with Memory Reduction

DOE PAGES

Kumar, B.; Huang, C. -H.; Sadayappan, P.; ...

1995-01-01

In this article, we present a program generation strategy of Strassen's matrix multiplication algorithm using a programming methodology based on tensor product formulas. In this methodology, block recursive programs such as the fast Fourier Transforms and Strassen's matrix multiplication algorithm are expressed as algebraic formulas involving tensor products and other matrix operations. Such formulas can be systematically translated to high-performance parallel/vector codes for various architectures. In this article, we present a nonrecursive implementation of Strassen's algorithm for shared memory vector processors such as the Cray Y-MP. A previous implementation of Strassen's algorithm synthesized from tensor product formulas required working storagemore » of size O(7 n ) for multiplying 2 n × 2 n matrices. We present a modified formulation in which the working storage requirement is reduced to O(4 n ). The modified formulation exhibits sufficient parallelism for efficient implementation on a shared memory multiprocessor. Performance results on a Cray Y-MP8/64 are presented.« less

Constraining the break of spatial diffeomorphism invariance with Planck data

NASA Astrophysics Data System (ADS)

Graef, L. L.; Benetti, M.; Alcaniz, J. S.

2017-07-01

The current most accepted paradigm for the early universe cosmology, the inflationary scenario, shows a good agreement with the recent Cosmic Microwave Background (CMB) and polarization data. However, when the inflation consistency relation is relaxed, these observational data exclude a larger range of red tensor tilt values, prevailing the blue ones which are not predicted by the minimal inflationary models. Recently, it has been shown that the assumption of spatial diffeomorphism invariance breaking (SDB) in the context of an effective field theory of inflation leads to interesting observational consequences. Among them, the possibility of generating a blue tensor spectrum, which can recover the specific consistency relation of the String Gas Cosmology, for a certain choice of parameters. We use the most recent CMB data to constrain the SDB model and test its observational viability through a Bayesian analysis assuming as reference an extended ΛCDM+tensor perturbation model, which considers a power-law tensor spectrum parametrized in terms of the tensor-to-scalar ratio, r, and the tensor spectral index, nt. If the inflation consistency relation is imposed, r=-8 nt, we obtain a strong evidence in favor of the reference model whereas if such relation is relaxed, a weak evidence in favor of the model with diffeomorphism breaking is found. We also use the same CMB data set to make an observational comparison between the SDB model, standard inflation and String Gas Cosmology.

Diffractive optics for precision alignment of Euclid space telescope optics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Asfour, Jean-Michel; Weidner, Frank; Bodendorf, Christof; Bode, Andreas; Poleshchuk, Alexander G.; Nasyrov, Ruslan K.; Grupp, Frank; Bender, Ralf

2017-09-01

We present a method for precise alignment of lens elements using specific Computer Generated Hologram (CGH) with an integrated Fizeau reference flat surface and a Fizeau interferometer. The method is used for aligning the so called Camera Lens Assembly for ESAs Euclid telescope. Each lens has a corresponding annular area on the diffractive optics, which is used to control the position of each lens. The lenses are subsequently positioned using individual annular rings of the CGH. The overall alignment accuracy is below 1 µm, the alignment sensitivity is in the range of 0.1 µm. The achieved alignment accuracy of the lenses relative to each other is mainly depending on the stability in time of the alignment tower. Error budgets when using computer generated holograms and physical limitations are explained. Calibration measurements of the alignment system and the typically reached alignment accuracies will be shown and discussed.

Grid-based lattice summation of electrostatic potentials by assembled rank-structured tensor approximation

NASA Astrophysics Data System (ADS)

Khoromskaia, Venera; Khoromskij, Boris N.

2014-12-01

Our recent method for low-rank tensor representation of sums of the arbitrarily positioned electrostatic potentials discretized on a 3D Cartesian grid reduces the 3D tensor summation to operations involving only 1D vectors however retaining the linear complexity scaling in the number of potentials. Here, we introduce and study a novel tensor approach for fast and accurate assembled summation of a large number of lattice-allocated potentials represented on 3D N × N × N grid with the computational requirements only weakly dependent on the number of summed potentials. It is based on the assembled low-rank canonical tensor representations of the collected potentials using pointwise sums of shifted canonical vectors representing the single generating function, say the Newton kernel. For a sum of electrostatic potentials over L × L × L lattice embedded in a box the required storage scales linearly in the 1D grid-size, O(N) , while the numerical cost is estimated by O(NL) . For periodic boundary conditions, the storage demand remains proportional to the 1D grid-size of a unit cell, n = N / L, while the numerical cost reduces to O(N) , that outperforms the FFT-based Ewald-type summation algorithms of complexity O(N3 log N) . The complexity in the grid parameter N can be reduced even to the logarithmic scale O(log N) by using data-sparse representation of canonical N-vectors via the quantics tensor approximation. For justification, we prove an upper bound on the quantics ranks for the canonical vectors in the overall lattice sum. The presented approach is beneficial in applications which require further functional calculus with the lattice potential, say, scalar product with a function, integration or differentiation, which can be performed easily in tensor arithmetics on large 3D grids with 1D cost. Numerical tests illustrate the performance of the tensor summation method and confirm the estimated bounds on the tensor ranks.

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

Casadio, Roberto; Orlandi, Alessio; Kühnel, Florian, E-mail: casadio@bo.infn.it, E-mail: florian.kuhnel@fysik.su.se, E-mail: aorlandi@bo.infn.it

Following a new quantum cosmological model proposed by Dvali and Gomez, we quantitatively investigate possible modifications to the Hubble parameter and following corrections to the cosmic microwave background spectrum. In this model, scalar and tensor perturbations are generated by the quantum depletion of the background inflaton and graviton condensate respectively. We show how the inflaton mass affects the power spectra and the tensor-to-scalar ratio. Masses approaching the Planck scale would lead to strong deviations, while standard spectra are recovered for an inflaton mass much smaller than the Planck mass.

Intermittency in small-scale turbulence: a velocity gradient approach

NASA Astrophysics Data System (ADS)

Meneveau, Charles; Johnson, Perry

2017-11-01

Intermittency of small-scale motions is an ubiquitous facet of turbulent flows, and predicting this phenomenon based on reduced models derived from first principles remains an important open problem. Here, a multiple-time scale stochastic model is introduced for the Lagrangian evolution of the full velocity gradient tensor in fluid turbulence at arbitrarily high Reynolds numbers. This low-dimensional model differs fundamentally from prior shell models and other empirically-motivated models of intermittency because the nonlinear gradient self-stretching and rotation A2 term vital to the energy cascade and intermittency development is represented exactly from the Navier-Stokes equations. With only one adjustable parameter needed to determine the model's effective Reynolds number, numerical solutions of the resulting set of stochastic differential equations show that the model predicts anomalous scaling for moments of the velocity gradient components and negative derivative skewness. It also predicts signature topological features of the velocity gradient tensor such as vorticity alignment trends with the eigen-directions of the strain-rate. This research was made possible by a graduate Fellowship from the National Science Foundation and by a Grant from The Gulf of Mexico Research Initiative.

A bulk viscosity approach for shock capturing on unstructured grids

NASA Astrophysics Data System (ADS)

Shoeybi, Mohammad; Larsson, Nils Johan; Ham, Frank; Moin, Parviz

2008-11-01

The bulk viscosity approach for shock capturing (Cook and Cabot, JCP, 2005) augments the bulk part of the viscous stress tensor. The intention is to capture shock waves without dissipating turbulent structures. The present work extends and modifies this method for unstructured grids. We propose a method that properly scales the bulk viscosity with the grid spacing normal to the shock for unstructured grid for which the shock is not necessarily aligned with the grid. The magnitude of the strain rate tensor used in the original formulation is replaced with the dilatation, which appears to be more appropriate in the vortical turbulent flow regions (Mani et al., 2008). The original form of the model is found to have an impact on dilatational motions away form the shock wave, which is eliminated by a proposed localization of the bulk viscosity. Finally, to allow for grid adaptation around shock waves, an explicit/implicit time advancement scheme has been developed that adaptively identifies the stiff regions. The full method has been verified with several test cases, including 2D shock-vorticity entropy interaction, homogenous isotropic turbulence, and turbulent flow over a cylinder.

Diffusion tensor eigenvector directional color imaging patterns in the evaluation of cerebral white matter tracts altered by tumor.

PubMed

Field, Aaron S; Alexander, Andrew L; Wu, Yu-Chien; Hasan, Khader M; Witwer, Brian; Badie, Behnam

2004-10-01

To categorize the varied appearances of tumor-altered white matter (WM) tracts on diffusion tensor eigenvector directional color maps. Diffusion tensor imaging (DTI) was obtained preoperatively in 13 patients with brain tumors ranging from benign to high-grade malignant, including primary and metastatic lesions, and maps of apparent diffusion coefficient (ADC), fractional anisotropy (FA), and major eigenvector direction were generated. Regions of interest (ROIs) were drawn within identifiable WM tracts affected by tumor, avoiding grossly cystic and necrotic regions, known fiber crossings, and gray matter. Patterns of WM tract alteration were categorized on the basis of qualitative analysis of directional color maps and correlation analysis of ADC and FA. Four basic patterns of WM alteration were identified: 1) normal or nearly normal FA and ADC, with abnormal tract location or tensor directions attributable to bulk mass displacement, 2) moderately decreased FA and increased ADC with normal tract locations and tensor directions, 3) moderately decreased FA and increased ADC with abnormal tensor directions, and 4) near isotropy. FA and ADC were inversely correlated for Patterns 1-3 but did not discriminate edema from infiltrating tumor. However, in the absence of mass displacement, infiltrating tumor was found to produce tensor directional changes that were not observed with vasogenic edema, suggesting the possibility of discrimination on the basis of directional statistics. Tumor alteration of WM tracts tends to produce one of four patterns on FA and directional color maps. Clinical application of these patterns must await further study. Copyright 2004 Wiley-Liss, Inc.

Nonlinear optical anisotropy and molecular orientational distribution in poly(p-phenylene benzobisthiazole) Langmuir-Blodgett films

NASA Astrophysics Data System (ADS)

Wang, Liming; Wada, Tatsuo; Yuba, Tomoyuki; Kakimoto, Masaaki; Imai, Yoshio; Sasabe, Hiroyuki

1996-06-01

The orientational distribution and packing of polymer chains were investigated in poly(p-phenylene benzobisthiazole) (PBT) Langmuir-Blodgett (LB) films by nonresonant third-harmonic generation measurement at a wavelength of 1907 nm. The tensor components of the third-harmonic susceptibility on the PBT LB film with a surface pressure of 50 mN/m were determined to be χ(3)XXXX=(16.6±2.5)×10-12 and χ(3)YYYY=(2.0±0.3)×10-12. The large nonlinear optical anisotropy can be explained as a result of highly oriented packing of the polymer chains induced by a flow orientation. A Gaussian distribution function with a standard deviation of σ=0.40 gives a practical description of the orientational distribution of PBT polymer chains. A maximum χ(3) value of (26.8±4.4)×10-12 esu is predicted assuming a perfect alignment of polymer chains. The χ(3)XXXX value increased by factor of 2 with the surface pressure from 30 to 50 mN/m mainly due to the packing density of the polymer chains, while the orientational degree did not change.

Intermediate Templates Guided Groupwise Registration of Diffusion Tensor Images

PubMed Central

Jia, Hongjun; Yap, Pew-Thian; Wu, Guorong; Wang, Qian; Shen, Dinggang

2010-01-01

Registration of a population of diffusion tensor images (DTIs) is one of the key steps in medical image analysis, and it plays an important role in the statistical analysis of white matter related neurological diseases. However, pairwise registration with respect to a pre-selected template may not give precise results if the selected template deviates significantly from the distribution of images. To cater for more accurate and consistent registration, a novel framework is proposed for groupwise registration with the guidance from one or more intermediate templates determined from the population of images. Specifically, we first use a Euclidean distance, defined as a combinative measure based on the FA map and ADC map, for gauging the similarity of each pair of DTIs. A fully connected graph is then built with each node denoting an image and each edge denoting the distance between a pair of images. The root template image is determined automatically as the image with the overall shortest path length to all other images on the minimum spanning tree (MST) of the graph. Finally, a sequence of registration steps is applied to progressively warping each image towards the root template image with the help of intermediate templates distributed along its path to the root node on the MST. Extensive experimental results using diffusion tensor images of real subjects indicate that registration accuracy and fiber tract alignment are significantly improved, compared with the direct registration from each image to the root template image. PMID:20851197

Magnetospheric convection during quiet or moderately disturbed times

NASA Technical Reports Server (NTRS)

Caudal, G.; Blanc, M.

1988-01-01

The processes which contribute to the large-scale plasma circulation in the earth's environment during quiet times, or during reasonable stable magnetic conditions are reviewed. The various sources of field-aligned current generation in the solar wind and the magnetosphere are presented. The generation of field-aligned currents on open field lines connected to either polar cap and the generation of closed field lines of the inner magnetosphere are examined. Consideration is given to the hypothesis of Caudal (1987) that loss processes of trapped particles are competing with adiabatic motions in the generation of field-aligned currents in the inner magnetosphere.

Unaligned instruction relocation

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

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unalignedmore » ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.« less

Unaligned instruction relocation

DOEpatents

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.; Sura, Zehra N.

2018-01-23

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unaligned ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.

N = (2,0) self-dual non-Abelian tensor multiplet in D = 3 + 3 generates N = (1,1) self-dual systems in D = 2 + 2

NASA Astrophysics Data System (ADS)

Nishino, Hitoshi; Rajpoot, Subhash

2018-03-01

We formulate an N = (2 , 0) system in D = 3 + 3 dimensions consisting of a Yang-Mills (YM)-multiplet (ˆ μ ˆ IA, λˆI), a self-dual non-Abelian tensor multiplet (ˆ μ ˆ ν ˆ IB, χˆI ,φˆI), and an extra vector multiplet (C ˆ μ ˆ IC, ρˆI). We next perform the dimensional reductions of this system into D = 2 + 2, and obtain N = (1 , 1) systems with a self-dual YM-multiplet (AIμ ,λI), a self-dual tensor multiplet (BIμν , χI , φI), and an extra vector multiplet (CIμ , ρI). In D = 2 + 2, we reach two distinct theories: 'Theory-I' and 'Theory-II'. The former has the self-dual field-strength Hμν(+)I of CIμ already presented in our recent paper, while the latter has anti-self-dual field strength Hμν(-)I. As an application, we show that Theory-II actually generates supersymmetric-KdV equations in D = 1 + 1. Our result leads to a new conclusion that the D = 3 + 3 theory with non-Abelian tensor multiplet can be a 'Grand Master Theory' for self-dual multiplet and self-dual YM-multiplet in D = 2 + 2, that in turn has been conjectured to be the 'Master Theory' for all supersymmetric integrable theories in D ≤ 3.

A Unified Approach to Diffusion Direction Sensitive Slice Registration and 3-D DTI Reconstruction From Moving Fetal Brain Anatomy

PubMed Central

Fogtmann, Mads; Seshamani, Sharmishtaa; Kroenke, Christopher; Cheng, Xi; Chapman, Teresa; Wilm, Jakob; Rousseau, François

2014-01-01

This paper presents an approach to 3-D diffusion tensor image (DTI) reconstruction from multi-slice diffusion weighted (DW) magnetic resonance imaging acquisitions of the moving fetal brain. Motion scatters the slice measurements in the spatial and spherical diffusion domain with respect to the underlying anatomy. Previous image registration techniques have been described to estimate the between slice fetal head motion, allowing the reconstruction of 3-D a diffusion estimate on a regular grid using interpolation. We propose Approach to Unified Diffusion Sensitive Slice Alignment and Reconstruction (AUDiSSAR) that explicitly formulates a process for diffusion direction sensitive DW-slice-to-DTI-volume alignment. This also incorporates image resolution modeling to iteratively deconvolve the effects of the imaging point spread function using the multiple views provided by thick slices acquired in different anatomical planes. The algorithm is implemented using a multi-resolution iterative scheme and multiple real and synthetic data are used to evaluate the performance of the technique. An accuracy experiment using synthetically created motion data of an adult head and a experiment using synthetic motion added to sedated fetal monkey dataset show a significant improvement in motion-trajectory estimation compared to a state-of-the-art approaches. The performance of the method is then evaluated on challenging but clinically typical in utero fetal scans of four different human cases, showing improved rendition of cortical anatomy and extraction of white matter tracts. While the experimental work focuses on DTI reconstruction (second-order tensor model), the proposed reconstruction framework can employ any 5-D diffusion volume model that can be represented by the spatial parameterizations of an orientation distribution function. PMID:24108711

Numerical study of comparison of vorticity and passive vectors in turbulence and inviscid flows

NASA Astrophysics Data System (ADS)

Ohkitani, Koji

2002-04-01

The nonlinear vortex stretching in incompressible Navier-Stokes turbulence is compared with a linear stretching process of passive vectors (PVs). In particular, we pay special attention to the difference of these processes under long and short time evolutions. For finite time evolution, we confirm our previous finding that the stretching effect of vorticity is weaker than that of general passive vectors for a majority of the initial conditions with the same energy spectra. The above difference can be explained qualitatively by examining the Biot-Savart formula. In order to see to what extent infinitesimal time development explains the above difference, we examine the probability density functions (PDFs) of the stretching rates of the passive vectors in the vicinity of a solution of Navier-Stokes equations. It is found that the PDFs are found to have a Gaussian distribution, suggesting that there are equally many PVs that stretched less and more than the vorticity. This suggests the importance of the vorticity-strain correlation built up over finite time in turbulence. We also discuss the case of Euler equations, where the dynamics of the Jacobian matrix relating the physical and material coordinates is examined numerically. A kind of alignment problem associated with the Cauchy-Green tensor is proposed and studied using the results of numerical simulations. It is found that vorticity tends to align itself with the most compressing eigenvector of the Cauchy-Green tensor. A two-dimensional counterpart of active-passive comparison is briefly studied. There is no essential difference between stretching of vorticity gradients and that of passive scalar gradients and a physical interpretation is given to it.

A combined numerical and experimental framework for determining permeability properties of the arterial media.

PubMed

Comerford, A; Chooi, K Y; Nowak, M; Weinberg, P D; Sherwin, S J

2015-04-01

The medial layer of the arterial wall may play an important role in the regulation of water and solute transport across the wall. In particular, a high medial resistance to transport could cause accumulation of lipid-carrying molecules in the inner wall. In this study, the water transport properties of medial tissue were characterised in a numerical model, utilising experimentally obtained data for the medial microstructure and the relative permeability of different constituents. For the model, a new solver for flow in porous materials, based on a high-order splitting scheme, was implemented in the spectral/hp element library nektar++ and validated. The data were obtained by immersing excised aortic bifurcations in a solution of fluorescent protein tracer and subsequently imaging them with a confocal microscope. Cuboidal regions of interest were selected in which the microstructure and relative permeability of different structures were transformed to a computational mesh. Impermeable objects were treated fictitiously in the numerical scheme. On this cube, a pressure drop was applied in the three coordinate directions and the principal components of the permeability tensor were determined. The reconstructed images demonstrated the arrangement of elastic lamellae and interspersed smooth muscle cells in rat aortic media; the distribution and alignment of the smooth muscle cells varied spatially within the extracellular matrix. The numerical simulations highlighted that the heterogeneity of the medial structure is important in determining local water transport properties of the tissue, resulting in regional and directional variation of the permeability tensor. A major factor in this variation is the alignment and density of smooth muscle cells in the media, particularly adjacent to the adventitial layer.

Van der Waals interaction in uniaxial anisotropic media.

PubMed

Kornilovitch, Pavel E

2013-01-23

Van der Waals interactions between flat surfaces in uniaxial anisotropic media are investigated in the nonretarded limit. The main focus is the effect of nonzero tilt between the optical axis and the surface normal on the strength of the van der Waals attraction. General expressions for the van der Waals free energy are derived using the surface mode method and the transfer-matrix formalism. To facilitate numerical calculations a temperature-dependent three-band parameterization of the dielectric tensor of the liquid crystal 5CB is developed. A solid slab immersed in a liquid crystal experiences a van der Waals torque that aligns the surface normal relative to the optical axis of the medium. The preferred orientation is different for different materials. Two solid slabs in close proximity experience a van der Waals attraction that is strongest for homeotropic alignment of the intervening liquid crystal for all the materials studied. The results have implications for the stability of plate-like colloids in liquid crystal hosts.

Hydrodynamics of isotropic and liquid crystalline active polymer solutions.

PubMed

Ahmadi, Aphrodite; Marchetti, M C; Liverpool, T B

2006-12-01

We describe the large-scale collective behavior of solutions of polar biofilaments and stationary and mobile crosslinkers. Both mobile and stationary crosslinkers induce filament alignment promoting either polar or nematic order. In addition, mobile crosslinkers, such as clusters of motor proteins, exchange forces and torques among the filaments and render the homogeneous states unstable via filament bundling. We start from a Smoluchowski equation for rigid filaments in solutions, where pairwise crosslink-mediated interactions among the filaments yield translational and rotational currents. The large-scale properties of the system are described in terms of continuum equations for filament and motor densities, polarization, and alignment tensor obtained by coarse-graining the Smoluchovski equation. The possible homogeneous and inhomogeneous states of the systems are obtained as stable solutions of the dynamical equations and are characterized in terms of experimentally accessible parameters. We make contact with work by other authors and show that our model allows for an estimate of the various parameters in the hydrodynamic equations in terms of physical properties of the crosslinkers.

Reynolds stress flow shear and turbulent energy transfer in reversed field pinch configuration

NASA Astrophysics Data System (ADS)

Vianello, Nicola; Spolaore, Monica; Serianni, Gianluigi; Regnoli, Giorgio; Spada, Emanuele; Antoni, Vanni; Bergsåker, Henric; Drake, James R.

2003-10-01

The role of Reynolds Stress tensor on flow generation in turbulent fluids and plasmas is still an open question and the comprehension of its behavior may assist the understanding of improved confinement scenario. It is generally believed that shear flow generation may occur by an interaction of the turbulent Reynolds stress with the shear flow. It is also generally believed that this mechanism may influence the generation of zonal flow shears. The evaluation of the complete Reynolds Stress tensor requires contemporary measurements of its electrostatic and magnetic part: this requirement is more restrictive for Reversed Field Pinch configuration where magnetic fluctuations are larger than in tokamak . A new diagnostic system which combines electrostatic and magnetic probes has been installed in the edge region of Extrap-T2R reversed field pinch. With this new probe the Reynolds stress tensor has been deduced and its radial profile has been reconstructed on a shot to shot basis exploring differen plasma conditions. These profiles have been compared with the naturally occurring velocity flow profile, in particular during Pulsed Poloidal Current Drive experiment, where a strong variation of ExB flow radial profile has been registered. The study of the temporal evolution of Reynolds stress reveals the appearance of strong localized bursts: these are considered in relation with global MHD relaxation phenomena, which naturally occur in the core of an RFP plasma sustaining its configuration.

An improved nearly-orthogonal structured mesh generation system with smoothness control functions

USDA-ARS?s Scientific Manuscript database

This paper presents an improved nearly-orthogonal structured mesh generation system with a set of smoothness control functions, which were derived based on the ratio between the Jacobian of the transformation matrix and the Jacobian of the metric tensor. The proposed smoothness control functions are...

Simultaneous tensor decomposition and completion using factor priors.

PubMed

Chen, Yi-Lei; Hsu, Chiou-Ting; Liao, Hong-Yuan Mark

2014-03-01

The success of research on matrix completion is evident in a variety of real-world applications. Tensor completion, which is a high-order extension of matrix completion, has also generated a great deal of research interest in recent years. Given a tensor with incomplete entries, existing methods use either factorization or completion schemes to recover the missing parts. However, as the number of missing entries increases, factorization schemes may overfit the model because of incorrectly predefined ranks, while completion schemes may fail to interpret the model factors. In this paper, we introduce a novel concept: complete the missing entries and simultaneously capture the underlying model structure. To this end, we propose a method called simultaneous tensor decomposition and completion (STDC) that combines a rank minimization technique with Tucker model decomposition. Moreover, as the model structure is implicitly included in the Tucker model, we use factor priors, which are usually known a priori in real-world tensor objects, to characterize the underlying joint-manifold drawn from the model factors. By exploiting this auxiliary information, our method leverages two classic schemes and accurately estimates the model factors and missing entries. We conducted experiments to empirically verify the convergence of our algorithm on synthetic data and evaluate its effectiveness on various kinds of real-world data. The results demonstrate the efficacy of the proposed method and its potential usage in tensor-based applications. It also outperforms state-of-the-art methods on multilinear model analysis and visual data completion tasks.

Constraining the break of spatial diffeomorphism invariance with Planck data

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

Graef, L.L.; Benetti, M.; Alcaniz, J.S., E-mail: leilagraef@on.br, E-mail: micolbenetti@on.br, E-mail: alcaniz@on.br

The current most accepted paradigm for the early universe cosmology, the inflationary scenario, shows a good agreement with the recent Cosmic Microwave Background (CMB) and polarization data. However, when the inflation consistency relation is relaxed, these observational data exclude a larger range of red tensor tilt values, prevailing the blue ones which are not predicted by the minimal inflationary models. Recently, it has been shown that the assumption of spatial diffeomorphism invariance breaking (SDB) in the context of an effective field theory of inflation leads to interesting observational consequences. Among them, the possibility of generating a blue tensor spectrum, whichmore » can recover the specific consistency relation of the String Gas Cosmology, for a certain choice of parameters. We use the most recent CMB data to constrain the SDB model and test its observational viability through a Bayesian analysis assuming as reference an extended ΛCDM+tensor perturbation model, which considers a power-law tensor spectrum parametrized in terms of the tensor-to-scalar ratio, r , and the tensor spectral index, n {sub t} . If the inflation consistency relation is imposed, r =−8 n {sub t} , we obtain a strong evidence in favor of the reference model whereas if such relation is relaxed, a weak evidence in favor of the model with diffeomorphism breaking is found. We also use the same CMB data set to make an observational comparison between the SDB model, standard inflation and String Gas Cosmology.« less

Waveform inversion of oscillatory signatures in long-period events beneath volcanoes

USGS Publications Warehouse

Kumagai, H.; Chouet, B.A.; Nakano, M.

2002-01-01

The source mechanism of long-period (LP) events is examined using synthetic waveforms generated by the acoustic resonance of a fluid-filled crack. We perform a series of numerical tests in which the oscillatory signatures of synthetic LP waveforms are used to determine the source time functions of the six moment tensor components from waveform inversions assuming a point source. The results indicate that the moment tensor representation is valid for the odd modes of crack resonance with wavelengths 2L/n, 2W/n, n = 3, 5, 7, ..., where L and W are the crack length and width, respectively. For the even modes with wavelengths 2L/n, 2W/n, n = 2, 4, 6,..., a generalized source representation using higher-order tensors is required, although the efficiency of seismic waves radiated by the even modes is expected to be small. We apply the moment tensor inversion to the oscillatory signatures of an LP event observed at Kusatsu-Shirane Volcano, central Japan. Our results point to the resonance of a subhorizontal crack located a few hundred meters beneath the summit crater lakes. The present approach may be useful to quantify the source location, geometry, and force system of LP events, and opens the way for moment tensor inversions of tremor.

Full moment tensors for small events (Mw < 3) at Uturuncu volcano, Bolivia

NASA Astrophysics Data System (ADS)

Alvizuri, Celso; Tape, Carl

2016-09-01

We present a catalogue of full seismic moment tensors for 63 events from Uturuncu volcano in Bolivia. The events were recorded during 2011-2012 in the PLUTONS seismic array of 24 broad-band stations. Most events had magnitudes between 0.5 and 2.0 and did not generate discernible surface waves; the largest event was Mw 2.8. For each event we computed the misfit between observed and synthetic waveforms, and we used first-motion polarity measurements to reduce the number of possible solutions. Each moment tensor solution was obtained using a grid search over the 6-D space of moment tensors. For each event, we show the misfit function in eigenvalue space, represented by a lune. We identify three subsets of the catalogue: (1) six isotropic events, (2) five tensional crack events, and (3) a swarm of 14 events southeast of the volcanic centre that appear to be double couples. The occurrence of positively isotropic events is consistent with other published results from volcanic and geothermal regions. Several of these previous results, as well as our results, cannot be interpreted within the context of either an oblique opening crack or a crack-plus-double-couple model. Proper characterization of uncertainties for full moment tensors is critical for distinguishing among physical models of source processes.

Subcortical pathways serving cortical language sites: initial experience with diffusion tensor imaging fiber tracking combined with intraoperative language mapping.

PubMed

Henry, Roland G; Berman, Jeffrey I; Nagarajan, Srikantan S; Mukherjee, Pratik; Berger, Mitchel S

2004-02-01

The combination of mapping functional cortical neurons by intraoperative cortical stimulation and axonal architecture by diffusion tensor MRI fiber tracking can be used to delineate the pathways between functional regions. In this study the authors investigated the feasibility of combining these techniques to yield connectivity associated with motor speech and naming. Diffusion tensor MRI fiber tracking provides maps of axonal bundles and was combined with intraoperative mapping of eloquent cortex for a patient undergoing brain tumor surgery. Tracks from eight stimulated sites in the inferior frontal cortex including mouth motor, speech arrest, and anomia were generated from the diffusion tensor MRI data. The regions connected by the fiber tracking were compared to foci from previous functional imaging reports on language tasks. Connections were found between speech arrest, mouth motor, and anomia sites and the SMA proper and cerebral peduncle. The speech arrest and a mouth motor site were also seen to connect to the putamen via the external capsule. This is the first demonstration of delineation of subcortical pathways using diffusion tensor MRI fiber tracking with intraoperative cortical stimulation. The combined techniques may provide improved preservation of eloquent regions during neurological surgery, and may provide access to direct connectivity information between functional regions of the brain.

Subcortical pathways serving cortical language sites: initial experience with diffusion tensor imaging fiber tracking combined with intraoperative language mapping

PubMed Central

Henry, Roland G.; Berman, Jeffrey I.; Nagarajan, Srikantan S.; Mukherjee, Pratik; Berger, Mitchel S.

2014-01-01

The combination of mapping functional cortical neurons by intraoperative cortical stimulation and axonal architecture by diffusion tensor MRI fiber tracking can be used to delineate the pathways between functional regions. In this study the authors investigated the feasibility of combining these techniques to yield connectivity associated with motor speech and naming. Diffusion tensor MRI fiber tracking provides maps of axonal bundles and was combined with intraoperative mapping of eloquent cortex for a patient undergoing brain tumor surgery. Tracks from eight stimulated sites in the inferior frontal cortex including mouth motor, speech arrest, and anomia were generated from the diffusion tensor MRI data. The regions connected by the fiber tracking were compared to foci from previous functional imaging reports on language tasks. Connections were found between speech arrest, mouth motor, and anomia sites and the SMA proper and cerebral peduncle. The speech arrest and a mouth motor site were also seen to connect to the putamen via the external capsule. This is the first demonstration of delineation of subcortical pathways using diffusion tensor MRI fiber tracking with intraoperative cortical stimulation. The combined techniques may provide improved preservation of eloquent regions during neurological surgery, and may provide access to direct connectivity information between functional regions of the brain. PMID:14980564

Spin correlations in the {Lambda}{Lambda} and {Lambda}{Lambda}-bar systems generated in relativistic heavy-ion collisions

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

Lyuboshitz, V. L.; Lyuboshitz, V. V., E-mail: Valery.Lyuboshitz@jinr.r

2010-05-15

Spin correlations for the {Lambda}{Lambda} and {Lambda}{Lambda}-bar pairs, generated in relativistic heavy-ion collisions, and related angular correlations at the joint registration of hadronic decays of two hyperons, in which space parity is not conserved, are analyzed. The correlation tensor components can be derived from the double angular distribution of products of two decays by the method of 'moments'. The properties of the 'trace' of the correlation tensor (a sum of three diagonal components), determining the relative fractions of the triplet states and singlet state of respective pairs, are discussed. Spin correlations for two identical particles ({Lambda}{Lambda}) and two nonidentical particlesmore » ({Lambda}{Lambda}-bar) are considered from the viewpoint of the conventional model of one-particle sources. In the framework of this model, correlations vanish at sufficiently large relative momenta. However, under these conditions, in the case of two nonidentical particles ({Lambda}{Lambda}-bar) a noticeable role is played by two-particle annihilation (two-quark, two-gluon) sources, which lead to the difference of the correlation tensor from zero. In particular, such a situation may arise when the system passes through the 'mixed phase.'« less

Detection of the Velocity Shear Effect on the Spatial Distributions of the Galactic Satellites in Isolated Systems

NASA Astrophysics Data System (ADS)

Lee, Jounghun; Choi, Yun-Young

2015-02-01

We report a detection of the effect of the large-scale velocity shear on the spatial distributions of the galactic satellites around the isolated hosts. Identifying the isolated galactic systems, each of which consists of a single host galaxy and its satellites, from the Seventh Data Release of the Sloan Digital Sky Survey and reconstructing linearly the velocity shear field in the local universe, we measure the alignments between the relative positions of the satellites from their isolated hosts and the principal axes of the local velocity shear tensors projected onto the plane of sky. We find a clear signal that the galactic satellites in isolated systems are located preferentially along the directions of the minor principal axes of the large-scale velocity shear field. Those galactic satellites that are spirals, are brighter, are located at distances larger than the projected virial radii of the hosts, and belong to the spiral hosts yield stronger alignment signals, which implies that the alignment strength depends on the formation and accretion epochs of the galactic satellites. It is also shown that the alignment strength is quite insensitive to the cosmic web environment, as well as the size and luminosity of the isolated hosts. Although this result is consistent with the numerical finding of Libeskind et al. based on an N-body experiment, owing to the very low significance of the observed signals, it remains inconclusive whether or not the velocity shear effect on the satellite distribution is truly universal.

ELATE: an open-source online application for analysis and visualization of elastic tensors

NASA Astrophysics Data System (ADS)

Gaillac, Romain; Pullumbi, Pluton; Coudert, François-Xavier

2016-07-01

We report on the implementation of a tool for the analysis of second-order elastic stiffness tensors, provided with both an open-source Python module and a standalone online application allowing the visualization of anisotropic mechanical properties. After describing the software features, how we compute the conventional elastic constants and how we represent them graphically, we explain our technical choices for the implementation. In particular, we focus on why a Python module is used to generate the HTML web page with embedded Javascript for dynamical plots.

Stress Energy tensor in LCFT and the Logarithmic Sugawara construction

NASA Astrophysics Data System (ADS)

Kogan, Ian I.; Nichols, Alexander

2002-01-01

We discuss the partners of the stress energy tensor and their structure in Logarithmic conformal field theories. In particular we draw attention to the fundamental differences between theories with zero and non-zero central charge. However they are both characterised by at least two independent parameters. We show how, by using a generalised Sugawara construction, one can calculate the logarithmic partner of T. We show that such a construction works in the c = -2 theory using the conformal dimension one primary currents which generate a logarithmic extension of the Kac-Moody algebra.

A tensor approach to modeling of nonhomogeneous nonlinear systems

NASA Technical Reports Server (NTRS)

Yurkovich, S.; Sain, M.

1980-01-01

Model following control methodology plays a key role in numerous application areas. Cases in point include flight control systems and gas turbine engine control systems. Typical uses of such a design strategy involve the determination of nonlinear models which generate requested control and response trajectories for various commands. Linear multivariable techniques provide trim about these motions; and protection logic is added to secure the hardware from excursions beyond the specification range. This paper reports upon experience in developing a general class of such nonlinear models based upon the idea of the algebraic tensor product.

Micro-Stress Bound Estimate Enabled Optimization of Structural Composite Repair for the Next Generation Aircraft

DTIC Science & Technology

2007-02-28

where they exhibited the maximum values, which were the midsurface and 0/-0 surface for two laminates with 0=150 and 0=400. a) 50000 40000 - 0 30000...the first and second invariants of the strain tensor calculated at the midsurface in the x=O cross section as a function of distance from the hole edge...Y Figure 7. Comparison of the distributions of strain tensor invariants predicted in the matrix phase at the midsurface at x=0 as a function of

Tensor scale-based fuzzy connectedness image segmentation

NASA Astrophysics Data System (ADS)

Saha, Punam K.; Udupa, Jayaram K.

2003-05-01

Tangible solutions to image segmentation are vital in many medical imaging applications. Toward this goal, a framework based on fuzzy connectedness was developed in our laboratory. A fundamental notion called "affinity" - a local fuzzy hanging togetherness relation on voxels - determines the effectiveness of this segmentation framework in real applications. In this paper, we introduce the notion of "tensor scale" - a recently developed local morphometric parameter - in affinity definition and study its effectiveness. Although, our previous notion of "local scale" using the spherical model successfully incorporated local structure size into affinity and resulted in measureable improvements in segmentation results, a major limitation of the previous approach was that it ignored local structural orientation and anisotropy. The current approach of using tensor scale in affinity computation allows an effective utilization of local size, orientation, and ansiotropy in a unified manner. Tensor scale is used for computing both the homogeneity- and object-feature-based components of affinity. Preliminary results of the proposed method on several medical images and computer generated phantoms of realistic shapes are presented. Further extensions of this work are discussed.

Diffusion with finite-helicity field tensor: A mechanism of generating heterogeneity

NASA Astrophysics Data System (ADS)

Sato, N.; Yoshida, Z.

2018-02-01

Topological constraints on a dynamical system often manifest themselves as breaking of the Hamiltonian structure; well-known examples are nonholonomic constraints on Lagrangian mechanics. The statistical mechanics under such topological constraints is the subject of this study. Conventional arguments based on phase spaces, Jacobi identity, invariant measure, or the H theorem are no longer applicable since all these notions stem from the symplectic geometry underlying canonical Hamiltonian systems. Remembering that Hamiltonian systems are endowed with field tensors (canonical 2-forms) that have zero helicity, our mission is to extend the scope toward the class of systems governed by finite-helicity field tensors. Here, we introduce a class of field tensors that are characterized by Beltrami vectors. We prove an H theorem for this Beltrami class. The most general class of energy-conserving systems are non-Beltrami, for which we identify the "field charge" that prevents the entropy to maximize, resulting in creation of heterogeneous distributions. The essence of the theory can be delineated by classifying three-dimensional dynamics. We then generalize to arbitrary (finite) dimensions.

Relativistic fluid dynamics with spin

NASA Astrophysics Data System (ADS)

Florkowski, Wojciech; Friman, Bengt; Jaiswal, Amaresh; Speranza, Enrico

2018-04-01

Using the conservation laws for charge, energy, momentum, and angular momentum, we derive hydrodynamic equations for the charge density, local temperature, and fluid velocity, as well as for the polarization tensor, starting from local equilibrium distribution functions for particles and antiparticles with spin 1/2. The resulting set of differential equations extends the standard picture of perfect-fluid hydrodynamics with a conserved entropy current in a minimal way. This framework can be used in space-time analyses of the evolution of spin and polarization in various physical systems including high-energy nuclear collisions. We demonstrate that a stationary vortex, which exhibits vorticity-spin alignment, corresponds to a special solution of the spin-hydrodynamical equations.

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

PubMed

Tong, Jing; Pei, Jimin; Grishin, Nick V

2015-09-03

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

Site-resolved multiple-quantum filtered correlations and distance measurements by magic-angle spinning NMR: Theory and applications to spins with weak to vanishing quadrupolar couplings

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

Eliav, U., E-mail: amirgo@tau.ac.il, E-mail: eliav@tau.ac.il; Haimovich, A.; Goldbourt, A., E-mail: amirgo@tau.ac.il, E-mail: eliav@tau.ac.il

2016-01-14

We discuss and analyze four magic-angle spinning solid-state NMR methods that can be used to measure internuclear distances and to obtain correlation spectra between a spin I = 1/2 and a half-integer spin S > 1/2 having a small quadrupolar coupling constant. Three of the methods are based on the heteronuclear multiple-quantum and single-quantum correlation experiments, that is, high rank tensors that involve the half spin and the quadrupolar spin are generated. Here, both zero and single-quantum coherence of the half spins are allowed and various coherence orders of the quadrupolar spin are generated, and filtered, via active recoupling ofmore » the dipolar interaction. As a result of generating coherence orders larger than one, the spectral resolution for the quadrupolar nucleus increases linearly with the coherence order. Since the formation of high rank tensors is independent of the existence of a finite quadrupolar interaction, these experiments are also suitable to materials in which there is high symmetry around the quadrupolar spin. A fourth experiment is based on the initial quadrupolar-driven excitation of symmetric high order coherences (up to p = 2S, where S is the spin number) and subsequently generating by the heteronuclear dipolar interaction higher rank (l + 1 or higher) tensors that involve also the half spins. Due to the nature of this technique, it also provides information on the relative orientations of the quadrupolar and dipolar interaction tensors. For the ideal case in which the pulses are sufficiently strong with respect to other interactions, we derive analytical expressions for all experiments as well as for the transferred echo double resonance experiment involving a quadrupolar spin. We show by comparison of the fitting of simulations and the analytical expressions to experimental data that the analytical expressions are sufficiently accurate to provide experimental {sup 7}Li–{sup 13}C distances in a complex of lithium, glycine, and water. Discussion of the regime for which such an approach is valid is given.« less

BatMis: a fast algorithm for k-mismatch mapping.

PubMed

Tennakoon, Chandana; Purbojati, Rikky W; Sung, Wing-Kin

2012-08-15

Second-generation sequencing (SGS) generates millions of reads that need to be aligned to a reference genome allowing errors. Although current aligners can efficiently map reads allowing a small number of mismatches, they are not well suited for handling a large number of mismatches. The efficiency of aligners can be improved using various heuristics, but the sensitivity and accuracy of the alignments are sacrificed. In this article, we introduce Basic Alignment tool for Mismatches (BatMis)--an efficient method to align short reads to a reference allowing k mismatches. BatMis is a Burrows-Wheeler transformation based aligner that uses a seed and extend approach, and it is an exact method. Benchmark tests show that BatMis performs better than competing aligners in solving the k-mismatch problem. Furthermore, it can compete favorably even when compared with the heuristic modes of the other aligners. BatMis is a useful alternative for applications where fast k-mismatch mappings, unique mappings or multiple mappings of SGS data are required. BatMis is written in C/C++ and is freely available from http://code.google.com/p/batmis/

Structural Assembly of Multidomain Proteins and Protein Complexes Guided by the Overall Rotational Diffusion Tensor

PubMed Central

Ryabov, Yaroslav; Fushman, David

2008-01-01

We present a simple and robust approach that uses the overall rotational diffusion tensor as a structural constraint for domain positioning in multidomain proteins and protein-protein complexes. This method offers the possibility to use NMR relaxation data for detailed structure characterization of such systems provided the structures of individual domains are available. The proposed approach extends the concept of using long-range information contained in the overall rotational diffusion tensor. In contrast to the existing approaches, we use both the principal axes and principal values of protein’s rotational diffusion tensor to determine not only the orientation but also the relative positioning of the individual domains in a protein. This is achieved by finding the domain arrangement in a molecule that provides the best possible agreement with all components of the overall rotational diffusion tensor derived from experimental data. The accuracy of the proposed approach is demonstrated for two protein systems with known domain arrangement and parameters of the overall tumbling: the HIV-1 protease homodimer and Maltose Binding Protein. The accuracy of the method and its sensitivity to domain positioning is also tested using computer-generated data for three protein complexes, for which the experimental diffusion tensors are not available. In addition, the proposed method is applied here to determine, for the first time, the structure of both open and closed conformations of Lys48-linked di-ubiquitin chain, where domain motions render impossible accurate structure determination by other methods. The proposed method opens new avenues for improving structure characterization of proteins in solution. PMID:17550252

A Catalog of Moment Tensors and Source-type Characterization for Small Events at Uturuncu Volcano, Bolivia

NASA Astrophysics Data System (ADS)

Alvizuri, C. R.; Tape, C.

2015-12-01

We present a catalog of full seismic moment tensors for 63 events from Uturuncu volcano in Bolivia. The events were recorded during 2011-2012 in the PLUTONS seismic array of 24 broadband stations. Most events had magnitudes between 0.5 and 2.0 and did not generate discernible surface waves; the largest event was Mw 2.8. For each event we computed the misfit between observed and synthetic waveforms, and we also used first-motion polarity measurements to reduce the number of possible solutions. Each moment tensor solution was obtained using a grid search over the six-dimensional space of moment tensors. For each event we characterize the variation of moment tensor source type by plotting the misfit function in eigenvalue space, represented by a lune. We plot the optimal solutions for the 63 events on the lune in order to identify three subsets of the catalog: (1) a set of isotropic events, (2) a set of tensional crack events, and (3) a swarm of events southeast of the volcanic center that appear to be double couples. The occurrence of positively isotropic events is consistent with other published results from volcanic and geothermal regions. Several of these previous results, as well as our results, cannot be interpreted within the context of either an oblique opening crack or a crack-plus-double-couple model; instead they require a multiple-process source model. Our study emphasizes the importance of characterizing uncertainties for full moment tensors, and it provides strong support for isotropic events at Uturuncu volcano.

Tensor contraction engine: Abstraction and automated parallel implementation of configuration-interaction, coupled-cluster, and many-body perturbation theories

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

Hirata, So

2003-11-20

We develop a symbolic manipulation program and program generator (Tensor Contraction Engine or TCE) that automatically derives the working equations of a well-defined model of second-quantized many-electron theories and synthesizes efficient parallel computer programs on the basis of these equations. Provided an ansatz of a many-electron theory model, TCE performs valid contractions of creation and annihilation operators according to Wick's theorem, consolidates identical terms, and reduces the expressions into the form of multiple tensor contractions acted by permutation operators. Subsequently, it determines the binary contraction order for each multiple tensor contraction with the minimal operation and memory cost, factorizes commonmore » binary contractions (defines intermediate tensors), and identifies reusable intermediates. The resulting ordered list of binary tensor contractions, additions, and index permutations is translated into an optimized program that is combined with the NWChem and UTChem computational chemistry software packages. The programs synthesized by TCE take advantage of spin symmetry, Abelian point-group symmetry, and index permutation symmetry at every stage of calculations to minimize the number of arithmetic operations and storage requirement, adjust the peak local memory usage by index range tiling, and support parallel I/O interfaces and dynamic load balancing for parallel executions. We demonstrate the utility of TCE through automatic derivation and implementation of parallel programs for various models of configuration-interaction theory (CISD, CISDT, CISDTQ), many-body perturbation theory [MBPT(2), MBPT(3), MBPT(4)], and coupled-cluster theory (LCCD, CCD, LCCSD, CCSD, QCISD, CCSDT, and CCSDTQ).« less

Use of non-fault fractures in stress tensor reconstruction using the Mohr Circle with the Win-tensor program

NASA Astrophysics Data System (ADS)

Delvaux, Damien

2016-04-01

Paleostress inversion of geological fault-slip data is usually done using the directional part of the applied stress tensor on a slip plane and comparing it with the observed slip lines. However, this method do not fully exploit the brittle data sets as those are composed of shear and tension fractures, in addition to faults. Brittle deformation can be decomposed in two steps. An initial fracture/failure in previously intact rock generate extension/tensile fractures or shear fractures, both without visible opening or displacement. This first step may or not be followed by fracture opening to form tension joints, frictional shearing to form shear faults, or a combination of opening and shearing which produces hybrid fractures. Fractured rock outcrop contain information of the stress conditions that acted during both brittle deformation steps. The purpose here is to investigate how the fracture pattern generated during the initial fracture/failure step might be used in paleostress reconstruction. Each fracture is represented on the Mohr Circle by its resolved normal and shear stress magnitudes. We consider the typical domains on the Mohr circle where the different types de fractures nucleate (tension, hybrid, shear and compression fractures), as well the domain which contain reactivated fractures (faults reactivating an initial fracture plane). In function of the fracture type defined in the field, a "distance" is computed on the Mohr circle between each point and its expected corresponding nucleation/reactivation domain. This "Mohr Distance" is then used as function to minimize during the inversion. We implemented this new function in the Win-Tensor program, and tested it with natural and synthetic data sets from different stress regimes. It can be used alone using only the Mohr Distance on each plane (function F10), or combined with the angular misfit between observed striae and resolved shear directions (composite function F11). When used alone (F10), only the 3 stress axes can be determined and the stress ratio R (sigma 2-3)/sigma1-3) has to be pre-determined. With the combined function (F11), it provide an additional constrain to the classical angular misfit. With data sets composed of a majority of neoformed fractures, stress inversion using the Mohr Distance F10 function provide a good approximation of the 3 stress axes (using only the fracture data) as compared with the results of the F11 composite function (using also the observed slip lines). Tensor program is available at (http://www.damiendelvaux.be/Tensor/tensor-index.html).

Field-aligned currents and large scale magnetospheric electric fields

NASA Technical Reports Server (NTRS)

Dangelo, N.

1980-01-01

D'Angelo's model of polar cap electric fields (1977) was used to visualize how high-latitude field-aligned currents are driven by the solar wind generator. The region 1 and region 2 currents of Iijima and Potemra (1976) and the cusp field-aligned currents of Wilhjelm et al. (1978) and McDiarmid et al. (1978) are apparently driven by different generators, although in both cases the solar wind is their ultimate source.

Towards Interactive Construction of Topical Hierarchy: A Recursive Tensor Decomposition Approach

PubMed Central

Wang, Chi; Liu, Xueqing; Song, Yanglei; Han, Jiawei

2015-01-01

Automatic construction of user-desired topical hierarchies over large volumes of text data is a highly desirable but challenging task. This study proposes to give users freedom to construct topical hierarchies via interactive operations such as expanding a branch and merging several branches. Existing hierarchical topic modeling techniques are inadequate for this purpose because (1) they cannot consistently preserve the topics when the hierarchy structure is modified; and (2) the slow inference prevents swift response to user requests. In this study, we propose a novel method, called STROD, that allows efficient and consistent modification of topic hierarchies, based on a recursive generative model and a scalable tensor decomposition inference algorithm with theoretical performance guarantee. Empirical evaluation shows that STROD reduces the runtime of construction by several orders of magnitude, while generating consistent and quality hierarchies. PMID:26705505

Towards Interactive Construction of Topical Hierarchy: A Recursive Tensor Decomposition Approach.

PubMed

Wang, Chi; Liu, Xueqing; Song, Yanglei; Han, Jiawei

2015-08-01

Automatic construction of user-desired topical hierarchies over large volumes of text data is a highly desirable but challenging task. This study proposes to give users freedom to construct topical hierarchies via interactive operations such as expanding a branch and merging several branches. Existing hierarchical topic modeling techniques are inadequate for this purpose because (1) they cannot consistently preserve the topics when the hierarchy structure is modified; and (2) the slow inference prevents swift response to user requests. In this study, we propose a novel method, called STROD, that allows efficient and consistent modification of topic hierarchies, based on a recursive generative model and a scalable tensor decomposition inference algorithm with theoretical performance guarantee. Empirical evaluation shows that STROD reduces the runtime of construction by several orders of magnitude, while generating consistent and quality hierarchies.

Controllable 3D architectures of aligned carbon nanotube arrays by multi-step processes

NASA Astrophysics Data System (ADS)

Huang, Shaoming

2003-06-01

An effective way to fabricate large area three-dimensional (3D) aligned CNTs pattern based on pyrolysis of iron(II) phthalocyanine (FePc) by two-step processes is reported. The controllable generation of different lengths and selective growth of the aligned CNT arrays on metal-patterned (e.g., Ag and Au) substrate are the bases for generating such 3D aligned CNTs architectures. By controlling experimental conditions 3D aligned CNT arrays with different lengths/densities and morphologies/structures as well as multi-layered architectures can be fabricated in large scale by multi-step pyrolysis of FePc. These 3D architectures could have interesting properties and be applied for developing novel nanotube-based devices.

Insights from echocardiography, magnetic resonance imaging, and microcomputed tomography relative to the mid-myocardial left ventricular echogenic zone.

PubMed

Agger, Peter; Stephenson, Robert S; Dobrzynski, Halina; Atkinson, Andrew; Iaizzo, Paul A; Anderson, Robert H; Jarvis, Jonathan C; Allan, Sarah L; Partridge, John B; Zhao, Jichao; Zhang, Henggui; MacIver, David H

2016-10-01

The anatomical substrate for the mid-mural ventricular hyperechogenic zone remains uncertain, but it may represent no more than ultrasound reflected from cardiomyocytes orientated orthogonally to the ultrasonic beam. We sought to ascertain the relationship between the echogenic zone and the orientation of the cardiomyocytes. We used 3D echocardiography, diffusion tensor imaging, and microcomputed tomography to analyze the location and orientation of cardiomyocytes within the echogenic zone. We demonstrated that visualization of the echogenic zone is dependent on the position of the transducer and is most clearly seen from the apical window. Diffusion tensor imaging and microcomputed tomography show that the echogenic zone seen from the apical window corresponds to the position of the circumferentially orientated cardiomyocytes. An oblique band seen in the parasternal view relates to cardiomyocytes orientated orthogonally to the ultrasonic beam. The mid-mural ventricular hyperechogenic zone represents reflected ultrasound from cardiomyocytes aligned orthogonal to the ultrasonic beam. The echogenic zone does not represent a space, a connective tissue sheet, a boundary between ascending and descending limbs of a hypothetical helical ventricular myocardial band, nor an abrupt change in cardiomyocyte orientation. © 2016, Wiley Periodicals, Inc.

Influences of the Darrieus-Landau instability on premixed turbulent flames

NASA Astrophysics Data System (ADS)

Patyal, Advitya; Matalon, Moshe

2017-11-01

The propagation of turbulent flames in three-dimensional turbulent flows is studied within the context of the hydrodynamic theory. The flame is treated as a surface of density discontinuity with the flow modified by gas expansion resulting from heat released during combustion. The flame is tracked using a level-set method with a propagation speed that depends on the local flame stretch, modulated by a Markstein length. Impact of the Darrieus-Landau instability on the topology of the flame surface is studied. It is shown that similar to passive interfaces, flames under the influence of the hydrodynamic instability resort to cylindrical structures with increasing turbulence intensity, even in 3D. The mechanism of modification of vortical structures in the burned gas is identified in terms of the alignments between the vorticity vector, flame surface normal and eigenvectors of the strain rate tensor. The results indicate that the strain rate tensor is intricately coupled with the normal to the flame surface and creates anisotropy in the orientation of vortical structures, which begins to weaken as the turbulent intensity increases. Furthermore, vorticity budgets are used to highlight the relative importance of baroclinic torque due to Darrieus-Landau instability.

Interpolation of orientation distribution functions in diffusion weighted imaging using multi-tensor model.

PubMed

Afzali, Maryam; Fatemizadeh, Emad; Soltanian-Zadeh, Hamid

2015-09-30

Diffusion weighted imaging (DWI) is a non-invasive method for investigating the brain white matter structure and can be used to evaluate fiber bundles. However, due to practical constraints, DWI data acquired in clinics are low resolution. This paper proposes a method for interpolation of orientation distribution functions (ODFs). To this end, fuzzy clustering is applied to segment ODFs based on the principal diffusion directions (PDDs). Next, a cluster is modeled by a tensor so that an ODF is represented by a mixture of tensors. For interpolation, each tensor is rotated separately. The method is applied on the synthetic and real DWI data of control and epileptic subjects. Both experiments illustrate capability of the method in increasing spatial resolution of the data in the ODF field properly. The real dataset show that the method is capable of reliable identification of differences between temporal lobe epilepsy (TLE) patients and normal subjects. The method is compared to existing methods. Comparison studies show that the proposed method generates smaller angular errors relative to the existing methods. Another advantage of the method is that it does not require an iterative algorithm to find the tensors. The proposed method is appropriate for increasing resolution in the ODF field and can be applied to clinical data to improve evaluation of white matter fibers in the brain. Copyright © 2015 Elsevier B.V. All rights reserved.

The TT, TB, EB and BB correlations in anisotropic inflation

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

Chen, Xingang; Emami, Razieh; Firouzjahi, Hassan

2014-08-01

The ongoing and future experiments will measure the B-mode from different sky coverage and frequency bands, with the potential to reveal non-trivial features in polarization map. In this work we study the TT, TB, EB and BB correlations associated with the B-mode polarization of CMB map in models of charged anisotropic inflation. The model contains a chaotic-type large field complex inflaton which is charged under the U(1) gauge field. We calculate the statistical anisotropies generated in the power spectra of the curvature perturbation, the tensor perturbation and their cross-correlation. It is shown that the asymmetry in tensor power spectrum ismore » a very sensitive probe of the gauge coupling. While the level of statistical anisotropy in temperature power spectrum can be small and satisfy the observational bounds, the interactions from the gauge coupling can induce large directional dependence in tensor modes. This will leave interesting anisotropic fingerprints in various correlations involving the B-mode polarization such as the TB cross-correlation which may be detected in upcoming Planck polarization data. In addition, the TT correlation receives an anisotropic contribution from the tensor sector which naturally decays after l ∼> 100. We expect that the mechanism of using tensor sector to induce asymmetry at low l to be generic which can also be applied to address other low l CMB anomalies.« less

Time-Optimized High-Resolution Readout-Segmented Diffusion Tensor Imaging

PubMed Central

Reishofer, Gernot; Koschutnig, Karl; Langkammer, Christian; Porter, David; Jehna, Margit; Enzinger, Christian; Keeling, Stephen; Ebner, Franz

2013-01-01

Readout-segmented echo planar imaging with 2D navigator-based reacquisition is an uprising technique enabling the sampling of high-resolution diffusion images with reduced susceptibility artifacts. However, low signal from the small voxels and long scan times hamper the clinical applicability. Therefore, we introduce a regularization algorithm based on total variation that is applied directly on the entire diffusion tensor. The spatially varying regularization parameter is determined automatically dependent on spatial variations in signal-to-noise ratio thus, avoiding over- or under-regularization. Information about the noise distribution in the diffusion tensor is extracted from the diffusion weighted images by means of complex independent component analysis. Moreover, the combination of those features enables processing of the diffusion data absolutely user independent. Tractography from in vivo data and from a software phantom demonstrate the advantage of the spatially varying regularization compared to un-regularized data with respect to parameters relevant for fiber-tracking such as Mean Fiber Length, Track Count, Volume and Voxel Count. Specifically, for in vivo data findings suggest that tractography results from the regularized diffusion tensor based on one measurement (16 min) generates results comparable to the un-regularized data with three averages (48 min). This significant reduction in scan time renders high resolution (1×1×2.5 mm3) diffusion tensor imaging of the entire brain applicable in a clinical context. PMID:24019951

Primordial perturbations from dilaton-induced gauge fields

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

Choi, Kiwoon; Choi, Ki-Young; Kim, Hyungjin

2015-10-01

We study the primordial scalar and tensor perturbations in inflation scenario involving a spectator dilaton field. In our setup, the rolling spectator dilaton causes a tachyonic instability of gauge fields, leading to a copious production of gauge fields in the superhorizon regime, which generates additional scalar and tensor perturbations through gravitational interactions. Our prime concern is the possibility to enhance the tensor-to-scalar ratio r relative to the standard result, while satisfying the observational constraints. To this end, we allow the dilaton field to be stabilized before the end of inflation, but after the CMB scales exit the horizon. We showmore » that for the inflaton slow roll parameter ε ∼> 10{sup −3}, the tensor-to-scalar ratio in our setup can be enhanced only by a factor of O(1) compared to the standard result. On the other hand, for smaller ε corresponding to a lower inflation energy scale, a much bigger enhancement can be achieved, so that our setup can give rise to an observably large r∼> 10{sup −2} even when ε|| 10{sup −3}. The tensor perturbation sourced by the spectator dilaton can have a strong scale dependence, and is generically red-tilted. We also discuss a specific model to realize our scenario, and identify the parameter region giving an observably large r for relatively low inflation energy scales.« less

ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

PubMed

Sadygov, Rovshan G; Maroto, Fernando Martin; Hühmer, Andreas F R

2006-12-15

We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

White matter tractography using diffusion tensor deflection.

PubMed

Lazar, Mariana; Weinstein, David M; Tsuruda, Jay S; Hasan, Khader M; Arfanakis, Konstantinos; Meyerand, M Elizabeth; Badie, Benham; Rowley, Howard A; Haughton, Victor; Field, Aaron; Alexander, Andrew L

2003-04-01

Diffusion tensor MRI provides unique directional diffusion information that can be used to estimate the patterns of white matter connectivity in the human brain. In this study, the behavior of an algorithm for white matter tractography is examined. The algorithm, called TEND, uses the entire diffusion tensor to deflect the estimated fiber trajectory. Simulations and imaging experiments on in vivo human brains were performed to investigate the behavior of the tractography algorithm. The simulations show that the deflection term is less sensitive than the major eigenvector to image noise. In the human brain imaging experiments, estimated tracts were generated in corpus callosum, corticospinal tract, internal capsule, corona radiata, superior longitudinal fasciculus, inferior longitudinal fasciculus, fronto-occipital fasciculus, and uncinate fasciculus. This approach is promising for mapping the organizational patterns of white matter in the human brain as well as mapping the relationship between major fiber trajectories and the location and extent of brain lesions. Copyright 2003 Wiley-Liss, Inc.

Conformal killing tensors and covariant Hamiltonian dynamics

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

Cariglia, M., E-mail: marco@iceb.ufop.br; Gibbons, G. W., E-mail: G.W.Gibbons@damtp.cam.ac.uk; LE STUDIUM, Loire Valley Institute for Advanced Studies, Tours and Orleans

2014-12-15

A covariant algorithm for deriving the conserved quantities for natural Hamiltonian systems is combined with the non-relativistic framework of Eisenhart, and of Duval, in which the classical trajectories arise as geodesics in a higher dimensional space-time, realized by Brinkmann manifolds. Conserved quantities which are polynomial in the momenta can be built using time-dependent conformal Killing tensors with flux. The latter are associated with terms proportional to the Hamiltonian in the lower dimensional theory and with spectrum generating algebras for higher dimensional quantities of order 1 and 2 in the momenta. Illustrations of the general theory include the Runge-Lenz vector formore » planetary motion with a time-dependent gravitational constant G(t), motion in a time-dependent electromagnetic field of a certain form, quantum dots, the Hénon-Heiles and Holt systems, respectively, providing us with Killing tensors of rank that ranges from one to six.« less

Intrinsic Viscosity of Dendrimers via Equilibrium Molecular Dynamics

NASA Astrophysics Data System (ADS)

Drew, Phil; Adolf, David

2004-03-01

Equilibrium molecular dynamics simulations of dendrimers in dilute solution have been performed using dl-poly. Analysis of the system stress tensor via the Green-Kubo formula produces the viscosity of the dendrimer solution which, when coupled with that of a solvent only system leads to the intrinsic viscosity of the dendrimer solute. Particular attention has been paid to error analysis as the auto-correlation of the stress tensor exhibits a long time tail, potentially leading to large uncertainties in the solution, and hence intrinsic, viscosities. In order to counter this effect and provide reliable statistical averaging, simulations have been run spanning very many times the longest system relaxation. Comparison is made to previous studies, using different techniques, which suggest a peak in the intrinsic viscosity of dendrimers at around generation four. Results are also presented from investigations in to the individual contributions to the system stress tensor from the solvent and the solute.

Topological regularization and self-duality in four-dimensional anti-de Sitter gravity

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

Miskovic, Olivera; Olea, Rodrigo; Instituto de Fisica, Pontificia Universidad Catolica de Valparaiso, Casilla 4059, Valparaiso

2009-06-15

It is shown that the addition of a topological invariant (Gauss-Bonnet term) to the anti-de Sitter gravity action in four dimensions recovers the standard regularization given by the holographic renormalization procedure. This crucial step makes possible the inclusion of an odd parity invariant (Pontryagin term) whose coupling is fixed by demanding an asymptotic (anti) self-dual condition on the Weyl tensor. This argument allows one to find the dual point of the theory where the holographic stress tensor is related to the boundary Cotton tensor as T{sub j}{sup i}={+-}(l{sup 2}/8{pi}G)C{sub j}{sup i}, which has been observed in recent literature in solitonicmore » solutions and hydrodynamic models. A general procedure to generate the counterterm series for anti-de Sitter gravity in any even dimension from the corresponding Euler term is also briefly discussed.« less

Conflation: a new type of accelerated expansion

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

Fertig, Angelika; Lehners, Jean-Luc; Mallwitz, Enno

2016-08-31

In the framework of scalar-tensor theories of gravity, we construct a new kind of cosmological model that conflates inflation and ekpyrosis. During a phase of conflation, the universe undergoes accelerated expansion, but with crucial differences compared to ordinary inflation. In particular, the potential energy is negative, which is of interest for supergravity and string theory where both negative potentials and the required scalar-tensor couplings are rather natural. A distinguishing feature of the model is that, for a large parameter range, it does not significantly amplify adiabatic scalar and tensor fluctuations, and in particular does not lead to eternal inflation andmore » the associated infinities. We also show how density fluctuations in accord with current observations may be generated by adding a second scalar field to the model. Conflation may be viewed as complementary to the recently proposed anamorphic universe of Ijjas and Steinhardt.« less

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

PubMed Central

Wright, Imogen A.; Travers, Simon A.

2014-01-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. PMID:24861618

Design, development and clinical validation of computer-aided surgical simulation system for streamlined orthognathic surgical planning.

PubMed

Yuan, Peng; Mai, Huaming; Li, Jianfu; Ho, Dennis Chun-Yu; Lai, Yingying; Liu, Siting; Kim, Daeseung; Xiong, Zixiang; Alfi, David M; Teichgraeber, John F; Gateno, Jaime; Xia, James J

2017-12-01

There are many proven problems associated with traditional surgical planning methods for orthognathic surgery. To address these problems, we developed a computer-aided surgical simulation (CASS) system, the AnatomicAligner, to plan orthognathic surgery following our streamlined clinical protocol. The system includes six modules: image segmentation and three-dimensional (3D) reconstruction, registration and reorientation of models to neutral head posture, 3D cephalometric analysis, virtual osteotomy, surgical simulation, and surgical splint generation. The accuracy of the system was validated in a stepwise fashion: first to evaluate the accuracy of AnatomicAligner using 30 sets of patient data, then to evaluate the fitting of splints generated by AnatomicAligner using 10 sets of patient data. The industrial gold standard system, Mimics, was used as the reference. When comparing the results of segmentation, virtual osteotomy and transformation achieved with AnatomicAligner to the ones achieved with Mimics, the absolute deviation between the two systems was clinically insignificant. The average surface deviation between the two models after 3D model reconstruction in AnatomicAligner and Mimics was 0.3 mm with a standard deviation (SD) of 0.03 mm. All the average surface deviations between the two models after virtual osteotomy and transformations were smaller than 0.01 mm with a SD of 0.01 mm. In addition, the fitting of splints generated by AnatomicAligner was at least as good as the ones generated by Mimics. We successfully developed a CASS system, the AnatomicAligner, for planning orthognathic surgery following the streamlined planning protocol. The system has been proven accurate. AnatomicAligner will soon be available freely to the boarder clinical and research communities.

Design, development and clinical validation of computer-aided surgical simulation system for streamlined orthognathic surgical planning

PubMed Central

Yuan, Peng; Mai, Huaming; Li, Jianfu; Ho, Dennis Chun-Yu; Lai, Yingying; Liu, Siting; Kim, Daeseung; Xiong, Zixiang; Alfi, David M.; Teichgraeber, John F.; Gateno, Jaime

2017-01-01

Purpose There are many proven problems associated with traditional surgical planning methods for orthognathic surgery. To address these problems, we developed a computer-aided surgical simulation (CASS) system, the AnatomicAligner, to plan orthognathic surgery following our streamlined clinical protocol. Methods The system includes six modules: image segmentation and three-dimensional (3D) reconstruction, registration and reorientation of models to neutral head posture, 3D cephalometric analysis, virtual osteotomy, surgical simulation, and surgical splint generation. The accuracy of the system was validated in a stepwise fashion: first to evaluate the accuracy of AnatomicAligner using 30 sets of patient data, then to evaluate the fitting of splints generated by AnatomicAligner using 10 sets of patient data. The industrial gold standard system, Mimics, was used as the reference. Result When comparing the results of segmentation, virtual osteotomy and transformation achieved with AnatomicAligner to the ones achieved with Mimics, the absolute deviation between the two systems was clinically insignificant. The average surface deviation between the two models after 3D model reconstruction in AnatomicAligner and Mimics was 0.3 mm with a standard deviation (SD) of 0.03 mm. All the average surface deviations between the two models after virtual osteotomy and transformations were smaller than 0.01 mm with a SD of 0.01 mm. In addition, the fitting of splints generated by AnatomicAligner was at least as good as the ones generated by Mimics. Conclusion We successfully developed a CASS system, the AnatomicAligner, for planning orthognathic surgery following the streamlined planning protocol. The system has been proven accurate. AnatomicAligner will soon be available freely to the boarder clinical and research communities. PMID:28432489

The nonlocal elastomagnetoelectrostatics of disordered micropolar media

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

Kabychenkov, A. F.; Lisiovskii, F. V., E-mail: lisf@rambler.ru

The interactions of electric, magnetic, and elastic subsystems in nonlinear disordered micropolar media that possess a bending–torsion tensor and an nonsymmetric strain tensor have been studied in the framework of phenomenological elastomagnetoelectrostatics. A system of nonlinear equations for determining the ground state of these media has been obtained by the variational method. It is shown that nonuniform external and internal rotations not only create elastic stresses, but also generate additional electric and magnetic fields, while nonuniform elastic stresses and external fields induce internal rotations. The nonlocal character of the micropolar media significantly influences elementary excitations and nonlinear dynamic processes.

Dark energy simulacrum in nonlinear electrodynamics

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

Labun, Lance; Rafelski, Johann

2010-03-15

Quasiconstant external fields in nonlinear electromagnetism generate a global contribution proportional to g{sup {mu}{nu}}in the energy-momentum tensor, thus a simulacrum of dark energy. To provide a thorough understanding of the origin and strength of its effects, we undertake a complete theoretical and numerical study of the energy-momentum tensor T{sup {mu}{nu}}for nonlinear electromagnetism. The Euler-Heisenberg nonlinearity due to quantum fluctuations of spinor and scalar matter fields is considered and contrasted with the properties of classical nonlinear Born-Infeld electromagnetism. We address modifications of charged particle kinematics by strong background fields.

HSA: a heuristic splice alignment tool.

PubMed

Bu, Jingde; Chi, Xuebin; Jin, Zhong

2013-01-01

RNA-Seq methodology is a revolutionary transcriptomics sequencing technology, which is the representative of Next generation Sequencing (NGS). With the high throughput sequencing of RNA-Seq, we can acquire much more information like differential expression and novel splice variants from deep sequence analysis and data mining. But the short read length brings a great challenge to alignment, especially when the reads span two or more exons. A two steps heuristic splice alignment tool is generated in this investigation. First, map raw reads to reference with unspliced aligner--BWA; second, split initial unmapped reads into three equal short reads (seeds), align each seed to the reference, filter hits, search possible split position of read and extend hits to a complete match. Compare with other splice alignment tools like SOAPsplice and Tophat2, HSA has a better performance in call rate and efficiency, but its results do not as accurate as the other software to some extent. HSA is an effective spliced aligner of RNA-Seq reads mapping, which is available at https://github.com/vlcc/HSA.

Numerical simulation of large-scale field-aligned current generation from finite-amplitude magnetosonic waves

NASA Technical Reports Server (NTRS)

Yamauchi, M.

1994-01-01

A two-dimensional numerical simulation of finite-amplitude magnetohydrodynamic (MHD) magnetosonic waves is performed under a finite-velocity background convection condition. Isothermal cases are considered for simplicity. External dissipation is introduced by assuming that the field-aligned currents are generated in proportion to the accumulated charges. The simulation results are as follows: Paired field-aligned currents are found from the simulated waves. The flow directions of these field-aligned currents depend on the angle between the background convection and the wave normal, and hence two pairs of field-aligned currents are found from a bowed wave if we look at the overall structure. The majority of these field-aligned currents are closed within each pair rather than between two wings. These features are not observed under slow background convection. The result could be applied to the cusp current system and the substorm current system.

A distributed system for fast alignment of next-generation sequencing data.

PubMed

Srimani, Jaydeep K; Wu, Po-Yen; Phan, John H; Wang, May D

2010-12-01

We developed a scalable distributed computing system using the Berkeley Open Interface for Network Computing (BOINC) to align next-generation sequencing (NGS) data quickly and accurately. NGS technology is emerging as a promising platform for gene expression analysis due to its high sensitivity compared to traditional genomic microarray technology. However, despite the benefits, NGS datasets can be prohibitively large, requiring significant computing resources to obtain sequence alignment results. Moreover, as the data and alignment algorithms become more prevalent, it will become necessary to examine the effect of the multitude of alignment parameters on various NGS systems. We validate the distributed software system by (1) computing simple timing results to show the speed-up gained by using multiple computers, (2) optimizing alignment parameters using simulated NGS data, and (3) computing NGS expression levels for a single biological sample using optimal parameters and comparing these expression levels to that of a microarray sample. Results indicate that the distributed alignment system achieves approximately a linear speed-up and correctly distributes sequence data to and gathers alignment results from multiple compute clients.

B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis

PubMed Central

Towfic, Fadi; Gupta, Shakti; Honavar, Vasant; Subramaniam, Shankar

2012-01-01

The initiation of B-cell ligand recognition is a critical step for the generation of an immune response against foreign bodies. We sought to identify the biochemical pathways involved in the B-cell ligand recognition cascade and sets of ligands that trigger similar immunological responses. We utilized several comparative approaches to analyze the gene coexpression networks generated from a set of microarray experiments spanning 33 different ligands. First, we compared the degree distributions of the generated networks. Second, we utilized a pairwise network alignment algorithm, BiNA, to align the networks based on the hubs in the networks. Third, we aligned the networks based on a set of KEGG pathways. We summarized our results by constructing a consensus hierarchy of pathways that are involved in B cell ligand recognition. The resulting pathways were further validated through literature for their common physiological responses. Collectively, the results based on our comparative analyses of degree distributions, alignment of hubs, and alignment based on KEGG pathways provide a basis for molecular characterization of the immune response states of B-cells and demonstrate the power of comparative approaches (e.g., gene coexpression network alignment algorithms) in elucidating biochemical pathways involved in complex signaling events in cells. PMID:22917187

Quantum corrections to the stress-energy tensor in thermodynamic equilibrium with acceleration

NASA Astrophysics Data System (ADS)

Becattini, F.; Grossi, E.

2015-08-01

We show that the stress-energy tensor has additional terms with respect to the ideal form in states of global thermodynamic equilibrium in flat spacetime with nonvanishing acceleration and vorticity. These corrections are of quantum origin and their leading terms are second order in the gradients of the thermodynamic fields. Their relevant coefficients can be expressed in terms of correlators of the stress-energy tensor operator and the generators of the Lorentz group. With respect to previous assessments, we find that there are more second-order coefficients and that all thermodynamic functions including energy density receive acceleration and vorticity dependent corrections. Notably, also the relation between ρ and p , that is, the equation of state, is affected by acceleration and vorticity. We have calculated the corrections for a free real scalar field—both massive and massless—and we have found that they increase, particularly for a massive field, at very high acceleration and vorticity and very low temperature. Finally, these nonideal terms depend on the explicit form of the stress-energy operator, implying that different stress-energy tensors of the scalar field—canonical or improved—are thermodynamically inequivalent.

Tensor integrand reduction via Laurent expansion

DOE PAGES

Hirschi, Valentin; Peraro, Tiziano

2016-06-09

We introduce a new method for the application of one-loop integrand reduction via the Laurent expansion algorithm, as implemented in the public C++ library Ninja. We show how the coefficients of the Laurent expansion can be computed by suitable contractions of the loop numerator tensor with cut-dependent projectors, making it possible to interface Ninja to any one-loop matrix element generator that can provide the components of this tensor. We implemented this technique in the Ninja library and interfaced it to MadLoop, which is part of the public MadGraph5_aMC@NLO framework. We performed a detailed performance study, comparing against other public reductionmore » tools, namely CutTools, Samurai, IREGI, PJFry++ and Golem95. We find that Ninja out-performs traditional integrand reduction in both speed and numerical stability, the latter being on par with that of the tensor integral reduction tool Golem95 which is however more limited and slower than Ninja. Lastly, we considered many benchmark multi-scale processes of increasing complexity, involving QCD and electro-weak corrections as well as effective non-renormalizable couplings, showing that Ninja’s performance scales well with both the rank and multiplicity of the considered process.« less

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

PubMed Central

Margulies, Elliott H.; Cooper, Gregory M.; Asimenos, George; Thomas, Daryl J.; Dewey, Colin N.; Siepel, Adam; Birney, Ewan; Keefe, Damian; Schwartz, Ariel S.; Hou, Minmei; Taylor, James; Nikolaev, Sergey; Montoya-Burgos, Juan I.; Löytynoja, Ari; Whelan, Simon; Pardi, Fabio; Massingham, Tim; Brown, James B.; Bickel, Peter; Holmes, Ian; Mullikin, James C.; Ureta-Vidal, Abel; Paten, Benedict; Stone, Eric A.; Rosenbloom, Kate R.; Kent, W. James; Bouffard, Gerard G.; Guan, Xiaobin; Hansen, Nancy F.; Idol, Jacquelyn R.; Maduro, Valerie V.B.; Maskeri, Baishali; McDowell, Jennifer C.; Park, Morgan; Thomas, Pamela J.; Young, Alice C.; Blakesley, Robert W.; Muzny, Donna M.; Sodergren, Erica; Wheeler, David A.; Worley, Kim C.; Jiang, Huaiyang; Weinstock, George M.; Gibbs, Richard A.; Graves, Tina; Fulton, Robert; Mardis, Elaine R.; Wilson, Richard K.; Clamp, Michele; Cuff, James; Gnerre, Sante; Jaffe, David B.; Chang, Jean L.; Lindblad-Toh, Kerstin; Lander, Eric S.; Hinrichs, Angie; Trumbower, Heather; Clawson, Hiram; Zweig, Ann; Kuhn, Robert M.; Barber, Galt; Harte, Rachel; Karolchik, Donna; Field, Matthew A.; Moore, Richard A.; Matthewson, Carrie A.; Schein, Jacqueline E.; Marra, Marco A.; Antonarakis, Stylianos E.; Batzoglou, Serafim; Goldman, Nick; Hardison, Ross; Haussler, David; Miller, Webb; Pachter, Lior; Green, Eric D.; Sidow, Arend

2007-01-01

A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization. PMID:17567995

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

PubMed

Terashi, Genki; Takeda-Shitaka, Mayuko

2015-01-01

Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both single and multi-domain comparisons. The CAB-align software is freely available to academic users as stand-alone software at http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Publications.html.

BarraCUDA - a fast short read sequence aligner using graphics processing units

PubMed Central

2012-01-01

Background With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. Findings Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. Conclusions BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available from http://seqbarracuda.sf.net PMID:22244497

Moment Tensor Inversions of the M1.7+ Earthquakes in Basel. Switzerland Reveal Predominant Shear Dislocations

NASA Astrophysics Data System (ADS)

Guilhem, A.; Walter, F. T.

2013-12-01

We investigate moment tensor solutions of nearly 30 magnitude (M) 1.7+ earthquakes that occurred in Basel, Switzerland during and after the simulation of the geothermal enhanced system between December 2nd and 8th 2006. In 2009, Deichmann and Ernst determined the focal mechanisms for these events using P-wave first-motions. They found clear evidence for double-couple mechanisms with no indications for substantial volumetric changes. This differs from evidences of composite type ruptures (i.e., shearing with isotropic motion) observed in other geothermal environments. Here, we use a similar approach for the computation of the moment tensor inversions to the one used by Guilhem et al. (2012) for M3 earthquakes in Geysers. We use a dataset from strong-motion stations located within 7 km from the epicenters, with data filtered between 0.5 and 3 Hz and integrated twice to displacement. The waveforms are inverted for both deviatoric and full moment tensor solutions. In addition, we perform a network sensitivity test (NSS) by computing 100 million random moment tensors for each event thus testing the sensitivity of the moment tensor solutions. Finally, because the injection of fluids in the ground can promote crack growth generating seismic events, we also compute a crack + double-couple inversion (Minson et al., 2007) for each of the studied earthquakes between December 2006 and May 2007. From this extensive search we find that the results of our different techniques converge. Moment tensor solutions are very similar to the first-motion focal mechanisms of Deichmann and Ernst (2009) and accordingly do not exhibit dominant volumetric changes except for a subset of events, which we discuss in some detail. References: Deichmann, N. and Ernst, J. (2009), Swiss J. Geosc. Guilhem, A., Dreger, D.S., Hutchings, L. J., and Johnson, L. (2012), AGU Fall meeting Minson, S. E., Dreger, D. S., Bürgmann, R., Kanamori, H., Larson, K. M. (2007), J. Geophys. Res.

An Analysis of Elliptic Grid Generation Techniques Using an Implicit Euler Solver.

DTIC Science & Technology

1986-06-09

automatic determination of the control fu.nction, . elements of covariant metric tensor in the elliptic grid generation system , from the Cm = 1,2,3...computational fluid d’nan1-cs code. Tne code Inclues a tnree-dimensional current research is aimed primaril: at algebraic generation system based on transfinite...start the iterative solution of the f. ow, nea, transfer, and combustion proble:s. elliptic generation system . Tn13 feature also .:ven-.ts :.t be made

Theoretically informed Monte Carlo simulation of liquid crystals by sampling of alignment-tensor fields.

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

Armas-Perez, Julio C.; Londono-Hurtado, Alejandro; Guzman, Orlando

2015-07-27

A theoretically informed coarse-grained Monte Carlo method is proposed for studying liquid crystals. The free energy functional of the system is described in the framework of the Landau-de Gennes formalism. The alignment field and its gradients are approximated by finite differences, and the free energy is minimized through a stochastic sampling technique. The validity of the proposed method is established by comparing the results of the proposed approach to those of traditional free energy minimization techniques. Its usefulness is illustrated in the context of three systems, namely, a nematic liquid crystal confined in a slit channel, a nematic liquid crystalmore » droplet, and a chiral liquid crystal in the bulk. It is found that for systems that exhibit multiple metastable morphologies, the proposed Monte Carlo method is generally able to identify lower free energy states that are often missed by traditional approaches. Importantly, the Monte Carlo method identifies such states from random initial configurations, thereby obviating the need for educated initial guesses that can be difficult to formulate.« less

Theoretically informed Monte Carlo simulation of liquid crystals by sampling of alignment-tensor fields

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

Armas-Pérez, Julio C.; Londono-Hurtado, Alejandro; Guzmán, Orlando

2015-07-28

A theoretically informed coarse-grained Monte Carlo method is proposed for studying liquid crystals. The free energy functional of the system is described in the framework of the Landau-de Gennes formalism. The alignment field and its gradients are approximated by finite differences, and the free energy is minimized through a stochastic sampling technique. The validity of the proposed method is established by comparing the results of the proposed approach to those of traditional free energy minimization techniques. Its usefulness is illustrated in the context of three systems, namely, a nematic liquid crystal confined in a slit channel, a nematic liquid crystalmore » droplet, and a chiral liquid crystal in the bulk. It is found that for systems that exhibit multiple metastable morphologies, the proposed Monte Carlo method is generally able to identify lower free energy states that are often missed by traditional approaches. Importantly, the Monte Carlo method identifies such states from random initial configurations, thereby obviating the need for educated initial guesses that can be difficult to formulate.« less

Testing statistical isotropy in cosmic microwave background polarization maps

NASA Astrophysics Data System (ADS)

Rath, Pranati K.; Samal, Pramoda Kumar; Panda, Srikanta; Mishra, Debesh D.; Aluri, Pavan K.

2018-04-01

We apply our symmetry based Power tensor technique to test conformity of PLANCK Polarization maps with statistical isotropy. On a wide range of angular scales (l = 40 - 150), our preliminary analysis detects many statistically anisotropic multipoles in foreground cleaned full sky PLANCK polarization maps viz., COMMANDER and NILC. We also study the effect of residual foregrounds that may still be present in the Galactic plane using both common UPB77 polarization mask, as well as the individual component separation method specific polarization masks. However, some of the statistically anisotropic modes still persist, albeit significantly in NILC map. We further probed the data for any coherent alignments across multipoles in several bins from the chosen multipole range.

Constraining primordial vector mode from B-mode polarization

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

Saga, Shohei; Ichiki, Kiyotomo; Shiraishi, Maresuke, E-mail: saga.shohei@nagoya-u.jp, E-mail: maresuke.shiraishi@pd.infn.it, E-mail: ichiki@a.phys.nagoya-u.ac.jp

The B-mode polarization spectrum of the Cosmic Microwave Background (CMB) may be the smoking gun of not only the primordial tensor mode but also of the primordial vector mode. If there exist nonzero vector-mode metric perturbations in the early Universe, they are known to be supported by anisotropic stress fluctuations of free-streaming particles such as neutrinos, and to create characteristic signatures on both the CMB temperature, E-mode, and B-mode polarization anisotropies. We place constraints on the properties of the primordial vector mode characterized by the vector-to-scalar ratio r{sub v} and the spectral index n{sub v} of the vector-shear power spectrum,more » from the Planck and BICEP2 B-mode data. We find that, for scale-invariant initial spectra, the ΛCDM model including the vector mode fits the data better than the model including the tensor mode. The difference in χ{sup 2} between the vector and tensor models is Δχ{sup 2} = 3.294, because, on large scales the vector mode generates smaller temperature fluctuations than the tensor mode, which is preferred for the data. In contrast, the tensor mode can fit the data set equally well if we allow a significantly blue-tilted spectrum. We find that the best-fitting tensor mode has a large blue tilt and leads to an indistinct reionization bump on larger angular scales. The slightly red-tilted vector mode supported by the current data set can also create O(10{sup -22})-Gauss magnetic fields at cosmological recombination. Our constraints should motivate research that considers models of the early Universe that involve the vector mode.« less

Separability of massive field equations for spin-0 and spin-1/2 charged particles in the general nonextremal rotating charged black hole spacetimes in minimal five-dimensional gauged supergravity

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

Wu Shuangqing

We continue to investigate the separability of massive field equations for spin-0 and spin-1/2 charged particles in the general, nonextremal, rotating, charged, Chong-Cvetic-Lue-Pope black holes with two independent angular momenta and a nonzero cosmological constant in minimal D=5 gauged supergravity theory. We show that the complex Klein-Gordon equation and the modified Dirac equation with the inclusion of an extra counterterm can be separated by variables into purely radial and purely angular parts in this general Einstein-Maxwell-Chern-Simons background spacetime. A second-order symmetry operator that commutes with the complex Laplacian operator is constructed from the separated solutions and expressed compactly in termsmore » of a rank-2 Staeckel-Killing tensor which admits a simple diagonal form in the chosen pentad one-forms so that it can be understood as the square of a rank-3 totally antisymmetric tensor. A first-order symmetry operator that commutes with the modified Dirac operator is expressed in terms of a rank-3 generalized Killing-Yano tensor and its covariant derivative. The Hodge dual of this generalized Killing-Yano tensor is a generalized principal conformal Killing-Yano tensor of rank-2, which can generate a 'tower' of generalized (conformal) Killing-Yano and Staeckel-Killing tensors that are responsible for the whole hidden symmetries of this general, rotating, charged, Kerr-anti-de Sitter black hole geometry. In addition, the first laws of black hole thermodynamics have been generalized to the case that the cosmological constant can be viewed as a thermodynamical variable.« less

Microseismic Full Waveform Modeling in Anisotropic Media with Moment Tensor Implementation

NASA Astrophysics Data System (ADS)

Shi, Peidong; Angus, Doug; Nowacki, Andy; Yuan, Sanyi; Wang, Yanyan

2018-03-01

Seismic anisotropy which is common in shale and fractured rocks will cause travel-time and amplitude discrepancy in different propagation directions. For microseismic monitoring which is often implemented in shale or fractured rocks, seismic anisotropy needs to be carefully accounted for in source location and mechanism determination. We have developed an efficient finite-difference full waveform modeling tool with an arbitrary moment tensor source. The modeling tool is suitable for simulating wave propagation in anisotropic media for microseismic monitoring. As both dislocation and non-double-couple source are often observed in microseismic monitoring, an arbitrary moment tensor source is implemented in our forward modeling tool. The increments of shear stress are equally distributed on the staggered grid to implement an accurate and symmetric moment tensor source. Our modeling tool provides an efficient way to obtain the Green's function in anisotropic media, which is the key of anisotropic moment tensor inversion and source mechanism characterization in microseismic monitoring. In our research, wavefields in anisotropic media have been carefully simulated and analyzed in both surface array and downhole array. The variation characteristics of travel-time and amplitude of direct P- and S-wave in vertical transverse isotropic media and horizontal transverse isotropic media are distinct, thus providing a feasible way to distinguish and identify the anisotropic type of the subsurface. Analyzing the travel-times and amplitudes of the microseismic data is a feasible way to estimate the orientation and density of the induced cracks in hydraulic fracturing. Our anisotropic modeling tool can be used to generate and analyze microseismic full wavefield with full moment tensor source in anisotropic media, which can help promote the anisotropic interpretation and inversion of field data.

Microseismic Full Waveform Modeling in Anisotropic Media with Moment Tensor Implementation

NASA Astrophysics Data System (ADS)

Shi, Peidong; Angus, Doug; Nowacki, Andy; Yuan, Sanyi; Wang, Yanyan

2018-07-01

Seismic anisotropy which is common in shale and fractured rocks will cause travel-time and amplitude discrepancy in different propagation directions. For microseismic monitoring which is often implemented in shale or fractured rocks, seismic anisotropy needs to be carefully accounted for in source location and mechanism determination. We have developed an efficient finite-difference full waveform modeling tool with an arbitrary moment tensor source. The modeling tool is suitable for simulating wave propagation in anisotropic media for microseismic monitoring. As both dislocation and non-double-couple source are often observed in microseismic monitoring, an arbitrary moment tensor source is implemented in our forward modeling tool. The increments of shear stress are equally distributed on the staggered grid to implement an accurate and symmetric moment tensor source. Our modeling tool provides an efficient way to obtain the Green's function in anisotropic media, which is the key of anisotropic moment tensor inversion and source mechanism characterization in microseismic monitoring. In our research, wavefields in anisotropic media have been carefully simulated and analyzed in both surface array and downhole array. The variation characteristics of travel-time and amplitude of direct P- and S-wave in vertical transverse isotropic media and horizontal transverse isotropic media are distinct, thus providing a feasible way to distinguish and identify the anisotropic type of the subsurface. Analyzing the travel-times and amplitudes of the microseismic data is a feasible way to estimate the orientation and density of the induced cracks in hydraulic fracturing. Our anisotropic modeling tool can be used to generate and analyze microseismic full wavefield with full moment tensor source in anisotropic media, which can help promote the anisotropic interpretation and inversion of field data.

Inversion of calcite twin data for paleostress orientations and magnitudes: A new technique tested and calibrated on numerically-generated and natural data

NASA Astrophysics Data System (ADS)

Parlangeau, Camille; Lacombe, Olivier; Schueller, Sylvie; Daniel, Jean-Marc

2018-01-01

The inversion of calcite twin data is a powerful tool to reconstruct paleostresses sustained by carbonate rocks during their geological history. Following Etchecopar's (1984) pioneering work, this study presents a new technique for the inversion of calcite twin data that reconstructs the 5 parameters of the deviatoric stress tensors from both monophase and polyphase twin datasets. The uncertainties in the parameters of the stress tensors reconstructed by this new technique are evaluated on numerically-generated datasets. The technique not only reliably defines the 5 parameters of the deviatoric stress tensor, but also reliably separates very close superimposed stress tensors (30° of difference in maximum principal stress orientation or switch between σ3 and σ2 axes). The technique is further shown to be robust to sampling bias and to slight variability in the critical resolved shear stress. Due to our still incomplete knowledge of the evolution of the critical resolved shear stress with grain size, our results show that it is recommended to analyze twin data subsets of homogeneous grain size to minimize possible errors, mainly those concerning differential stress values. The methodological uncertainty in principal stress orientations is about ± 10°; it is about ± 0.1 for the stress ratio. For differential stresses, the uncertainty is lower than ± 30%. Applying the technique to vein samples within Mesozoic limestones from the Monte Nero anticline (northern Apennines, Italy) demonstrates its ability to reliably detect and separate tectonically significant paleostress orientations and magnitudes from naturally deformed polyphase samples, hence to fingerprint the regional paleostresses of interest in tectonic studies.

A high-order strong stability preserving Runge-Kutta method for three-dimensional full waveform modeling and inversion of anelastic models

NASA Astrophysics Data System (ADS)

Wang, N.; Shen, Y.; Yang, D.; Bao, X.; Li, J.; Zhang, W.

2017-12-01

Accurate and efficient forward modeling methods are important for high resolution full waveform inversion. Compared with the elastic case, solving anelastic wave equation requires more computational time, because of the need to compute additional material-independent anelastic functions. A numerical scheme with a large Courant-Friedrichs-Lewy (CFL) condition number enables us to use a large time step to simulate wave propagation, which improves computational efficiency. In this work, we apply the fourth-order strong stability preserving Runge-Kutta method with an optimal CFL coeffiecient to solve the anelastic wave equation. We use a fourth order DRP/opt MacCormack scheme for the spatial discretization, and we approximate the rheological behaviors of the Earth by using the generalized Maxwell body model. With a larger CFL condition number, we find that the computational efficient is significantly improved compared with the traditional fourth-order Runge-Kutta method. Then, we apply the scattering-integral method for calculating travel time and amplitude sensitivity kernels with respect to velocity and attenuation structures. For each source, we carry out one forward simulation and save the time-dependent strain tensor. For each station, we carry out three `backward' simulations for the three components and save the corresponding strain tensors. The sensitivity kernels at each point in the medium are the convolution of the two sets of the strain tensors. Finally, we show several synthetic tests to verify the effectiveness of the strong stability preserving Runge-Kutta method in generating accurate synthetics in full waveform modeling, and in generating accurate strain tensors for calculating sensitivity kernels at regional and global scales.

Sum-Frequency Generation from a Thin Cylindrical Layer

NASA Astrophysics Data System (ADS)

Shamyna, A. A.; Kapshai, V. N.

2018-01-01

In the Rayleigh-Gans-Debye approximation, we have solved the problem of the sum-frequency generation by two plane elliptically polarized electromagnetic waves from the surface of a dielectric particle of a cylindrical shape that is coated by a thin layer possessing nonlinear optical properties. The formulas that describe the sum-frequency field have been presented in the tensor and vector forms for the second-order nonlinear dielectric susceptibility tensor, which was chosen in the general form, containing chiral components. Expressions describing the sum-frequency field from the cylindrical particle ends have been obtained for the case of a nonlinear layer possessing chiral properties. Three-dimensional directivity patterns of the sum-frequency radiation have been analyzed for different combinations of parameters (angles of incidence, degrees of ellipticity, orientations of polarization ellipses, cylindrical particle dimensions). The mathematical properties of the spatial distribution functions of the sum-frequency field, which characterize the symmetry of directivity patterns, have been revealed.

Generation of large-scale magnetic fields, non-Gaussianity, and primordial gravitational waves in inflationary cosmology

NASA Astrophysics Data System (ADS)

Bamba, Kazuharu

2015-02-01

The generation of large-scale magnetic fields in inflationary cosmology is explored, in particular, in a kind of moduli inflation motivated by racetrack inflation in the context of the type IIB string theory. In this model, the conformal invariance of the hypercharge electromagnetic fields is broken thanks to the coupling of both the scalar and pseudoscalar fields to the hypercharge electromagnetic fields. The following three cosmological observable quantities are first evaluated: the current magnetic field strength on the Hubble horizon scale, which is much smaller than the upper limit from the backreaction problem, local non-Gaussianity of the curvature perturbations due to the existence of the massive gauge fields, and the tensor-to-scalar ratio. It is explicitly demonstrated that the resultant values of local non-Gaussianity and the tensor-to-scalar ratio are consistent with the Planck data.

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA.

PubMed

Wright, Imogen A; Travers, Simon A

2014-07-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search

NASA Technical Reports Server (NTRS)

Wheeler, Ward C.

2003-01-01

A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

Anisotropic Developments for Homogeneous Shear Flows

NASA Technical Reports Server (NTRS)

Cambon, Claude; Rubinstein, Robert

2006-01-01

The general decomposition of the spectral correlation tensor R(sub ij)(k) by Cambon et al. (J. Fluid Mech., 202, 295; J. Fluid Mech., 337, 303) into directional and polarization components is applied to the representation of R(sub ij)(k) by spherically averaged quantities. The decomposition splits the deviatoric part H(sub ij)(k) of the spherical average of R(sub ij)(k) into directional and polarization components H(sub ij)(sup e)(k) and H(sub ij)(sup z)(k). A self-consistent representation of the spectral tensor in the limit of weak anisotropy is constructed in terms of these spherically averaged quantities. The directional polarization components must be treated independently: models that attempt the same representation of the spectral tensor using the spherical average H(sub ij)(k) alone prove to be inconsistent with Navier-Stokes dynamics. In particular, a spectral tensor consistent with a prescribed Reynolds stress is not unique. The degree of anisotropy permitted by this theory is restricted by realizability requirements. Since these requirements will be less severe in a more accurate theory, a preliminary account is given of how to generalize the formalism of spherical averages to higher expansion of the spectral tensor. Directionality is described by a conventional expansion in spherical harmonics, but polarization requires an expansion in tensorial spherical harmonics generated by irreducible representations of the spatial rotation group SO(exp 3). These expansions are considered in more detail in the special case of axial symmetry.

enoLOGOS: a versatile web tool for energy normalized sequence logos

PubMed Central

Workman, Christopher T.; Yin, Yutong; Corcoran, David L.; Ideker, Trey; Stormo, Gary D.; Benos, Panayiotis V.

2005-01-01

enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a set of aligned sequences. Each position of the alignment is represented by a column of stacked symbols with its total height reflecting the information content in this position. Currently, the available web servers are able to create logo images from a set of aligned sequences, but none of them generates weighted sequence logos directly from energy measurements or other sources. With the advent of high-throughput technologies for estimating the contact energy of different DNA sequences, tools that can create logos directly from binding affinity data are useful to researchers. enoLOGOS generates sequence logos from a variety of input data, including energy measurements, probability matrices, alignment matrices, count matrices and aligned sequences. Furthermore, enoLOGOS can represent the mutual information of different positions of the consensus sequence, a unique feature of this tool. Another web interface for our software, C2H2-enoLOGOS, generates logos for the DNA-binding preferences of the C2H2 zinc-finger transcription factor family members. enoLOGOS and C2H2-enoLOGOS are accessible over the web at . PMID:15980495

On the Landau-de Gennes Elastic Energy of a Q-Tensor Model for Soft Biaxial Nematics

NASA Astrophysics Data System (ADS)

Mucci, Domenico; Nicolodi, Lorenzo

2017-12-01

In the Landau-de Gennes theory of liquid crystals, the propensities for alignments of molecules are represented at each point of the fluid by an element Q of the vector space S_0 of 3× 3 real symmetric traceless matrices, or Q-tensors. According to Longa and Trebin (1989), a biaxial nematic system is called soft biaxial if the tensor order parameter Q satisfies the constraint tr(Q^2) = {const}. After the introduction of a Q-tensor model for soft biaxial nematic systems and the description of its geometric structure, we address the question of coercivity for the most common four-elastic-constant form of the Landau-de Gennes elastic free-energy (Iyer et al. 2015) in this model. For a soft biaxial nematic system, the tensor field Q takes values in a four-dimensional sphere S^4_ρ of radius ρ ≤ √{2/3} in the five-dimensional space S_0 with inner product < Q, P > = tr(QP). The rotation group it{SO}(3) acts orthogonally on S_0 by conjugation and hence induces an action on S^4_ρ \\subset {S}_0. This action has generic orbits of codimension one that are diffeomorphic to an eightfold quotient S^3/H of the unit three-sphere S^3, where H={± 1, ± i, ± j, ± k} is the quaternion group, and has two degenerate orbits of codimension two that are diffeomorphic to the projective plane RP^2. Each generic orbit can be interpreted as the order parameter space of a constrained biaxial nematic system and each singular orbit as the order parameter space of a constrained uniaxial nematic system. It turns out that S^4_ρ is a cohomogeneity one manifold, i.e., a manifold with a group action whose orbit space is one-dimensional. Another important geometric feature of the model is that the set Σ _ρ of diagonal Q-tensors of fixed norm ρ is a (geodesic) great circle in S^4_ρ which meets every orbit of S^4_ρ orthogonally and is then a section for S^4_ρ in the sense of the general theory of canonical forms. We compute necessary and sufficient coercivity conditions for the elastic energy by exploiting the it{SO}(3)-invariance of the elastic energy (frame-indifference), the existence of the section Σ _ρ for S^4_ρ , and the geometry of the model, which allow us to reduce to a suitable invariant problem on (an arc of) Σ _ρ . Our approach can ultimately be seen as an application of the general method of reduction of variables, or cohomogeneity method.

n-D shape/texture optimal synthetic description and modeling by GEOGINE

NASA Astrophysics Data System (ADS)

Fiorini, Rodolfo A.; Dacquino, Gianfranco F.

2004-12-01

GEOGINE(GEOmetrical enGINE), a state-of-the-art OMG (Ontological Model Generator) based on n-D Tensor Invariants for multidimensional shape/texture optimal synthetic description and learning, is presented. Usually elementary geometric shape robust characterization, subjected to geometric transformation, on a rigorous mathematical level is a key problem in many computer applications in different interest areas. The past four decades have seen solutions almost based on the use of n-Dimensional Moment and Fourier descriptor invariants. The present paper introduces a new approach for automatic model generation based on n -Dimensional Tensor Invariants as formal dictionary. An ontological model is the kernel used for specifying ontologies so that how close an ontology can be from the real world depends on the possibilities offered by the ontological model. By this approach even chromatic information content can be easily and reliably decoupled from target geometric information and computed into robus colour shape parameter attributes. Main GEOGINEoperational advantages over previous approaches are: 1) Automated Model Generation, 2) Invariant Minimal Complete Set for computational efficiency, 3) Arbitrary Model Precision for robust object description.

Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

PubMed Central

Kosugi, Shunichi; Natsume, Satoshi; Yoshida, Kentaro; MacLean, Daniel; Cano, Liliana; Kamoun, Sophien; Terauchi, Ryohei

2013-01-01

Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in ‘targeted’ alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/. PMID:24116042

Homothetic matter collineations of LRS Bianchi type I spacetimes

NASA Astrophysics Data System (ADS)

Hussain, Tahir; Rahim, Waqas

2017-12-01

A complete classification of locally rotationally symmetric (LRS) Bianchi type I spacetimes via homothetic matter collineations (HMCs) is presented. For non-degenerate energy-momentum tensor, a general form of the vector field generating HMCs is found, subject to some integrability conditions. Solving the integrability conditions in different cases, it is found that the LRS Bianchi type I spacetimes admit 6-, 7-, 8-, 10- or 11-dimensional Lie algebra of HMCs. When the energy-momentum tensor is degenerate, two cases give 6 and 11 HMCs, while the remaining cases produce infinite number of HMCs. Some LRS Bianchi type I metrics are provided admitting HMCs.

Nonsingular, big-bounce cosmology from spinor-torsion coupling

NASA Astrophysics Data System (ADS)

Popławski, Nikodem

2012-05-01

The Einstein-Cartan-Sciama-Kibble theory of gravity removes the constraint of general relativity that the affine connection be symmetric by regarding its antisymmetric part, the torsion tensor, as a dynamical variable. The minimal coupling between the torsion tensor and Dirac spinors generates a spin-spin interaction which is significant in fermionic matter at extremely high densities. We show that such an interaction averts the unphysical big-bang singularity, replacing it with a cusp-like bounce at a finite minimum scale factor, before which the Universe was contracting. This scenario also explains why the present Universe at largest scales appears spatially flat, homogeneous and isotropic.

Clockwork inflation

NASA Astrophysics Data System (ADS)

Kehagias, Alex; Riotto, Antonio

2017-04-01

We investigate the recently proposed clockwork mechanism delivering light degrees of freedom with suppressed interactions and show, with various examples, that it can be efficiently implemented in inflationary scenarios to generate flat inflaton potentials and small density perturbations without fine-tunings. We also study the clockwork graviton in de Sitter and, interestingly, we find that the corresponding clockwork charge is site-dependent. As a consequence, the amount of tensor modes is generically suppressed with respect to the standard cases where the clockwork set-up is not adopted. This point can be made a virtue in resurrecting models of inflation which were supposed to be ruled out because of the excessive amount of tensor modes from inflation.

Killing spinors and related symmetries in six dimensions

NASA Astrophysics Data System (ADS)

Batista, Carlos

2016-03-01

Benefiting from the index spinorial formalism, the Killing spinor equation is integrated in six-dimensional spacetimes. The integrability conditions for the existence of a Killing spinor are worked out and the Killing spinors are classified into two algebraic types; in the first type the scalar curvature of the spacetime must be negative, while in the second type the spacetime must be an Einstein manifold. In addition, the equations that define Killing-Yano (KY) and closed conformal Killing-Yano (CCKY) tensors are expressed in the index notation and, as consequence, all nonvanishing KY and CCKY tensors that can be generated from a Killing spinor are made explicit.

Face Hallucination with Linear Regression Model in Semi-Orthogonal Multilinear PCA Method

NASA Astrophysics Data System (ADS)

Asavaskulkiet, Krissada

2018-04-01

In this paper, we propose a new face hallucination technique, face images reconstruction in HSV color space with a semi-orthogonal multilinear principal component analysis method. This novel hallucination technique can perform directly from tensors via tensor-to-vector projection by imposing the orthogonality constraint in only one mode. In our experiments, we use facial images from FERET database to test our hallucination approach which is demonstrated by extensive experiments with high-quality hallucinated color faces. The experimental results assure clearly demonstrated that we can generate photorealistic color face images by using the SO-MPCA subspace with a linear regression model.

Apparatus for monitoring X-ray beam alignment

DOEpatents

Steinmeyer, Peter A.

1991-10-08

A self-contained, hand-held apparatus is provided for minitoring alignment of an X-ray beam in an instrument employing an X-ray source. The apparatus includes a transducer assembly containing a photoresistor for providing a range of electrical signals responsive to a range of X-ray beam intensities from the X-ray beam being aligned. A circuit, powered by a 7.5 VDC power supply and containing an audio frequency pulse generator whose frequency varies with the resistance of the photoresistor, is provided for generating a range of audible sounds. A portion of the audible range corresponds to low X-ray beam intensity. Another portion of the audible range corresponds to high X-ray beam intensity. The transducer assembly may include an a photoresistor, a thin layer of X-ray fluorescent material, and a filter layer transparent to X-rays but opaque to visible light. X-rays from the beam undergoing alignment penetrate the filter layer and excite the layer of fluorescent material. The light emitted from the fluorescent material alters the resistance of the photoresistor which is in the electrical circuit including the audio pulse generator and a speaker. In employing the apparatus, the X-ray beam is aligned to a complete alignment by adjusting the X-ray beam to produce an audible sound of the maximum frequency.

Apparatus for monitoring X-ray beam alignment

DOEpatents

Steinmeyer, P.A.

1991-10-08

A self-contained, hand-held apparatus is provided for monitoring alignment of an X-ray beam in an instrument employing an X-ray source. The apparatus includes a transducer assembly containing a photoresistor for providing a range of electrical signals responsive to a range of X-ray beam intensities from the X-ray beam being aligned. A circuit, powered by a 7.5 VDC power supply and containing an audio frequency pulse generator whose frequency varies with the resistance of the photoresistor, is provided for generating a range of audible sounds. A portion of the audible range corresponds to low X-ray beam intensity. Another portion of the audible range corresponds to high X-ray beam intensity. The transducer assembly may include an a photoresistor, a thin layer of X-ray fluorescent material, and a filter layer transparent to X-rays but opaque to visible light. X-rays from the beam undergoing alignment penetrate the filter layer and excite the layer of fluorescent material. The light emitted from the fluorescent material alters the resistance of the photoresistor which is in the electrical circuit including the audio pulse generator and a speaker. In employing the apparatus, the X-ray beam is aligned to a complete alignment by adjusting the X-ray beam to produce an audible sound of the maximum frequency. 2 figures.

Combining cell sheet technology and electrospun scaffolding for engineered tubular, aligned, and contractile blood vessels.

PubMed

Rayatpisheh, Shahrzad; Heath, Daniel E; Shakouri, Amir; Rujitanaroj, Pim-On; Chew, Sing Yian; Chan-Park, Mary B

2014-03-01

Herein we combine cell sheet technology and electrospun scaffolding to rapidly generate circumferentially aligned tubular constructs of human aortic smooth muscles cells with contractile gene expression for use as tissue engineered blood vessel media. Smooth muscle cells cultured on micropatterned and N-isopropylacrylamide-grafted (pNIPAm) polydimethylsiloxane (PDMS), a small portion of which was covered by aligned electrospun scaffolding, resulted in a single sheet of unidirectionally aligned cells. Upon cooling to room temperature, the scaffold, its adherent cells, and the remaining cell sheet detached and were collected on a mandrel to generating tubular constructs with circumferentially aligned smooth muscle cells which possess contractile gene expression and a single layer of electrospun scaffold as an analogue to a small diameter blood vessel's internal elastic lamina (IEL). This method improves cell sheet handling, results in rapid circumferential alignment of smooth muscle cells which immediately express contractile genes, and introduction of an analogue to small diameter blood vessel IEL. Copyright © 2013 Elsevier Ltd. All rights reserved.

Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS.

PubMed

Warris, Sven; Yalcin, Feyruz; Jackson, Katherine J L; Nap, Jan Peter

2015-01-01

To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis. With the Parallel SW Alignment Software (PaSWAS) it is possible (a) to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs) to perform high-speed sequence alignments, and (b) retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1) tag recovery in next generation sequence data and (2) isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation.

Velocity model calibration as a tool to improve regional wave moment tensors: Application to the Basin and Range Province

NASA Astrophysics Data System (ADS)

Ichinose, G. A.

2006-12-01

Many scientific issues for the Basin and Range Province (BRP) remain unsettled including structural evolution, strain rates, slip partitioning and earthquake source physics. A catalog of earthquake source parameters including locations and moment tensors is the basis for tectonic and geophysical study. New instrumentation from the Advance National Seismic System, EarthScope Plate Boundary Observatory, Bigfoot and US-Array brings the opportunity for high quality research; therefore, a catalog is an underlying foundation for examining the BRP. We are continuing to generate a moment tensor catalog for the BRP (Mw<3.5) using long-period regional waves spanning back to 1990. Iterative waveform inversion method (e.g., Nolet et al., 1986, Randell, 1994) is used to calibrate the BRP velocity and density structure using two northern and southern BRP earthquakes. The calibrated models generate realistic synthetics for (f<0.5Hz) with ~50-80% variance reduction. We averaged all path specific models to construct a 1-D BRP community background model. The crust is relatively simple between 5-20km (~6.12km/s) and there is a strong velocity gradient in the upper 5- km. There are lower velocities in the upper crust but higher velocities in the mid-crust for the Sierra Nevada paths relative to BRP. There is also a lower crust high-velocity anomaly near Battle Mountain and Elko that is faster by ~5% and may indicate a wider area of under-plating by basaltic magmas. There are significant low velocity zones in the upper and mid crust mainly across the Walker Lane Belt that may indicate the presence of fluids. We are continuing to work on assessing the performance of these newly calibrated models in improving the estimation of moment tensors down to lower magnitudes and mapping out holes in the seismic network which can be filled to improve moment tensor catalog. We also are looking at how these models work at locating earthquakes and comparing synthetics with those computed from models constrained from different data including refraction, surface wave dispersion, and travel-time tomography.

Moment tensor inversion of recent local moderate sized Van Earthquakes: seismicity and active tectonics of the Van region : Eastern Turkey

NASA Astrophysics Data System (ADS)

Kalafat, D.; Suvarikli, M.; Ogutcu, Z.; Kekovali, K.; Ocal, M. F.; Gunes, Y.; Pinar, A.

2013-12-01

The study area of the present research, the Van Region is located at the norththern end of the collision zone between the Anatolia and Arabian plates. Therefore, the southeast border of the Anatolian plate collides with the Arabian plate along the Bitlis Suture Zone. This zone is formed by collision of Arabian and in large scale Eurasian plates at mid-Miocen age. This type of thrust generation as a result of compressional regime extends east-west. The largest recorded earthquakes have all taken place along Southern Turkey (e.g. Lice, 1971; Varto, 1966; Caldiran, 1976). On the 23th of October 2011, an earthquake shook the Van Lake, Eastern Turkey, following a seismic sequence of more than three months in an unprecedented episode for this region characterized by null or low seismicity. The October 23, 2011 Van-Ercis Earthquake (Mw=7.1) was the most devastating resulting in loss of life and destruction. In order to study the aftershocks' activity of this main event, we installed and kept a seismic network of 10 broad-band (BB) stations in the area for an interval of nearly fifteen months. We characterized the seismogenic structure of the zone by calculating a minimum 1-D local velocity model and obtaining precise hypocentre locations. We also calculated fault plane solutions for more than 200 moderate sized earthquakes based on first motion polarities and commonly Moment Tensor Inversion Methods. The seismogenic zone would be localized at aproximately 10 km depth. Generally, the distribution of the important moderate earthquakes and the aftershock distribution shows that the E-W and NE-SW oriented fault segments cause the earthquake activities. Aftershock events are located along the eastern border of Lake Van and mainly between 5 and 10 km depth and disposed in two alignments: a ~E-W-trending alignment that matches with the trace of the Van Trust fault Zone and a NE-trending which could correspond to an structure not previously seen. Selected focal mechanisms show a strong trust faulting which coincides with the nature of the Van fault. We were currently analysing an archive of over 5000 local events recorded by the KOERI seismic network of over 20 broadband stations between 2010 and 2013 in the whole Van Region. The Van Earthquake initiated and caused an increase in seismic activity of the region. Van Earthquake and its important aftershocks fault mechanism solutions show that the region is under compression and reverse faulting is a result of this regime which is effective on the active compressional tectonics of the region. This study was supported by Bogazici University Research Projects Commission under SRP/BAP project No. 6040.

Three-dimensional magnetotelluric inversion in practice—the electrical conductivity structure of the San Andreas Fault in Central California

NASA Astrophysics Data System (ADS)

Tietze, Kristina; Ritter, Oliver

2013-10-01

3-D inversion techniques have become a widely used tool in magnetotelluric (MT) data interpretation. However, with real data sets, many of the controlling factors for the outcome of 3-D inversion are little explored, such as alignment of the coordinate system, handling and influence of data errors and model regularization. Here we present 3-D inversion results of 169 MT sites from the central San Andreas Fault in California. Previous extensive 2-D inversion and 3-D forward modelling of the data set revealed significant along-strike variation of the electrical conductivity structure. 3-D inversion can recover these features but only if the inversion parameters are tuned in accordance with the particularities of the data set. Based on synthetic 3-D data we explore the model space and test the impacts of a wide range of inversion settings. The tests showed that the recovery of a pronounced regional 2-D structure in inversion of the complete impedance tensor depends on the coordinate system. As interdependencies between data components are not considered in standard 3-D MT inversion codes, 2-D subsurface structures can vanish if data are not aligned with the regional strike direction. A priori models and data weighting, that is, how strongly individual components of the impedance tensor and/or vertical magnetic field transfer functions dominate the solution, are crucial controls for the outcome of 3-D inversion. If deviations from a prior model are heavily penalized, regularization is prone to result in erroneous and misleading 3-D inversion models, particularly in the presence of strong conductivity contrasts. A `good' overall rms misfit is often meaningless or misleading as a huge range of 3-D inversion results exist, all with similarly `acceptable' misfits but producing significantly differing images of the conductivity structures. Reliable and meaningful 3-D inversion models can only be recovered if data misfit is assessed systematically in the frequency-space domain.

Compromise and Conciliation: Frame Alignment Theory in the Argument Class.

ERIC Educational Resources Information Center

Vandenberg, Peter

"Frame alignment"--the conscious process of creating correspondence between one's own "frame" (ways of making meaning out circumstances) and someone else's--is a necessary condition for participation in organized social movements. Frame alignment processes may offer a generative and useful alternative to the reductive…

Limits on tensor coupling from neutron β decay

NASA Astrophysics Data System (ADS)

Pattie, R. W., Jr.; Hickerson, K. P.; Young, A. R.

2013-10-01

Limits on the tensor couplings generating a Fierz interference term b in mixed Gamow-Teller Fermi decays can be derived by combining data from measurements of angular correlation parameters in neutron decay, the neutron lifetime, and GV=GFVud as extracted from measurements of the Ft values from the 0+→0+ superallowed decay data set. These limits are derived by comparing the neutron β-decay rate as predicted in the standard model with the measured decay rate while allowing for the existence of beyond the standard model (BSM) couplings. We analyze limits derived from the electron-neutrino asymmetry a, or the beta asymmetry A, finding that the most stringent limits for CT/CA under the assumption of no right-handed neutrinos is -0.0026

The Speech multi features fusion perceptual hash algorithm based on tensor decomposition

NASA Astrophysics Data System (ADS)

Huang, Y. B.; Fan, M. H.; Zhang, Q. Y.

2018-03-01

With constant progress in modern speech communication technologies, the speech data is prone to be attacked by the noise or maliciously tampered. In order to make the speech perception hash algorithm has strong robustness and high efficiency, this paper put forward a speech perception hash algorithm based on the tensor decomposition and multi features is proposed. This algorithm analyses the speech perception feature acquires each speech component wavelet packet decomposition. LPCC, LSP and ISP feature of each speech component are extracted to constitute the speech feature tensor. Speech authentication is done by generating the hash values through feature matrix quantification which use mid-value. Experimental results showing that the proposed algorithm is robust for content to maintain operations compared with similar algorithms. It is able to resist the attack of the common background noise. Also, the algorithm is highly efficiency in terms of arithmetic, and is able to meet the real-time requirements of speech communication and complete the speech authentication quickly.

Dark neutrino interactions make gravitational waves blue

NASA Astrophysics Data System (ADS)

Ghosh, Subhajit; Khatri, Rishi; Roy, Tuhin S.

2018-03-01

New interactions of neutrinos can stop them from free-streaming in the early Universe even after the weak decoupling epoch. This results in the enhancement of the primordial gravitational wave amplitude on small scales compared to the standard Λ CDM prediction. In this paper, we calculate the effect of dark matter neutrino interactions in CMB tensor B -modes spectrum. We show that the effect of new neutrino interactions generates a scale- or ℓ-dependent imprint in the CMB B -modes power spectrum at ℓ≳100 . In the event that primordial B -modes are detected by future experiments, a departure from scale invariance, with a blue spectrum, may not necessarily mean failure of simple inflationary models but instead may be a sign of nonstandard interactions of relativistic particles. New interactions of neutrinos also induce a phase shift in the CMB B -mode power spectrum which cannot be mimicked by simple modifications of the primordial tensor power spectrum. There is rich information hidden in the CMB B -modes spectrum beyond just the tensor-to-scalar ratio.

Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

PubMed Central

Schmitz, Christophe; Vernon, Robert; Otting, Gottfried; Baker, David; Huber, Thomas

2013-01-01

Paramagnetic metal ions generate pseudocontact shifts (PCSs) in nuclear magnetic resonance spectra that are manifested as easily measurable changes in chemical shifts. Metals can be incorporated into proteins through metal binding tags, and PCS data constitute powerful long-range restraints on the positions of nuclear spins relative to the coordinate system of the magnetic susceptibility anisotropy tensor (Δχ-tensor) of the metal ion. We show that three-dimensional structures of proteins can reliably be determined using PCS data from a single metal binding site combined with backbone chemical shifts. The program PCS-ROSETTA automatically determines the Δχ-tensor and metal position from the PCS data during the structure calculations, without any prior knowledge of the protein structure. The program can determine structures accurately for proteins of up to 150 residues, offering a powerful new approach to protein structure determination that relies exclusively on readily measurable backbone chemical shifts and easily discriminates between correctly and incorrectly folded conformations. PMID:22285518

Higher-order stochastic differential equations and the positive Wigner function

NASA Astrophysics Data System (ADS)

Drummond, P. D.

2017-12-01

General higher-order stochastic processes that correspond to any diffusion-type tensor of higher than second order are obtained. The relationship of multivariate higher-order stochastic differential equations with tensor decomposition theory and tensor rank is explained. Techniques for generating the requisite complex higher-order noise are proved to exist either using polar coordinates and γ distributions, or from products of Gaussian variates. This method is shown to allow the calculation of the dynamics of the Wigner function, after it is extended to a complex phase space. The results are illustrated physically through dynamical calculations of the positive Wigner distribution for three-mode parametric downconversion, widely used in quantum optics. The approach eliminates paradoxes arising from truncation of the higher derivative terms in Wigner function time evolution. Anomalous results of negative populations and vacuum scattering found in truncated Wigner quantum simulations in quantum optics and Bose-Einstein condensate dynamics are shown not to occur with this type of stochastic theory.

How Artificial Should the Treatment of a Plasma's Viscosity Be?

NASA Astrophysics Data System (ADS)

Whitney, K. G.; Velikovich, A. L.; Thornhill, J. W.; Davis, J.

1999-11-01

Electron viscosity dominates over ion viscosity and is important in describing the generation of shock fronts in highly ionizable plasmas. The sizes of shock front jumps in electron and ion temperature are determined from the magnitudes of the heat flow vector and pressure tensor, which, in turn, acquire non-negligible nonlinear contributions from the temperature and density gradients when these gradients are large. Thus, a consistent treatment of steep gradient formation in plasmas must come from investigations that include the effects of these nonlinear contributions to heat and momentum transport. Coefficients for each of five nonlinear contributions to the pressure tensor for an (r,z) Z-pinch geometry are presented and discussed in this talk. Hydrodynamic code calculations generally are not designed to provide a testbed for directly evaluating the kinetic energy dissipation that occurs at shock fronts; therefore, the strength of these nonlinear pressure tensor terms will be estimated by post-processing a Z-pinch hydrodynamics calculation and a steady-state planar shock wave calculation.

Performance of tensor decomposition-based modal identification under nonstationary vibration

NASA Astrophysics Data System (ADS)

Friesen, P.; Sadhu, A.

2017-03-01

Health monitoring of civil engineering structures is of paramount importance when they are subjected to natural hazards or extreme climatic events like earthquake, strong wind gusts or man-made excitations. Most of the traditional modal identification methods are reliant on stationarity assumption of the vibration response and posed difficulty while analyzing nonstationary vibration (e.g. earthquake or human-induced vibration). Recently tensor decomposition based methods are emerged as powerful and yet generic blind (i.e. without requiring a knowledge of input characteristics) signal decomposition tool for structural modal identification. In this paper, a tensor decomposition based system identification method is further explored to estimate modal parameters using nonstationary vibration generated due to either earthquake or pedestrian induced excitation in a structure. The effects of lag parameters and sensor densities on tensor decomposition are studied with respect to the extent of nonstationarity of the responses characterized by the stationary duration and peak ground acceleration of the earthquake. A suite of more than 1400 earthquakes is used to investigate the performance of the proposed method under a wide variety of ground motions utilizing both complete and partial measurements of a high-rise building model. Apart from the earthquake, human-induced nonstationary vibration of a real-life pedestrian bridge is also used to verify the accuracy of the proposed method.

Tensor integrand reduction via Laurent expansion

NASA Astrophysics Data System (ADS)

Hirschi, Valentin; Peraro, Tiziano

2016-06-01

We introduce a new method for the application of one-loop integrand reduction via the Laurent expansion algorithm, as implemented in the public C ++ library N inja. We show how the coefficients of the Laurent expansion can be computed by suitable contractions of the loop numerator tensor with cut-dependent projectors, making it possible to interface N inja to any one-loop matrix element generator that can provide the components of this tensor. We implemented this technique in the N inja library and interfaced it to M adL oop, which is part of the public M adG raph5_ aMC@NLO framework. We performed a detailed performance study, comparing against other public reduction tools, namely C utT ools, S amurai, IREGI, PJF ry++ and G olem95. We find that N inja out-performs traditional integrand reduction in both speed and numerical stability, the latter being on par with that of the tensor integral reduction tool Golem95 which is however more limited and slower than N inja. We considered many benchmark multi-scale processes of increasing complexity, involving QCD and electro-weak corrections as well as effective non-renormalizable couplings, showing that N inja's performance scales well with both the rank and multiplicity of the considered process.

A generalized electro-elastic theory of polymer networks

NASA Astrophysics Data System (ADS)

Cohen, Noy

2018-01-01

A rigorous multi-scale analysis of the electromechanical coupling in dielectric polymers is conducted. The body couples stemming from a misalignment between the electric field and the electric-dipole density vector are studied and the conservation laws for polymer networks are derived. Using variational principles, expressions for the polarization and the stress are determined. Interestingly, it is found that the stress tensor resulting from coupled loadings in which the electric field is misaligned with the principal stretch directions is not symmetric and the asymmetry arises from the body couples. Next, the electro-mechanical response of a chain is analyzed. The deformations of the individual polymer chains are related to the macroscopic deformation via two highly non-linear constraints - the first pertaining to the compatibility of the local deformations with the imposed macroscopic one and the second stems from the symmetric part of the stress at equilibrium. In accord with the proposed framework, an amended three-chains model is introduced. The predictions of this model are found to be in excellent agreement with experimental findings. Lastly, the behavior of a polymer subjected to a simple shear and an electric field is studied. The offset between the electric field and the principal directions gives rise to body couples, a polarization that is not aligned with the electric field, and an asymmetric stress tensor.

Attitude Ground System (AGS) for the Magnetospheric Multi-Scale (MMS) Mission

NASA Technical Reports Server (NTRS)

Raymond, Juan C.; Sedlak, Joseph E.; Vint, Babak

2015-01-01

MMS Overview Recall from Conrads presentation earlier today MMS launch: March 13, 2015 on an Atlas V from Space Launch Complex 40, Cape Canaveral, Florida MMS Observatory Separation: five minute intervals spinning at 3 rpm approximately 1.5 hours after launch MMS Science Goals: study magnetospheric plasma physics and understand the processes that cause power grids, communication disruptions and Aurora formation Mission: 4 identical spacecraft in tetrahedral formation with variable size1.2 x 12 RE in Phase 1, with apogee on dayside to observe bow shock1.2 x 25 RE in Phase 2, with apogee on night side to observe magneto tail Challenges Tight attitude control box, orbit and formation maintenance requirements Maneuvers on thrusters every two weeks Delta-H Spin axis direction and spin rate maintenance Delta-V Orbit and Formation maintenance Mission phase transitions AGS support Smart targeting prediction of Spin-Axis attitude in the presence of environmental torques to stay within the science attitude Determination of the spacecraft attitude and spin rate (sensitive to knowledge of inertia tensor)Calibrations to improve attitude determination results and improve orbit maneuvers Mass properties (Center of Mass, and inertia tensor for nutation and coning) Accelerometer bias (sensitive to the accuracy of the rate estimates) Sensor alignments.

Impact of heat release on strain rate field in turbulent premixed Bunsen flames

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

Coriton, Bruno Rene Leon; Frank, Jonathan H.

2016-08-10

The effects of combustion on the strain rate field are investigated in turbulent premixed CH 4/air Bunsen flames using simultaneous tomographic PIV and OH LIF measurements. Tomographic PIV provides three-dimensional velocity measurements, from which the complete strain rate tensor is determined. The OH LIF measurements are used to determine the position of the flame surface and the flame-normal orientation within the imaging plane. This combination of diagnostic techniques enables quantification of divergence as well as flame-normal and tangential strain rates, which are otherwise biased using only planar measurements. Measurements are compared in three lean-to-stoichiometric flames that have different amounts ofmore » heat release and Damköhler numbers greater than unity. The effects of heat release on the principal strain rates and their alignment relative to the local flame normal are analyzed. The extensive strain rate preferentially aligns with the flame normal in the reaction zone, which has been indicated by previous studies. The strength of this alignment increases with increasing heat release and, as a result, the flame-normal strain rate becomes highly extensive. These effects are associated with the gas expansion normal to the flame surface, which is largest for the stoichiometric flame. In the preheat zone, the compressive strain rate has a tendency to align with the flame normal. Away from the flame front, the flame – strain rate alignment is arbitrary in both the reactants and products. The flame-tangential strain rate is on average positive across the flame front, and therefore the turbulent strain rate field contributes to the enhancement of scalar gradients as in passive scalar turbulence. As a result, increases in heat release result in larger positive values of the divergence as well as flame-normal and tangential strain rates, the tangential strain rate has a weaker dependence on heat release than the flame-normal strain rate and the divergence.« less

Homogenized moment tensor and the effect of near-field heterogeneities on nonisotropic radiation in nuclear explosion

NASA Astrophysics Data System (ADS)

Burgos, Gaël.; Capdeville, Yann; Guillot, Laurent

2016-06-01

We investigate the effect of small-scale heterogeneities close to a seismic explosive source, at intermediate periods (20-50 s), with an emphasis on the resulting nonisotropic far-field radiation. First, using a direct numerical approach, we show that small-scale elastic heterogeneities located in the near-field of an explosive source, generate unexpected phases (i.e., long period S waves). We then demonstrate that the nonperiodic homogenization theory applied to 2-D and 3-D elastic models, with various pattern of small-scale heterogeneities near the source, leads to accurate waveforms at a reduced computational cost compared to direct modeling. Further, it gives an interpretation of how nearby small-scale features interact with the source at low frequencies, through an explicit correction to the seismic moment tensor. In 2-D simulations, we find a deviatoric contribution to the moment tensor, as high as 21% for near-source heterogeneities showing a 25% contrast of elastic values (relative to a homogeneous background medium). In 3-D this nonisotropic contribution reaches 27%. Second, we analyze intermediate-periods regional seismic waveforms associated with some underground nuclear explosions conducted at the Nevada National Security Site and invert for the full moment tensor, in order to quantify the relative contribution of the isotropic and deviatoric components of the tensor. The average value of the deviatoric part is about 35%. We conclude that the interactions between an explosive source and small-scale local heterogeneities of moderate amplitude may lead to a deviatoric contribution to the seismic moment, close to what is observed using regional data from nuclear test explosions.

Introduction to Vector Field Visualization

NASA Technical Reports Server (NTRS)

Kao, David; Shen, Han-Wei

2010-01-01

Vector field visualization techniques are essential to help us understand the complex dynamics of flow fields. These can be found in a wide range of applications such as study of flows around an aircraft, the blood flow in our heart chambers, ocean circulation models, and severe weather predictions. The vector fields from these various applications can be visually depicted using a number of techniques such as particle traces and advecting textures. In this tutorial, we present several fundamental algorithms in flow visualization including particle integration, particle tracking in time-dependent flows, and seeding strategies. For flows near surfaces, a wide variety of synthetic texture-based algorithms have been developed to depict near-body flow features. The most common approach is based on the Line Integral Convolution (LIC) algorithm. There also exist extensions of LIC to support more flexible texture generations for 3D flow data. This tutorial reviews these algorithms. Tensor fields are found in several real-world applications and also require the aid of visualization to help users understand their data sets. Examples where one can find tensor fields include mechanics to see how material respond to external forces, civil engineering and geomechanics of roads and bridges, and the study of neural pathway via diffusion tensor imaging. This tutorial will provide an overview of the different tensor field visualization techniques, discuss basic tensor decompositions, and go into detail on glyph based methods, deformation based methods, and streamline based methods. Practical examples will be used when presenting the methods; and applications from some case studies will be used as part of the motivation.

The structure and Gel'fand patterns inherent in the Heisenberg supergenerator algebra of dual Liouville-space ||kq{K-tilde.}(k1 - kn)[lambda- tilde],scriptn>> tensors and the Cayley algebra of scalar invariants over a (k1 - kn) field

NASA Astrophysics Data System (ADS)

Temme, F. P.

1991-06-01

For many-body spin cluster problems, dual-symmetry recoupled tensors over Liouville space provide suitable bases for a generalized torque formalism using the Sn-adapted density operator in which to discuss NMR and related techniques. The explicit structure of such tensors is considered in the context of the Cayley algebra of scalar invariants over a field, specified by the inner ki rank labels of the Tkq(kl-kn)s. The pertinence of both lexical combinatorial architectures over inner rank sets and SU2 propagative topologies in specifying the structure of dual recoupling tensors is considered in the context of the Sn partitional aspects of spin clusters. The form of Heisenberg superoperator generators whose algebra underlies the Gel'fand pattern algebra of SU(2) and SU(2)×Sn tensor bases over Liouville space is presented together with both the related s-boson algebras and a description of the associated {||2k 0>>} pattern sets of CF29H carrier space under the appropriate symmetry. These concepts are correlated with recent work on SU(2)×Sn induced symmetry hierarchies over Liouville spin space. The pertinence of this theoretical work to an understanding of multiquantum NMR in Liouville space formalisms is stressed in a discussion of the nature of pathways for intracluster J coupling, which also gives a valuable physical insight into the nature of coherence transfer in more general spin-1/2 systems.

Impact of the inherent separation of scales in the Navier-Stokes- alphabeta equations.

PubMed

Kim, Tae-Yeon; Cassiani, Massimo; Albertson, John D; Dolbow, John E; Fried, Eliot; Gurtin, Morton E

2009-04-01

We study the effect of the length scales alpha and beta in the Navier-Stokes- alphabeta equations on the energy spectrum and the alignment between the vorticity and the eigenvectors of the stretching tensor in three-dimensional homogeneous and isotropic turbulent flows in a periodic cubic domain, including the limiting cases of the Navier-Stokes- alpha and Navier-Stokes equations. A significant increase in the accuracy of the energy spectrum at large wave numbers arises for beta

DNAAlignEditor: DNA alignment editor tool

PubMed Central

Sanchez-Villeda, Hector; Schroeder, Steven; Flint-Garcia, Sherry; Guill, Katherine E; Yamasaki, Masanori; McMullen, Michael D

2008-01-01

Background With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naïve programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor. Results We have generated a nucleotide sequence alignment editor (DNAAlignEditor) that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected. Conclusion We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism. PMID:18366684

Distance-preserving rigidity penalty on deformable image registration of multiple skeletal components in the neck

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

Kim, Jihun, E-mail: jihun@umich.edu; Saitou, Kazuhiro; Matuszak, Martha M.

Purpose: This study aims at developing and testing a novel rigidity penalty suitable for the deformable registration of tightly located skeletal components in the head and neck from planning computed tomography (CT) and daily cone-beam CT (CBCT) scans of patients undergoing radiotherapy. Methods: The proposed rigidity penalty is designed to preserve intervoxel distances within each bony structure. This penalty was tested in the intensity-based B-spline deformable registration of five cervical vertebral bodies (C1–C5). The displacement vector fields (DVFs) from the registrations were compared to the DVFs generated by using rigid body motions of the cervical vertebrae, measured by the surfacemore » registration of vertebrae delineated on CT and CBCT images. Twenty five pairs of planning CT (reference) and treatment CBCTs (target) from five patients were aligned without and with the penalty. An existing penalty based on the orthonormality of the deformation gradient tensor was also tested and the effects of the penalties compared. Results: The mean magnitude of the maximum registration error with the proposed distance-preserving penalty was (0.86, 1.12, 1.33) mm compared to (2.11, 2.49, 2.46) without penalty and (1.53, 1.64, 1.64) with the existing orthonormality-based penalty. The improvement in the accuracy of the deformable image registration was also verified by comparing the Procrustes distance between the DVFs. With the proposed penalty, the average distance was 0.11 (σ 0.03 mm) which is smaller than 0.53 (0.1 mm) without penalty and 0.28 (0.04 mm) with the orthonormality-based penalty. Conclusions: The accuracy of aligning multiple bony elements was improved by using the proposed distance-preserving rigidity penalty. The voxel-based statistical analysis of the registration error shows that the proposed penalty improved the integrity of the DVFs within the vertebral bodies.« less

Distance-preserving rigidity penalty on deformable image registration of multiple skeletal components in the neck

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

Kim, Jihun, E-mail: jihun@umich.edu; Saitou, Kazuhiro; Matuszak, Martha M.

2013-12-15

Purpose: This study aims at developing and testing a novel rigidity penalty suitable for the deformable registration of tightly located skeletal components in the head and neck from planning computed tomography (CT) and daily cone-beam CT (CBCT) scans of patients undergoing radiotherapy. Methods: The proposed rigidity penalty is designed to preserve intervoxel distances within each bony structure. This penalty was tested in the intensity-based B-spline deformable registration of five cervical vertebral bodies (C1–C5). The displacement vector fields (DVFs) from the registrations were compared to the DVFs generated by using rigid body motions of the cervical vertebrae, measured by the surfacemore » registration of vertebrae delineated on CT and CBCT images. Twenty five pairs of planning CT (reference) and treatment CBCTs (target) from five patients were aligned without and with the penalty. An existing penalty based on the orthonormality of the deformation gradient tensor was also tested and the effects of the penalties compared. Results: The mean magnitude of the maximum registration error with the proposed distance-preserving penalty was (0.86, 1.12, 1.33) mm compared to (2.11, 2.49, 2.46) without penalty and (1.53, 1.64, 1.64) with the existing orthonormality-based penalty. The improvement in the accuracy of the deformable image registration was also verified by comparing the Procrustes distance between the DVFs. With the proposed penalty, the average distance was 0.11 (σ 0.03 mm) which is smaller than 0.53 (0.1 mm) without penalty and 0.28 (0.04 mm) with the orthonormality-based penalty. Conclusions: The accuracy of aligning multiple bony elements was improved by using the proposed distance-preserving rigidity penalty. The voxel-based statistical analysis of the registration error shows that the proposed penalty improved the integrity of the DVFs within the vertebral bodies.« less

Spin-adapted open-shell random phase approximation and time-dependent density functional theory. I. Theory.

PubMed

Li, Zhendong; Liu, Wenjian

2010-08-14

The spin-adaptation of single-reference quantum chemical methods for excited states of open-shell systems has been nontrivial. The primary reason is that the configuration space, generated by a truncated rank of excitations from only one component of a reference multiplet, is spin-incomplete. Those "missing" configurations are of higher ranks and can, in principle, be recaptured by a particular class of excitation operators. However, the resulting formalisms are then quite involved and there are situations [e.g., time-dependent density functional theory (TD-DFT) under the adiabatic approximation] that prevent one from doing so. To solve this issue, we propose here a tensor-coupling scheme that invokes all the components of a reference multiplet (i.e., a tensor reference) rather than increases the excitation ranks. A minimal spin-adapted n-tuply excited configuration space can readily be constructed by tensor products between the n-tuple tensor excitation operators and the chosen tensor reference. Further combined with the tensor equation-of-motion formalism, very compact expressions for excitation energies can be obtained. As a first application of this general idea, a spin-adapted open-shell random phase approximation is first developed. The so-called "translation rule" is then adopted to formulate a spin-adapted, restricted open-shell Kohn-Sham (ROKS)-based TD-DFT (ROKS-TD-DFT). Here, a particular symmetry structure has to be imposed on the exchange-correlation kernel. While the standard ROKS-TD-DFT can access only excited states due to singlet-coupled single excitations, i.e., only some of the singly excited states of the same spin (S(i)) as the reference, the new scheme can capture all the excited states of spin S(i)-1, S(i), or S(i)+1 due to both singlet- and triplet-coupled single excitations. The actual implementation and computation are very much like the (spin-contaminated) unrestricted Kohn-Sham-based TD-DFT. It is also shown that spin-contaminated spin-flip configuration interaction approaches can easily be spin-adapted via the tensor-coupling scheme.

Vertical decomposition with Genetic Algorithm for Multiple Sequence Alignment

PubMed Central

2011-01-01

Background Many Bioinformatics studies begin with a multiple sequence alignment as the foundation for their research. This is because multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence structure relationships. Results In this paper, we have proposed a Vertical Decomposition with Genetic Algorithm (VDGA) for Multiple Sequence Alignment (MSA). In VDGA, we divide the sequences vertically into two or more subsequences, and then solve them individually using a guide tree approach. Finally, we combine all the subsequences to generate a new multiple sequence alignment. This technique is applied on the solutions of the initial generation and of each child generation within VDGA. We have used two mechanisms to generate an initial population in this research: the first mechanism is to generate guide trees with randomly selected sequences and the second is shuffling the sequences inside such trees. Two different genetic operators have been implemented with VDGA. To test the performance of our algorithm, we have compared it with existing well-known methods, namely PRRP, CLUSTALX, DIALIGN, HMMT, SB_PIMA, ML_PIMA, MULTALIGN, and PILEUP8, and also other methods, based on Genetic Algorithms (GA), such as SAGA, MSA-GA and RBT-GA, by solving a number of benchmark datasets from BAliBase 2.0. Conclusions The experimental results showed that the VDGA with three vertical divisions was the most successful variant for most of the test cases in comparison to other divisions considered with VDGA. The experimental results also confirmed that VDGA outperformed the other methods considered in this research. PMID:21867510

MTpy: A Python toolbox for magnetotellurics

USGS Publications Warehouse

Krieger, Lars; Peacock, Jared R.

2014-01-01

In this paper, we introduce the structure and concept of MTpy  . Additionally, we show some examples from an everyday work-flow of MT data processing: the generation of standard EDI data files from raw electric (E-) and magnetic flux density (B-) field time series as input, the conversion into MiniSEED data format, as well as the generation of a graphical data representation in the form of a Phase Tensor pseudosection.

On hidden symmetries of extremal Kerr-NUT-AdS-dS black holes

NASA Astrophysics Data System (ADS)

Rasmussen, Jørgen

2011-05-01

It is well known that the Kerr-NUT-AdS-dS black hole admits two linearly independent Killing vectors and possesses a hidden symmetry generated by a rank-2 Killing tensor. The near-horizon geometry of an extremal Kerr-NUT-AdS-dS black hole admits four linearly independent Killing vectors, and we show how the hidden symmetry of the black hole itself is carried over by means of a modified Killing-Yano potential which is given explicitly. We demonstrate that the corresponding Killing tensor of the near-horizon geometry is reducible as it can be expressed in terms of the Casimir operators formed by the four Killing vectors.

The Bargmann-Wigner equations in spherical space

NASA Astrophysics Data System (ADS)

McKeon, D. G. C.; Sherry, T. N.

2006-01-01

The Bargmann-Wigner formalism is adapted to spherical surfaces embedded in three to eleven dimensions. This is demonstrated to generate wave equations in spherical space for a variety of antisymmetric tensor fields. Some of these equations are gauge invariant for particular values of the parameters characterizing them. For spheres embedded in three, four, and five dimensions, this gauge invariance can be generalized so as to become non-Abelian. This non-Abelian gauge invariance is shown to be a property of second-order models for two index antisymmetric tensor fields in any number of dimensions. The O(3) model is quantized and the two-point function is shown to vanish at the one-loop order.

Large-scale magnetic fields, non-Gaussianity, and gravitational waves from inflation

NASA Astrophysics Data System (ADS)

Bamba, Kazuharu

2017-12-01

We explore the generation of large-scale magnetic fields in the so-called moduli inflation. The hypercharge electromagnetic fields couple to not only a scalar field but also a pseudoscalar one, so that the conformal invariance of the hypercharge electromagnetic fields can be broken. We explicitly analyze the strength of the magnetic fields on the Hubble horizon scale at the present time, the local non-Gaussianity of the curvature perturbations originating from the massive gauge fields, and the tensor-to-scalar ratio of the density perturbations. As a consequence, we find that the local non-Gaussianity and the tensor-to-scalar ratio are compatible with the recent Planck results.

Corrected High-Frame Rate Anchored Ultrasound with Software Alignment

ERIC Educational Resources Information Center

Miller, Amanda L.; Finch, Kenneth B.

2011-01-01

Purpose: To improve lingual ultrasound imaging with the Corrected High Frame Rate Anchored Ultrasound with Software Alignment (CHAUSA; Miller, 2008) method. Method: A production study of the IsiXhosa alveolar click is presented. Articulatory-to-acoustic alignment is demonstrated using a Tri-Modal 3-ms pulse generator. Images from 2 simultaneous…

Educational Leaders' Doctoral Research That Informed Strategies to Steer Their Organizations towards Cultural Alignment

ERIC Educational Resources Information Center

Taysum, Alison

2016-01-01

This research generates new knowledge about how 24 educational leaders in the USA and England used their doctoral research to build narrative capital to inform strategies to steer their organizations towards cultural alignment. Cultural alignment prevents forms of segregation rooted in nation-states' wider historiography of education segregation…

JVM: Java Visual Mapping tool for next generation sequencing read.

PubMed

Yang, Ye; Liu, Juan

2015-01-01

We developed a program JVM (Java Visual Mapping) for mapping next generation sequencing read to reference sequence. The program is implemented in Java and is designed to deal with millions of short read generated by sequence alignment using the Illumina sequencing technology. It employs seed index strategy and octal encoding operations for sequence alignments. JVM is useful for DNA-Seq, RNA-Seq when dealing with single-end resequencing. JVM is a desktop application, which supports reads capacity from 1 MB to 10 GB.

Clustering of reads with alignment-free measures and quality values.

PubMed

Comin, Matteo; Leoni, Andrea; Schimd, Michele

2015-01-01

The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an important aspect is the reduction of data complexity by collapsing redundant reads in a single cluster to improve the run time, memory requirements, and quality of post-processing steps like assembly and error correction. Several alignment-free measures, based on k-mers counts, have been used to cluster reads. Quality scores produced by NGS platforms are fundamental for various analysis of NGS data like reads mapping and error detection. Moreover future-generation sequencing platforms will produce long reads but with a large number of erroneous bases (up to 15 %). In this scenario it will be fundamental to exploit quality value information within the alignment-free framework. To the best of our knowledge this is the first study that incorporates quality value information and k-mers counts, in the context of alignment-free measures, for the comparison of reads data. Based on this principles, in this paper we present a family of alignment-free measures called D (q) -type. A set of experiments on simulated and real reads data confirms that the new measures are superior to other classical alignment-free statistics, especially when erroneous reads are considered. Also results on de novo assembly and metagenomic reads classification show that the introduction of quality values improves over standard alignment-free measures. These statistics are implemented in a software called QCluster (http://www.dei.unipd.it/~ciompin/main/qcluster.html).

Gravitational waves during inflation from a 5D large-scale repulsive gravity model

NASA Astrophysics Data System (ADS)

Reyes, Luz M.; Moreno, Claudia; Madriz Aguilar, José Edgar; Bellini, Mauricio

2012-10-01

We investigate, in the transverse traceless (TT) gauge, the generation of the relic background of gravitational waves, generated during the early inflationary stage, on the framework of a large-scale repulsive gravity model. We calculate the spectrum of the tensor metric fluctuations of an effective 4D Schwarzschild-de Sitter metric on cosmological scales. This metric is obtained after implementing a planar coordinate transformation on a 5D Ricci-flat metric solution, in the context of a non-compact Kaluza-Klein theory of gravity. We found that the spectrum is nearly scale invariant under certain conditions. One interesting aspect of this model is that it is possible to derive the dynamical field equations for the tensor metric fluctuations, valid not just at cosmological scales, but also at astrophysical scales, from the same theoretical model. The astrophysical and cosmological scales are determined by the gravity-antigravity radius, which is a natural length scale of the model, that indicates when gravity becomes repulsive in nature.

A simple, direct derivation and proof of the validity of the SLLOD equations of motion for generalized homogeneous flows.

PubMed

Daivis, Peter J; Todd, B D

2006-05-21

We present a simple and direct derivation of the SLLOD equations of motion for molecular simulations of general homogeneous flows. We show that these equations of motion (1) generate the correct particle trajectories, (2) conserve the total thermal momentum without requiring the center of mass to be located at the origin, and (3) exactly generate the required energy dissipation. These equations of motion are compared with the g-SLLOD and p-SLLOD equations of motion, which are found to be deficient. Claims that the SLLOD equations of motion are incorrect for elongational flows are critically examined and found to be invalid. It is confirmed that the SLLOD equations are, in general, non-Hamiltonian. We derive a Hamiltonian from which they can be obtained in the special case of a symmetric velocity gradient tensor. In this case, it is possible to perform a canonical transformation that results in the well-known DOLLS tensor Hamiltonian.

A Few New 2+1-Dimensional Nonlinear Dynamics and the Representation of Riemann Curvature Tensors

NASA Astrophysics Data System (ADS)

Wang, Yan; Zhang, Yufeng; Zhang, Xiangzhi

2016-09-01

We first introduced a linear stationary equation with a quadratic operator in ∂x and ∂y, then a linear evolution equation is given by N-order polynomials of eigenfunctions. As applications, by taking N=2, we derived a (2+1)-dimensional generalized linear heat equation with two constant parameters associative with a symmetric space. When taking N=3, a pair of generalized Kadomtsev-Petviashvili equations with the same eigenvalues with the case of N=2 are generated. Similarly, a second-order flow associative with a homogeneous space is derived from the integrability condition of the two linear equations, which is a (2+1)-dimensional hyperbolic equation. When N=3, the third second flow associative with the homogeneous space is generated, which is a pair of new generalized Kadomtsev-Petviashvili equations. Finally, as an application of a Hermitian symmetric space, we established a pair of spectral problems to obtain a new (2+1)-dimensional generalized Schrödinger equation, which is expressed by the Riemann curvature tensors.

Simulation of Ground-Water Flow in the Shenandoah Valley, Virginia and West Virginia, Using Variable-Direction Anisotropy in Hydraulic Conductivity to Represent Bedrock Structure

USGS Publications Warehouse

Yager, Richard M.; Southworth, Scott C.; Voss, Clifford I.

2008-01-01

Ground-water flow was simulated using variable-direction anisotropy in hydraulic conductivity to represent the folded, fractured sedimentary rocks that underlie the Shenandoah Valley in Virginia and West Virginia. The anisotropy is a consequence of the orientations of fractures that provide preferential flow paths through the rock, such that the direction of maximum hydraulic conductivity is oriented within bedding planes, which generally strike N30 deg E; the direction of minimum hydraulic conductivity is perpendicular to the bedding. The finite-element model SUTRA was used to specify variable directions of the hydraulic-conductivity tensor in order to represent changes in the strike and dip of the bedding throughout the valley. The folded rocks in the valley are collectively referred to as the Massanutten synclinorium, which contains about a 5-km thick section of clastic and carbonate rocks. For the model, the bedrock was divided into four units: a 300-m thick top unit with 10 equally spaced layers through which most ground water is assumed to flow, and three lower units each containing 5 layers of increasing thickness that correspond to the three major rock units in the valley: clastic, carbonate and metamorphic rocks. A separate zone in the carbonate rocks that is overlain by colluvial gravel - called the western-toe carbonate unit - was also distinguished. Hydraulic-conductivity values were estimated through model calibration for each of the four rock units, using data from 354 wells and 23 streamflow-gaging stations. Conductivity tensors for metamorphic and western-toe carbonate rocks were assumed to be isotropic, while conductivity tensors for carbonate and clastic rocks were assumed to be anisotropic. The directions of the conductivity tensor for carbonate and clastic rocks were interpolated for each mesh element from a stack of 'form surfaces' that provided a three-dimensional representation of bedrock structure. Model simulations were run with (1) variable strike and dip, in which conductivity tensors were aligned with the strike and dip of the bedding, and (2) uniform strike in which conductivity tensors were assumed to be horizontally isotropic with the maximum conductivity direction parallel to the N30 deg E axis of the valley and the minimum conductivity direction perpendicular to the horizontal plane. Simulated flow penetrated deeper into the aquifer system with the uniform-strike tensor than with the variable-strike-and-dip tensor. Sensitivity analyses suggest that additional information on recharge rates would increase confidence in the estimated parameter values. Two applications of the model were conducted - the first, to determine depth of recent ground-water flow by simulating the distribution of ground-water ages, showed that most shallow ground water is less than 10 years old. Ground-water age distributions computed by variable-strike-and-dip and uniform-strike models were similar, but differed beneath Massanutten Mountain in the center of the valley. The variable-strike-and-dip model simulated flow from west to east parallel to the bedding of the carbonate rocks beneath Massanutten Mountain, while the uniform-strike model, in which flow was largely controlled by topography, simulated this same area as an east-west ground-water divide. The second application, which delineated capture zones for selected well fields in the valley, showed that capture zones delineated with both models were similar in plan view, but differed in vertical extent. Capture zones simulated by the variable-strike-and-dip model extended downdip with the bedding of carbonate rock and were relatively shallow, while those simulated by the uniform-strike model extended to the bottom of the flow system, which is unrealistic. These results suggest that simulations of ground-water flow through folded fractured rock can be constructed using SUTRA to represent variable orientations of the hydraulic-conductivity tensor and produce a

Simplified moment tensor analysis and unified decomposition of acoustic emission source: Application to in situ hydrofracturing test

NASA Astrophysics Data System (ADS)

Ohtsu, Masayasu

1991-04-01

An application of a moment tensor analysis to acoustic emission (AE) is studied to elucidate crack types and orientations of AE sources. In the analysis, simplified treatment is desirable, because hundreds of AE records are obtained from just one experiment and thus sophisticated treatment is realistically cumbersome. Consequently, a moment tensor inversion based on P wave amplitude is employed to determine six independent tensor components. Selecting only P wave portion from the full-space Green's function of homogeneous and isotropic material, a computer code named SiGMA (simplified Green's functions for the moment tensor analysis) is developed for the AE inversion analysis. To classify crack type and to determine crack orientation from moment tensor components, a unified decomposition of eigenvalues into a double-couple (DC) part, a compensated linear vector dipole (CLVD) part, and an isotropic part is proposed. The aim of the decomposition is to determine the proportion of shear contribution (DC) and tensile contribution (CLVD + isotropic) on AE sources and to classify cracks into a crack type of the dominant motion. Crack orientations determined from eigenvectors are presented as crack-opening vectors for tensile cracks and fault motion vectors for shear cracks, instead of stereonets. The SiGMA inversion and the unified decomposition are applied to synthetic data and AE waveforms detected during an in situ hydrofracturing test. To check the accuracy of the procedure, numerical experiments are performed on the synthetic waveforms, including cases with 10% random noise added. Results show reasonable agreement with assumed crack configurations. Although the maximum error is approximately 10% with respect to the ratios, the differences on crack orientations are less than 7°. AE waveforms detected by eight accelerometers deployed during the hydrofracturing test are analyzed. Crack types and orientations determined are in reasonable agreement with a predicted failure plane from borehole TV observation. The results suggest that tensile cracks are generated first at weak seams and then shear cracks follow on the opened joints.

Large eddy simulation of orientation and rotation of ellipsoidal particles in isotropic turbulent flows

NASA Astrophysics Data System (ADS)

Chen, Jincai; Jin, Guodong; Zhang, Jian

2016-03-01

The rotational motion and orientational distribution of ellipsoidal particles in turbulent flows are of significance in environmental and engineering applications. Whereas the translational motion of an ellipsoidal particle is controlled by the turbulent motions at large scales, its rotational motion is determined by the fluid velocity gradient tensor at small scales, which raises a challenge when predicting the rotational dispersion of ellipsoidal particles using large eddy simulation (LES) method due to the lack of subgrid scale (SGS) fluid motions. We report the effects of the SGS fluid motions on the orientational and rotational statistics, such as the alignment between the long axis of ellipsoidal particles and the vorticity, the mean rotational energy at various aspect ratios against those obtained with direct numerical simulation (DNS) and filtered DNS. The performances of a stochastic differential equation (SDE) model for the SGS velocity gradient seen by the particles and the approximate deconvolution method (ADM) for LES are investigated. It is found that the missing SGS fluid motions in LES flow fields have significant effects on the rotational statistics of ellipsoidal particles. Alignment between the particles and the vorticity is weakened; and the rotational energy of the particles is reduced in LES. The SGS-SDE model leads to a large error in predicting the alignment between the particles and the vorticity and over-predicts the rotational energy of rod-like particles. The ADM significantly improves the rotational energy prediction of particles in LES.

Cosmic Vorticity and the Origin Halo Spins

NASA Astrophysics Data System (ADS)

Libeskind, Noam I.; Hoffman, Yehuda; Steinmetz, Matthias; Gottlöber, Stefan; Knebe, Alexander; Hess, Steffen

2013-04-01

In the standard model of cosmology, structure emerges out of a non-rotational flow and the angular momentum of collapsing halos is induced by tidal torques. The growth of angular momentum in the linear and quasi-linear phases is associated with a shear, curl-free, flow and it is well described within the linear framework of tidal torque theory (TTT). However, TTT ceases to be applicable as halos approach turnaround when their ambient flow field becomes rotational. Subsequently, halos become embedded in a vortical flow field and the growth of their angular momentum is affected by the vorticity of their ambient velocity field. Using a cosmological simulation, we have examined the importance of the curl of the velocity field in determining halo spin, finding a significant alignment between the two: the vorticity tends to be perpendicular to the axis of the fastest collapse of the velocity shear tensor (e 1). This is independent of halo masses and cosmic web environment. Our results agree with previous findings on the tendency of halo spin to be perpendicular to e 1, and of the spin of (simulated) halos and (observed) galaxies to be aligned with the large-scale structure. It follows that angular momentum growth proceeds in two distinct phases. First, the angular momentum emerges out of a shear, curl-free, potential flow, as described by TTT. In the second phase, in which halos approach virialization, the angular momentum emerges out of a vortical flow and halo spin becomes partially aligned with the vorticity of the ambient flow field.

A similarity measure for partially folded proteins: application to unfolded and native-like conformational fluctuations

NASA Astrophysics Data System (ADS)

Larios, Edgar; Yang, Wei Y.; Schulten, K.; Gruebele, M.

2004-12-01

Computing the root-mean-square deviation (RMSD) of a partially folded protein structure from the folded state requires the two structures to be translationally and rotationally aligned. We examine the constraint matrix L that preserves orthogonality of the rotation matrix during minimization of the RMSD. L is proportional to the sensitivity of the RMSD to the rotational alignment matrix. Its trace yields an isotropic reaction coordinate, while its off-diagonal matrix elements are related to the moment of inertia derivative tensor that encodes anisotropic information about the structure. We use L to compare λ-repressor fragment 6-85 (λ 6-85) to several partially folded structures obtained from molecular dynamics simulation (MD), and find that L as a reaction coordinate indeed encodes some information about protein topology. We also apply C α RMSD, L and tryptophan sidechain mobility as criteria for native state structural fluctuations of several λ 6-85 mutants. The mutants' denaturation curves and fluorescence quenching are measured experimentally for comparison. The results are in accord with a recent proposal that structural fluctuations near the chromophore can induce increased native state fluorescence or hyperfluorescence during unfolding of proteins.

Alignment and focus of mirrored facets of a heliosat

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

Yellowhair, Julius E; Ho, Clifford Kuofei; Diver, Richard B

2013-11-12

Various technologies pertaining to aligning and focusing mirrored facets of a heliostat are described herein. Updating alignment and/or focus of mirrored facets is undertaken through generation of a theoretical image, wherein the theoretical image is indicative of a reflection of the target via the mirrored facets when the mirrored facets are properly aligned. This theoretical image includes reference points that are overlaid on an image of the target as reflected by the mirrored facets of the heliostat. A technician adjusts alignment/focus of a mirrored facet by causing reflected reference markings to become aligned with the reference points in the theoreticalmore » image.« less

A Novel Partial Sequence Alignment Tool for Finding Large Deletions

PubMed Central

Aruk, Taner; Ustek, Duran; Kursun, Olcay

2012-01-01

Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method. PMID:22566777

IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

PubMed

Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Naeem; Naveed, Nasir; Ahmad, Sarfraz; Muhammad, Shah; Qadri, Salman; Shahid, Muhammad; Hussain, Tanveer; Javed, Maryam

2015-01-01

IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

Advanced Magnetic Resonance Imaging techniques to probe muscle structure and function

NASA Astrophysics Data System (ADS)

Malis, Vadim

Structural and functional Magnetic Resonance Imaging (MRI) studies of skeletal muscle allow the elucidation of muscle physiology under normal and pathological conditions. Continuing on the efforts of the Muscle Imaging and Modeling laboratory, the focus of the thesis is to (i) extend and refine two challenging imaging modalities: structural imaging using Diffusion Tensor Imaging (DTI) and functional imaging based on Velocity Encoded Phase Contrast Imaging (VE-PC) and (ii) apply these methods to explore age related structure and functional differences of the gastrocnemius muscle. Diffusion Tensor Imaging allows the study of tissue microstructure as well as muscle fiber architecture. The images, based on an ultrafast single shot Echo Planar Imaging (EPI) sequence, suffer from geometric distortions and low signal to noise ratio. A processing pipeline was developed to correct for distortions and to improve image Signal to Noise Ratio (SNR). DTI acquired on a senior and young cohort of subjects were processed through the pipeline and differences in DTI derived indices and fiber architecture between the two cohorts were explored. The DTI indices indicated that at the microstructural level, fiber atrophy was accompanied with a reduction in fiber volume fraction. At the fiber architecture level, fiber length and pennation angles decreased with age that potentially contribute to the loss of muscle force with age. Velocity Encoded Phase Contrast imaging provides tissue (e.g. muscle) velocity at each voxel which allows the study of strain and Strain Rate (SR) under dynamic conditions. The focus of the thesis was to extract 2D strain rate tensor maps from the velocity images and apply the method to study age related differences. The tensor mapping can potentially provide unique information on the extracellular matrix and lateral transmission the role of these two elements has recently emerged as important determinants of force loss with age. In the cross sectional study on aging, strain rate during isometric contraction was significantly reduced in the seniors; presumably from decrease in muscle slack and increase in stiffness with age. Other parameters of interest from this study that allow inferences on the ECM and lateral transmission are the asymmetry of deformation in the fiber cross section as well as the angle between the SR and muscle fiber. The last part of thesis, which is a 'work-in-progress', is the extension to 3D SR tensor mapping using a 3D spatial, 3D velocity encoded imaging sequence. This is combined with Diffusion Tensor Imaging to obtain the lead eigenvector (muscle fiber direction) at each voxel. The 3D SR is then rotated to the basis of the DTI to obtain a 'Fiber Aligned Strain rate: FASR'. The off diagonal elements of FASR are shear strain terms. Detailed analysis of the shear strain will provide a unique non-invasive method to probe lateral transmission.

Diffusion Tensor Imaging of Heterotopia: Changes of Fractional Anisotropy during Radial Migration of Neurons

PubMed Central

Kim, Jinna

2010-01-01

Purpose Diffusion tensor imaging provides better understanding of pathophysiology of congenital anomalies, involving central nervous system. This study was aimed to specify the pathogenetic mechanism of heterotopia, proved by diffusion tensor imaging, and establish new findings of heterotopia on fractional anisotropy maps. Materials and Methods Diffusion-weighted imaging data from 11 patients (M : F = 7 : 4, aged from 1 to 22 years, mean = 12.3 years) who visited the epilepsy clinic and received a routine seizure protocol MRI exam were retrospectively analyzed. Fractional anisotropy (FA) maps were generated from diffusion tensor imaging of 11 patients with heterotopia. Regions of interests (ROI) were placed in cerebral cortex, heterotopic gray matter and deep gray matter, including putamen. ANOVA analysis was performed for comparison of different gray matter tissues. Results Heterotopic gray matter showed signal intensities similar to normal gray matter on T1 and T2 weighted MRI. The measured FA of heterotopic gray matter was higher than that of cortical gray matter (0.236 ± 0.011 vs. 0.169 ± 0.015, p < 0.01, one way ANOVA), and slightly lower than that of deep gray matter (0.236 ± 0.011 vs. 0.259 ± 0.016, p < 0.01). Conclusion Increased FA of heterotopic gray matter suggests arrested neuron during radial migration and provides better understanding of neurodevelopment. PMID:20499428

Second harmonic generation imaging - a new method for unraveling molecular information of starch.

PubMed

Zhuo, Zong-Yan; Liao, Chien-Sheng; Huang, Chen-Han; Yu, Jiun-Yann; Tzeng, Yu-Yi; Lo, Wen; Dong, Chen-Yuan; Chui, Hsiang-Chen; Huang, Yu-Chan; Lai, Hsi-Mei; Chu, Shi-Wei

2010-07-01

We present a new method, second harmonic generation (SHG) imaging for the study of starch structure. SHG imaging can provide the structural organization and molecular orientation information of bio-tissues without centrosymmetry. In recent years, SHG has proven its capability in the study of crystallized bio-molecules such as collagen and myosin. Starch, the most important food source and a promising future energy candidate, has, for a decade, been shown to exhibit strong SHG response. By comparing SHG intensity from different starch species, we first identified that the SHG-active molecule is amylopectin, which accounts for the crystallinity in starch granules. With the aid of SHG polarization anisotropy, we extracted the complete χ((2)) tensor of amylopectin, which reflects the underlying molecular details. Through χ((2)) tensor analysis, three-dimensional orientation and packing symmetry of amylopectin are determined. The helical angle of the double-helix in amylopectin is also deduced from the tensor, and the value corresponds well to previous X-ray studies, further verifying amylopectin as SHG source. It is noteworthy that the nm-sized structure of amylopectin inside a starch granule can be determined by this far-field optical method with 1-μm excitation wavelength. Since SHG is a relatively new tool for plant research, a detailed understanding of SHG in starch structure will be useful for future high-resolution imaging and quantitative analyses for food/energy applications. Copyright © 2010 Elsevier Inc. All rights reserved.

Second-order cosmological perturbations. I. Produced by scalar-scalar coupling in synchronous gauge

NASA Astrophysics Data System (ADS)

Wang, Bo; Zhang, Yang

2017-11-01

We present a systematic study of the 2nd-order scalar, vector, and tensor metric perturbations in the Einstein-de Sitter Universe in synchronous coordinates. For the scalar-scalar coupling between 1st-order perturbations, we decompose the 2nd-order perturbed Einstein equation into the respective field equations of 2nd-order scalar, vector, and tensor perturbations, and obtain their solutions with general initial conditions. In particular, the decaying modes of solution are included, the 2nd-order vector is generated even if the 1st-order vector is absent, and the solution of the 2nd-order tensor corrects that in literature. We perform general synchronous-to-synchronous gauge transformations up to 2nd order generated by a 1st-order vector field ξ(1 )μ and a 2nd-order ξ(2 )μ . All the residual gauge modes of 2nd-order metric perturbations and density contrast are found, and their number is substantially reduced when the transformed 3-velocity of dust is set to zero. Moreover, we show that only ξ(2 )μ is effective in carrying out 2nd-order transformations that we consider, because ξ(1 )μ has been used in obtaining the 1st-order perturbations. Holding the 1st-order perturbations fixed, the transformations by ξ(2 )μ on the 2nd-order perturbations have the same structure as those by ξ(1 )μ on the 1st-order perturbations.

Aptaligner: automated software for aligning pseudorandom DNA X-aptamers from next-generation sequencing data.

PubMed

Lu, Emily; Elizondo-Riojas, Miguel-Angel; Chang, Jeffrey T; Volk, David E

2014-06-10

Next-generation sequencing results from bead-based aptamer libraries have demonstrated that traditional DNA/RNA alignment software is insufficient. This is particularly true for X-aptamers containing specialty bases (W, X, Y, Z, ...) that are identified by special encoding. Thus, we sought an automated program that uses the inherent design scheme of bead-based X-aptamers to create a hypothetical reference library and Markov modeling techniques to provide improved alignments. Aptaligner provides this feature as well as length error and noise level cutoff features, is parallelized to run on multiple central processing units (cores), and sorts sequences from a single chip into projects and subprojects.

Fracture characterization by hybrid enumerative search and Gauss-Newton least-squares inversion methods

NASA Astrophysics Data System (ADS)

Alkharji, Mohammed N.

Most fracture characterization methods provide a general description of the fracture parameters as part of the reservoirs parameters; the fracture interaction and geometry within the reservoir is given less attention. T-Matrix and Linear Slip effective medium fracture models are implemented to invert the elastic tensor for the parameters and geometries of the fractures within the reservoir. The fracture inverse problem has an ill-posed, overdetermined, underconstrained rank-deficit system of equations. Least-squares inverse methods are used to solve the problem. A good starting initial model for the parameters is a key factor in the reliability of the inversion. Most methods assume that the starting parameters are close to the solution to avoid inaccurate local minimum solutions. The prior knowledge of the fracture parameters and their geometry is not available. We develop a hybrid, enumerative and Gauss-Newton, method that estimates the fracture parameters and geometry from the elastic tensor with no prior knowledge of the initial parameter values. The fracture parameters are separated into two groups. The first group contains the fracture parameters with no prior information, and the second group contains the parameters with known prior information. Different models are generated from the first group parameters by sampling the solution space over a predefined range of possible solutions for each parameter. Each model generated by the first group is fixed and used as a starting model to invert for the second group of parameters using the Gauss-Newton method. The least-squares residual between the observed elastic tensor and the estimated elastic tensor is calculated for each model. The model parameters that yield the least-squares residual corresponds to the correct fracture reservoir parameters and geometry. Two synthetic examples of fractured reservoirs with oil and gas saturations were inverted with no prior information about the fracture properties. The results showed that the hybrid algorithm successfully predicted the fracture parametrization, geometry, and the fluid content within the modeled reservoir. The method was also applied on an elastic tensor extracted from the Weyburn field in Saskatchewan, Canada. The solution suggested no presence of fractures but only a VTI system caused by the shale layering in the targeted reservoir, this interpretation is supported by other Weyburn field data.

Modeling the effects of structure on seismic anisotropy in the Chester gneiss dome, southeast Vermont

NASA Astrophysics Data System (ADS)

Saif, S.; Brownlee, S. J.

2017-12-01

Compositional and structural heterogeneity in the continental crust are factors that contribute to the complex expression of crustal seismic anisotropy. Understanding deformation and flow in the crust using seismic anisotropy has thus proven difficult. Seismic anisotropy is affected by rock microstructure and mineralogy, and a number of studies have begun to characterize the full elastic tensors of crustal rocks in an attempt to increase our understanding of these intrinsic factors. However, there is still a large gap in length-scale between laboratory characterization on the scale of centimeters and seismic wavelengths on the order of kilometers. To address this length-scale gap we are developing a 3D crustal model that will help us determine the effects of rotating laboratory-scale elastic tensors into field-scale structures. The Chester gneiss dome in southeast Vermont is our primary focus. The model combines over 2000 structural data points from field measurements and published USGS structural data with elastic tensors of Chester dome rocks derived from electron backscatter diffraction data. We created a uniformly spaced grid by averaging structural measurements together in equally spaced grid boxes. The surface measurements are then projected into the third dimension using existing subsurface interpretations. A measured elastic tensor for the specific rock type is rotated according to its unique structural input at each point in the model. The goal is to use this model to generate artificial seismograms using existing numerical wave propagation codes. Once completed, the model input can be varied to examine the effects of different subsurface structure interpretations, as well as heterogeneity in rock composition and elastic tensors. Our goal is to be able to make predictions for how specific structures will appear in seismic data, and how that appearance changes with variations in rock composition.

Complex brittle deformation pattern along the Southern Patagonian Andes (Argentina)

NASA Astrophysics Data System (ADS)

Barberón, Vanesa; Sue, Christian; Ronda, Gonzalo; Ghiglione, Matías

2016-04-01

The Southern Patagonian Andes is located in the southern extreme of the Pacific subduction zone, where the Antartic oceanic plate sinks underneath South America. The history of the area begins with compression during Paleozoic, Jurassic extension associated to the rift and opening of the South Atlantic Ocean, then a sag stage in the Lower Cretaceous followed by a foreland phase as a result of plate tectonics (Ghiglione et al., 2016). The kinematic study is concentrated in the Argentinean foothills, between 46°40' and 48° SL. We measured around 800 fault planes and their striaes with the sense of movement in order to characterize the stress field. The software used to make the stress inversion were Tensor (Delvaux, 2011) and Multiple Inverse Method MIM (Yamaji et al., 2011). The stress field map was built with the results of the MIM. We present new data from 48 sites located in the northern sector of the Southern Patagonian Andes. The measurements were made in several rocks from Paleozoic to Lower Cretaceous, even though most were taken in pyroclastic jurassic rocks from El Quemado Complex. Paleostress tensors obtained are mostly strike-slip, although a 25% is normal and there are a few compresional. The pattern of faults found is complex. In some sites the tensor can be locally linked to satellite images and observations from the field or be related to a major thrust front. There is no clear correlation between the age and/or lithology with the tensor since the youngest rocks measured are Lower Cretaceous. Probably there are several generations of family faults connected to different and recent tectonic phases then the paleostress tensors might correspond to the latest tectonic events.

On the `simple' form of the gravitational action and the self-interacting graviton

NASA Astrophysics Data System (ADS)

Tomboulis, E. T.

2017-09-01

The so-called ΓΓ-form of the gravitational Lagrangian, long known to provide its most compact expression as well as the most efficient generation of the graviton vertices, is taken as the starting point for discussing General Relativity as a theory of the self-interacting graviton. A straightforward but general method of converting to a covariant formulation by the introduction of a reference metric is given. It is used to recast the Einstein field equation as the equation of motion of a spin-2 particle interacting with the canonical energy-momentum tensor symmetrized by the standard Belinfante method applicable to any field carrying nonzero spin. This represents the graviton field equation in a form complying with the precepts of standard field theory. It is then shown how representations based on other, at face value completely unrelated definitions of energy-momentum (pseudo)tensors are all related by the addition of appropriate superpotential terms. Specifically, the superpotentials are explicitly constructed which connect to: i) the common definition consisting simply of the nonlinear part of the Einstein tensor; ii) the Landau-Lifshitz definition.

On synthetic gravitational waves from multi-field inflation

NASA Astrophysics Data System (ADS)

Ozsoy, Ogan

2018-04-01

We revisit the possibility of producing observable tensor modes through a continuous particle production process during inflation. Particularly, we focus on the multi-field realization of inflation where a spectator pseudoscalar σ induces a significant amplification of the U(1) gauge fields through the coupling propto σFμνtilde Fμν. In this model, both the scalar σ and the Abelian gauge fields are gravitationally coupled to the inflaton sector, therefore they can only affect the primordial scalar and tensor fluctuations through their mixing with gravitational fluctuations. Recent studies on this scenario show that the sourced contributions to the scalar correlators can be dangerously large to invalidate a large tensor power spectrum through the particle production mechanism. In this paper, we re-examine these recent claims by explicitly calculating the dominant contribution to the scalar power and bispectrum. Particularly, we show that once the current limits from CMB data are taken into account, it is still possible to generate a signal as large as r ≈ 10‑3 and the limitations on the model building are more relaxed than what was considered before.

Evading the Lyth bound in hybrid natural inflation

NASA Astrophysics Data System (ADS)

Hebecker, A.; Kraus, S. C.; Westphal, A.

2013-12-01

Generically, the gravitational-wave or tensor-mode contribution to the primordial curvature spectrum of inflation is tiny if the field range of the inflaton is much smaller than the Planck scale. We show that this pessimistic conclusion is naturally avoided in a rather broad class of small-field models. More specifically, we consider models where an axionlike shift symmetry keeps the inflaton potential flat (up to nonperturbative cosine-shaped modulations), but inflation nevertheless ends in a waterfall regime, as is typical for hybrid inflation. In such hybrid natural inflation scenarios (examples are provided by Wilson line inflation and fluxbrane inflation), the slow-roll parameter ɛ can be sizable during an early period (relevant for the cosmic microwave background spectrum). Subsequently, ɛ quickly becomes very small before the tachyonic instability eventually terminates the slow-roll regime. In this scenario, one naturally generates a considerable tensor-mode contribution in the curvature spectrum, collecting nevertheless the required amount of e-foldings during the final period of inflation. While nonobservation of tensors by Planck is certainly not a problem, a discovery in the medium- to long-term future is realistic.

Interaction of weakly compressible isotropic turbulence with planar expansion waves: Flow anisotropy and vorticity alignment

NASA Astrophysics Data System (ADS)

Xanthos, Savvas; Gong, Minwei; Andreopoulos, Yiannis

2010-01-01

Further analysis of the experimental data of the velocity gradient tensor first published by Xanthos et al. [J. Fluid Mech. 584, 301 (2007)] has been carried out and new results are reported here to provide additional insights on the effects of expansion waves interacting with isotropic turbulence. The flow field was generated by the reflection of an incoming shock wave at the open end of a large scale shock tube facility which interacted with the induced flow behind the incident shock wave which passed through a turbulence generating grid. In the present configuration the interaction is free from streamline curvature effects, which cause additional effects on turbulence. The strength of the applied expansive straining was 240 s-1. Rectangular pattern grids of different mesh sizes were used to generate isotropic and homogeneous turbulence with turbulent Reynolds number Reλ based on Taylor's microscale between 450 and 488. Lateral vorticity fluctuations and fluctuations of enstrophy and all stretching vector components are drastically reduced during the interaction. Residual attenuation in the postinteraction flow field was found only in the lateral vorticity fluctuations and in the longitudinal stretching term S11Ω1. Helicity and the helicity angle were computed from the data and the orientation angle of the vorticity vector in reference to the velocity vector was determined. Large fluctuations of the helicity angle were observed which extend from 0° to 180° with most probable values close to 30° and 130° and a mean value of 85°. Rotational dissipation rate was found to be high at these angles. The time-dependent signals of enstrophy, vortex stretching/tilting vector, and dissipation rate were found to exhibit a rather strong intermittent behavior which is characterized by high amplitude bursts followed by low level activities. It was found that the observed strong dissipative events are mostly associated with strong activities in the longitudinal stretching S11Ω1 rather than with events in the lateral components.

Explicit robust schemes for implementation of a class of principal value-based constitutive models: Theoretical development

NASA Technical Reports Server (NTRS)

Saleeb, A. F.; Arnold, S. M.

1991-01-01

The issue of developing effective and robust schemes to implement a class of the Ogden-type hyperelastic constitutive models is addressed. To this end, explicit forms for the corresponding material tangent stiffness tensors are developed, and these are valid for the entire deformation range; i.e., with both distinct as well as repeated principal-stretch values. Throughout the analysis the various implications of the underlying property of separability of the strain-energy functions are exploited, thus leading to compact final forms of the tensor expressions. In particular, this facilitated the treatment of complex cases of uncoupled volumetric/deviatoric formulations for incompressible materials. The forms derived are also amenable for use with symbolic-manipulation packages for systematic code generation.

Strain-induced three-photon effects

NASA Astrophysics Data System (ADS)

Jeong, Jae-Woo; Shin, Sung-Chul; Lyubchanskii, I. L.; Varyukhin, V. N.

2000-11-01

Strain-induced three-photon effects such as optical second-harmonic generation and hyper-Rayleigh light scattering, characterized by electromagnetic radiation at the double frequency of an incident light, are phenomenologically investigated by adopting a nonlinear photoelastic interaction. The relations between the strain and the nonlinear optical susceptibility for crystal surfaces with point symmetries of 4mm and 3m are described by a symmetry analysis of the nonlinear photoelastic tensor. We theoretically demonstrate a possibility of determining the strain components by measuring the rotational anisotropy of radiation at the second-harmonic frequency. Hyper-Rayleigh light scattering by dislocation strain is also described using a nonlinear photoelastic tensor. The angular dependencies of light scattered at the double frequency of an incident light for different scattering geometries are analyzed.

Stress Energy Tensor in LCFT and LOGARITHMIC Sugawara Construction

NASA Astrophysics Data System (ADS)

Kogan, Ian I.; Nichols, Alexander

We discuss the partners of the stress energy tensor and their structure in Logarithmic conformal field theories. In particular we draw attention to the fundamental differences between theories with zero and non-zero central charge. However they are both characterised by at least two independent parameters. We show how, by using a generalised Sugawara construction, one can calculate the logarithmic partner of T. We show that such a construction works in the c=-2 theory using the conformal dimension one primary currents which generate a logarithmic extension of the Kac-Moody algebra. This is an expanded version of a talk presented by A. Nichols at the conference on Logarithmic Conformal Field Theory and its Applications in Tehran Iran, 2001.

Frictional Magneto-Coulomb Drag in Graphene Double-Layer Heterostructures.

PubMed

Liu, Xiaomeng; Wang, Lei; Fong, Kin Chung; Gao, Yuanda; Maher, Patrick; Watanabe, Kenji; Taniguchi, Takashi; Hone, James; Dean, Cory; Kim, Philip

2017-08-04

Coulomb interaction between two closely spaced parallel layers of conductors can generate the frictional drag effect by interlayer Coulomb scattering. Employing graphene double layers separated by few-layer hexagonal boron nitride, we investigate density tunable magneto- and Hall drag under strong magnetic fields. The observed large magnetodrag and Hall-drag signals can be related with Laudau level filling status of the drive and drag layers. We find that the sign and magnitude of the drag resistivity tensor can be quantitatively correlated to the variation of magnetoresistivity tensors in the drive and drag layers, confirming a theoretical formula for magnetodrag in the quantum Hall regime. The observed weak temperature dependence and ∼B^{2} dependence of the magnetodrag are qualitatively explained by Coulomb scattering phase-space argument.

Generation of arbitrary vector beams with liquid crystal polarization converters and vector-photoaligned q-plates

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

Chen, Peng; Ji, Wei; Wei, Bing-Yan

Arbitrary vector beams (VBs) are realized by the designed polarization converters and corresponding vector-photoaligned q-plates. The polarization converter is a specific twisted nematic cell with one substrate homogeneously aligned and the other space-variantly aligned. By combining a polarization-sensitive alignment agent with a dynamic micro-lithography system, various categories of liquid crystal polarization converters are demonstrated. Besides, traditional radially/azimuthally polarized light, high-order and multi-ringed VBs, and a VB array with different orders are generated. The obtained converters are further utilized as polarization masks to implement vector-photoaligning. The technique facilitates both the volume duplication of these converters and the generation of another promisingmore » optical element, the q-plate, which is suitable for the generation of VBs for coherent lasers. The combination of proposed polarization converters and correspondingly fabricated q-plates would drastically enhance the capability of polarization control and may bring more possibilities for the design of photonic devices.« less

A new Weyl-like tensor of geometric origin

NASA Astrophysics Data System (ADS)

Vishwakarma, Ram Gopal

2018-04-01

A set of new tensors of purely geometric origin have been investigated, which form a hierarchy. A tensor of a lower rank plays the role of the potential for the tensor of one rank higher. The tensors have interesting mathematical and physical properties. The highest rank tensor of the hierarchy possesses all the geometrical properties of the Weyl tensor.

Theoretical study of dynamic electron-spin-polarization via the doublet-quartet quantum-mixed state and time-resolved ESR spectra of the quartet high-spin state.

PubMed

Teki, Yoshio; Matsumoto, Takafumi

2011-04-07

The mechanism of the unique dynamic electron polarization of the quartet (S = 3/2) high-spin state via a doublet-quartet quantum-mixed state and detail theoretical calculations of the population transfer are reported. By the photo-induced electron transfer, the quantum-mixed charge-separate state is generated in acceptor-donor-radical triad (A-D-R). This mechanism explains well the unique dynamic electron polarization of the quartet state of A-D-R. The generation of the selectively populated quantum-mixed state and its transfer to the strongly coupled pure quartet and doublet states have been treated both by a perturbation approach and by exact numerical calculations. The analytical solutions show that generation of the quantum-mixed states with the selective populations after de-coherence and/or accompanying the (complete) dephasing during the charge-recombination are essential for the unique dynamic electron polarization. Thus, the elimination of the quantum coherence (loss of the quantum information) is the key process for the population transfer from the quantum-mixed state to the quartet state. The generation of high-field polarization on the strongly coupled quartet state by the charge-recombination process can be explained by a polarization transfer from the quantum-mixed charge-separate state. Typical time-resolved ESR patterns of the quantum-mixed state and of the strongly coupled quartet state are simulated based on the generation mechanism of the dynamic electron polarization. The dependence of the spectral pattern of the quartet high-spin state has been clarified for the fine-structure tensor and the exchange interaction of the quantum-mixed state. The spectral pattern of the quartet state is not sensitive towards the fine-structure tensor of the quantum-mixed state, because this tensor contributes only as a perturbation in the population transfer to the spin-sublevels of the quartet state. Based on the stochastic Liouville equation, it is also discussed why the selective population in the quantum-mixed state is generated for the "finite field" spin-sublevels. The numerical calculations of the elimination of the quantum coherence (de-coherence and/or dephasing) are demonstrated. A new possibility of the enhanced intersystem crossing pathway in solution is also proposed.

Development of the Tensoral Computer Language

NASA Technical Reports Server (NTRS)

Ferziger, Joel; Dresselhaus, Eliot

1996-01-01

The research scientist or engineer wishing to perform large scale simulations or to extract useful information from existing databases is required to have expertise in the details of the particular database, the numerical methods and the computer architecture to be used. This poses a significant practical barrier to the use of simulation data. The goal of this research was to develop a high-level computer language called Tensoral, designed to remove this barrier. The Tensoral language provides a framework in which efficient generic data manipulations can be easily coded and implemented. First of all, Tensoral is general. The fundamental objects in Tensoral represent tensor fields and the operators that act on them. The numerical implementation of these tensors and operators is completely and flexibly programmable. New mathematical constructs and operators can be easily added to the Tensoral system. Tensoral is compatible with existing languages. Tensoral tensor operations co-exist in a natural way with a host language, which may be any sufficiently powerful computer language such as Fortran, C, or Vectoral. Tensoral is very-high-level. Tensor operations in Tensoral typically act on entire databases (i.e., arrays) at one time and may, therefore, correspond to many lines of code in a conventional language. Tensoral is efficient. Tensoral is a compiled language. Database manipulations are simplified optimized and scheduled by the compiler eventually resulting in efficient machine code to implement them.

A seismicity boundary in the low-strain region of Alentejo, south Portugal

NASA Astrophysics Data System (ADS)

Matos, Catarina; Zahradník, Jirí; Arroucau, Pierre; Silveira, Graça; Custódio, Susana

2017-04-01

Mainland Portugal lays on a stable continental setting characterized by low strain rates (convergence velocities < 1 mm/yr). However, the region has been the source of documented moderate magnitude earthquakes. The Alentejo region (south Portugal) presents belts of high epicenter density, the two main ones being (1) the Viana do Alentejo cluster in the south and (2) the NW-SE oriented Arraiolos alignment in the north. The latter appears as a sharp transition between a nearly aseismic area to the north and a seismically active area to the south. Active fault studies based on geological observations have not identified tectonic features able to explain the observed seismicity patterns. Our objective is to contribute to the understanding of the deformation pattern in south Portugal. Several hypotheses need to be addressed: (1) Are those clusters the expression of a broad region of distributed deformation?; (2) Do they mark structures that might have the potential to generate moderate magnitude events? We use a high-quality dataset recorded by a temporary array deployed in the area to produce a robust image of earthquake locations and to compute focal mechanisms. Newly detected events match well the previously identified earthquake alignments. The local network provides good control of the focal depths. We observe a spatial variation in the depth distribution. The Arraiolos alignment seems to produce deeper earthquakes than the Viana do Alentejo cluster. Earthquake locations inferred using 1D and 3D velocity models show a persistent concentration of seismicity at middle to lower crust depths (15 - 30 km) in the SE section of that alignment. We also present relocation of instrumental seismicity for the period (1970-2016). Previous studies show that a strike-slip faulting regime dominates mainland Portugal. IPMA (Instituto Português do Mar e da Atmosfera) routinely computes focal mechanisms for earthquakes with reported local magnitudes of 3.5 or greater using the permanent network. However, little is known about small-scale faulting in mainland Portugal. The temporary deployment allowed us to model waveforms of small earthquakes (ML < 3.0) at relatively high frequencies (1.0 - 2.0 Hz). We computed focal mechanisms for ML > 1.5 events. We tested the stability of moment tensor solutions using two velocity models. Minimal diferences in focal plane orientations were observed. The results show a tendency for both strike-slip and reverse faulting. We discuss the small-scale fault structure of the Alentejo region taking into account other relevant geological and geodetic data. This work is supported by the project SPIDER (PTDC/GEO-FIQ/2590/2014) and by the research fellowship PD/BD/106019/2014.

Measurement of residual chemical shift anisotropies in compressed polymethylmethacrylate gels. Automatic compensation of gel isotropic shift contribution.

PubMed

Hallwass, Fernando; Teles, Rubens R; Hellemann, Erich; Griesinger, Christian; Gil, Roberto R; Navarro-Vázquez, Armando

2018-05-01

Mechanical compression of polymer gels provides a simple way for the measurement of residual chemical shift anisotropies, which then can be employed, on its own, or in combination with residual dipolar couplings, for structural elucidation purposes. Residual chemical shift anisotropies measured using compression devices needed a posteriori correction to account for the increase of the polymer to solvent ratio inside the swollen gel. This correction has been cast before in terms of a single-free parameter which, as shown here, can be simultaneously optimized along with the components of the alignment tensor while still retaining discriminating power of the different relative configurations as illustrated in the stereochemical analysis of α-santonin and 10-epi-8-deoxycumambrin B. Copyright © 2018 John Wiley & Sons, Ltd.

Scale-Similar Models for Large-Eddy Simulations

NASA Technical Reports Server (NTRS)

Sarghini, F.

1999-01-01

Scale-similar models employ multiple filtering operations to identify the smallest resolved scales, which have been shown to be the most active in the interaction with the unresolved subgrid scales. They do not assume that the principal axes of the strain-rate tensor are aligned with those of the subgrid-scale stress (SGS) tensor, and allow the explicit calculation of the SGS energy. They can provide backscatter in a numerically stable and physically realistic manner, and predict SGS stresses in regions that are well correlated with the locations where large Reynolds stress occurs. In this paper, eddy viscosity and mixed models, which include an eddy-viscosity part as well as a scale-similar contribution, are applied to the simulation of two flows, a high Reynolds number plane channel flow, and a three-dimensional, nonequilibrium flow. The results show that simulations without models or with the Smagorinsky model are unable to predict nonequilibrium effects. Dynamic models provide an improvement of the results: the adjustment of the coefficient results in more accurate prediction of the perturbation from equilibrium. The Lagrangian-ensemble approach [Meneveau et al., J. Fluid Mech. 319, 353 (1996)] is found to be very beneficial. Models that included a scale-similar term and a dissipative one, as well as the Lagrangian ensemble averaging, gave results in the best agreement with the direct simulation and experimental data.

Functional MRI registration with tissue-specific patch-based functional correlation tensors.

PubMed

Zhou, Yujia; Zhang, Han; Zhang, Lichi; Cao, Xiaohuan; Yang, Ru; Feng, Qianjin; Yap, Pew-Thian; Shen, Dinggang

2018-06-01

Population studies of brain function with resting-state functional magnetic resonance imaging (rs-fMRI) rely on accurate intersubject registration of functional areas. This is typically achieved through registration using high-resolution structural images with more spatial details and better tissue contrast. However, accumulating evidence has suggested that such strategy cannot align functional regions well because functional areas are not necessarily consistent with anatomical structures. To alleviate this problem, a number of registration algorithms based directly on rs-fMRI data have been developed, most of which utilize functional connectivity (FC) features for registration. However, most of these methods usually extract functional features only from the thin and highly curved cortical grey matter (GM), posing great challenges to accurate estimation of whole-brain deformation fields. In this article, we demonstrate that additional useful functional features can also be extracted from the whole brain, not restricted to the GM, particularly the white-matter (WM), for improving the overall functional registration. Specifically, we quantify local anisotropic correlation patterns of the blood oxygenation level-dependent (BOLD) signals using tissue-specific patch-based functional correlation tensors (ts-PFCTs) in both GM and WM. Functional registration is then performed by integrating the features from different tissues using the multi-channel large deformation diffeomorphic metric mapping (mLDDMM) algorithm. Experimental results show that our method achieves superior functional registration performance, compared with conventional registration methods. © 2018 Wiley Periodicals, Inc.

Second harmonic generation in a molecular magnetic chain

NASA Astrophysics Data System (ADS)

Cavigli, L.; Sessoli, R.; Gurioli, M.; Bogani, L.

2006-05-01

A setup for the determination of all the components of the second harmonic generation tensor in molecular materials is presented. It allows overcoming depletion problems, which one can expect to be common in molecular systems. A preliminary characterization of the nonlinear properties of the single chain magnet CoPhOMe is carried out. We observe a high second harmonic signal, comparable to that of urea, and show that the bulk contributions are dominant over the surface ones.

The 1/ N Expansion of Tensor Models with Two Symmetric Tensors

NASA Astrophysics Data System (ADS)

Gurau, Razvan

2018-06-01

It is well known that tensor models for a tensor with no symmetry admit a 1/ N expansion dominated by melonic graphs. This result relies crucially on identifying jackets, which are globally defined ribbon graphs embedded in the tensor graph. In contrast, no result of this kind has so far been established for symmetric tensors because global jackets do not exist. In this paper we introduce a new approach to the 1/ N expansion in tensor models adapted to symmetric tensors. In particular we do not use any global structure like the jackets. We prove that, for any rank D, a tensor model with two symmetric tensors and interactions the complete graph K D+1 admits a 1/ N expansion dominated by melonic graphs.

The Weyl curvature tensor, Cotton-York tensor and gravitational waves: A covariant consideration

NASA Astrophysics Data System (ADS)

Osano, Bob

1 + 3 covariant approach to cosmological perturbation theory often employs the electric part (Eab), the magnetic part (Hab) of the Weyl tensor or the shear tensor (σab) in a phenomenological description of gravitational waves. The Cotton-York tensor is rarely mentioned in connection with gravitational waves in this approach. This tensor acts as a source for the magnetic part of the Weyl tensor which should not be neglected in studies of gravitational waves in the 1 + 3 formalism. The tensor is only mentioned in connection with studies of “silent model” but even there the connection with gravitational waves is not exhaustively explored. In this study, we demonstrate that the Cotton-York tensor encodes contributions from both electric and magnetic parts of the Weyl tensor and in directly from the shear tensor. In our opinion, this makes the Cotton-York tensor arguably the natural choice for linear gravitational waves in the 1 + 3 covariant formalism. The tensor is cumbersome to work with but that should negate its usefulness. It is conceivable that the tensor would equally be useful in the metric approach, although we have not demonstrated this in this study. We contend that the use of only one of the Weyl tensor or the shear tensor, although phenomenologically correct, leads to loss of information. Such information is vital particularly when examining the contribution of gravitational waves to the anisotropy of an almost-Friedmann-Lamitre-Robertson-Walker (FLRW) universe. The recourse to this loss is the use Cotton-York tensor.

Efficient Tensor Completion for Color Image and Video Recovery: Low-Rank Tensor Train.

PubMed

Bengua, Johann A; Phien, Ho N; Tuan, Hoang Duong; Do, Minh N

2017-05-01

This paper proposes a novel approach to tensor completion, which recovers missing entries of data represented by tensors. The approach is based on the tensor train (TT) rank, which is able to capture hidden information from tensors thanks to its definition from a well-balanced matricization scheme. Accordingly, new optimization formulations for tensor completion are proposed as well as two new algorithms for their solution. The first one called simple low-rank tensor completion via TT (SiLRTC-TT) is intimately related to minimizing a nuclear norm based on TT rank. The second one is from a multilinear matrix factorization model to approximate the TT rank of a tensor, and is called tensor completion by parallel matrix factorization via TT (TMac-TT). A tensor augmentation scheme of transforming a low-order tensor to higher orders is also proposed to enhance the effectiveness of SiLRTC-TT and TMac-TT. Simulation results for color image and video recovery show the clear advantage of our method over all other methods.

A Review of Tensors and Tensor Signal Processing

NASA Astrophysics Data System (ADS)

Cammoun, L.; Castaño-Moraga, C. A.; Muñoz-Moreno, E.; Sosa-Cabrera, D.; Acar, B.; Rodriguez-Florido, M. A.; Brun, A.; Knutsson, H.; Thiran, J. P.

Tensors have been broadly used in mathematics and physics, since they are a generalization of scalars or vectors and allow to represent more complex properties. In this chapter we present an overview of some tensor applications, especially those focused on the image processing field. From a mathematical point of view, a lot of work has been developed about tensor calculus, which obviously is more complex than scalar or vectorial calculus. Moreover, tensors can represent the metric of a vector space, which is very useful in the field of differential geometry. In physics, tensors have been used to describe several magnitudes, such as the strain or stress of materials. In solid mechanics, tensors are used to define the generalized Hooke’s law, where a fourth order tensor relates the strain and stress tensors. In fluid dynamics, the velocity gradient tensor provides information about the vorticity and the strain of the fluids. Also an electromagnetic tensor is defined, that simplifies the notation of the Maxwell equations. But tensors are not constrained to physics and mathematics. They have been used, for instance, in medical imaging, where we can highlight two applications: the diffusion tensor image, which represents how molecules diffuse inside the tissues and is broadly used for brain imaging; and the tensorial elastography, which computes the strain and vorticity tensor to analyze the tissues properties. Tensors have also been used in computer vision to provide information about the local structure or to define anisotropic image filters.

Characterizing dielectric tensors of anisotropic materials from a single measurement

NASA Astrophysics Data System (ADS)

Smith, Paula Kay

Ellipsometry techniques look at changes in polarization states to measure optical properties of thin film materials. A beam reflected from a substrate measures the real and imaginary parts of the index of the material represented as n and k, respectively. Measuring the substrate at several angles gives additional information that can be used to measure multilayer thin film stacks. However, the outstanding problem in standard ellipsometry is that it uses a limited number of incident polarization states (s and p). This limits the technique to isotropic materials. The technique discussed in this paper extends the standard process to measure anisotropic materials by using a larger set of incident polarization states. By using a polarimeter to generate several incident polarization states and measure the polarization properties of the sample, ellipsometry can be performed on biaxial materials. Use of an optimization algorithm in conjunction with biaxial ellipsometry can more accurately determine the dielectric tensor of individual layers in multilayer structures. Biaxial ellipsometry is a technique that measures the dielectric tensors of a biaxial substrate, single-layer thin film, or multi-layer structure. The dielectric tensor of a biaxial material consists of the real and imaginary parts of the three orthogonal principal indices (n x + ikx, ny +iky and nz + i kz) as well as three Euler angles (alpha, beta and gamma) to describe its orientation. The method utilized in this work measures an angle-of-incidence Mueller matrix from a Mueller matrix imaging polarimeter equipped with a pair of microscope objectives that have low polarization properties. To accurately determine the dielectric tensors for multilayer samples, the angle-of-incidence Mueller matrix images are collected for multiple wavelengths. This is done in either a transmission mode or a reflection mode, each incorporates an appropriate dispersion model. Given approximate a priori knowledge of the dielectric tensor and film thickness, a Jones reflectivity matrix is calculated by solving Maxwell's equations at each surface. Converting the Jones matrix into a Mueller matrix provides a starting point for optimization. An optimization algorithm then finds the best fit dielectric tensor based on the measured angle-of-incidence Mueller matrix image. This process can be applied to polarizing materials, birefringent crystals and the multilayer structures of liquid crystal displays. In particular, the need for such accuracy in liquid crystal displays is growing as their applications in industry evolve.

Geometric decomposition of the conformation tensor in viscoelastic turbulence

NASA Astrophysics Data System (ADS)

Hameduddin, Ismail; Meneveau, Charles; Zaki, Tamer A.; Gayme, Dennice F.

2018-05-01

This work introduces a mathematical approach to analysing the polymer dynamics in turbulent viscoelastic flows that uses a new geometric decomposition of the conformation tensor, along with associated scalar measures of the polymer fluctuations. The approach circumvents an inherent difficulty in traditional Reynolds decompositions of the conformation tensor: the fluctuating tensor fields are not positive-definite and so do not retain the physical meaning of the tensor. The geometric decomposition of the conformation tensor yields both mean and fluctuating tensor fields that are positive-definite. The fluctuating tensor in the present decomposition has a clear physical interpretation as a polymer deformation relative to the mean configuration. Scalar measures of this fluctuating conformation tensor are developed based on the non-Euclidean geometry of the set of positive-definite tensors. Drag-reduced viscoelastic turbulent channel flow is then used an example case study. The conformation tensor field, obtained using direct numerical simulations, is analysed using the proposed framework.

Switchable radioactive neutron source device

DOEpatents

Boyar, Robert E.; DeVolpi, Alexander; Stanford, George S.; Rhodes, Edgar A.

1989-01-01

This invention is a switchable neutron generating apparatus comprised of a pair of plates, the first plate having an alpha emitter section on it and the second plate having a target material portion on it which generates neutrons when its nuclei absorb an alpha particle. In operation, the alpha portion of the first plate is aligned with the neutron portion of the second plate to produce neutrons and brought out of alignment to cease production of neutrons.

Rheologic effects of crystal preferred orientation in upper mantle flow near plate boundaries

NASA Astrophysics Data System (ADS)

Blackman, Donna; Castelnau, Olivier; Dawson, Paul; Boyce, Donald

2016-04-01

Observations of anisotropy provide insight into upper mantle processes. Flow-induced mineral alignment provides a link between mantle deformation patterns and seismic anisotropy. Our study focuses on the rheologic effects of crystal preferred orientation (CPO), which develops during mantle flow, in order to assess whether corresponding anisotropic viscosity could significantly impact the pattern of flow. We employ a coupled nonlinear numerical method to link CPO and the flow model via a local viscosity tensor field that quantifies the stress/strain-rate response of a textured mineral aggregate. For a given flow field, the CPO is computed along streamlines using a self-consistent texture model and is then used to update the viscosity tensor field. The new viscosity tensor field defines the local properties for the next flow computation. This iteration produces a coupled nonlinear model for which seismic signatures can be predicted. Results thus far confirm that CPO can impact flow pattern by altering rheology in directionally-dependent ways, particularly in regions of high flow gradient. Multiple iterations run for an initial, linear stress/strain-rate case (power law exponent n=1) converge to a flow field and CPO distribution that are modestly different from the reference, scalar viscosity case. Upwelling rates directly below the spreading axis are slightly reduced and flow is focused somewhat toward the axis. Predicted seismic anisotropy differences are modest. P-wave anisotropy is a few percent greater in the flow 'corner', near the spreading axis, below the lithosphere and extending 40-100 km off axis. Predicted S-wave splitting differences would be below seafloor measurement limits. Calculations with non-linear stress/strain-rate relation, which is more realistic for olivine, indicate that effects are stronger than for the linear case. For n=2-3, the distribution and strength of CPO for the first iteration are greater than for n=1, although the fast seismic axis directions are similar. The greatest difference in CPO for the nonlinear cases develop at the flow 'corner' at depths of 10-30 km and 20-100 km off-axis. J index values up to 10% greater than the linear case are predicted near the lithosphere base in that region. Viscosity tensor components are notably altered in the nonlinear cases. Iterations between the texture and flow calculations for the non-linear cases are underway this winter; results will be reported in the presentation.

Tensor Algebra Library for NVidia Graphics Processing Units

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

Liakh, Dmitry

This is a general purpose math library implementing basic tensor algebra operations on NVidia GPU accelerators. This software is a tensor algebra library that can perform basic tensor algebra operations, including tensor contractions, tensor products, tensor additions, etc., on NVidia GPU accelerators, asynchronously with respect to the CPU host. It supports a simultaneous use of multiple NVidia GPUs. Each asynchronous API function returns a handle which can later be used for querying the completion of the corresponding tensor algebra operation on a specific GPU. The tensors participating in a particular tensor operation are assumed to be stored in local RAMmore » of a node or GPU RAM. The main research area where this library can be utilized is the quantum many-body theory (e.g., in electronic structure theory).« less

Retrospective Correction of Physiological Noise in DTI Using an Extended Tensor Model and Peripheral Measurements

PubMed Central

Mohammadi, Siawoosh; Hutton, Chloe; Nagy, Zoltan; Josephs, Oliver; Weiskopf, Nikolaus

2013-01-01

Diffusion tensor imaging is widely used in research and clinical applications, but this modality is highly sensitive to artefacts. We developed an easy-to-implement extension of the original diffusion tensor model to account for physiological noise in diffusion tensor imaging using measures of peripheral physiology (pulse and respiration), the so-called extended tensor model. Within the framework of the extended tensor model two types of regressors, which respectively modeled small (linear) and strong (nonlinear) variations in the diffusion signal, were derived from peripheral measures. We tested the performance of four extended tensor models with different physiological noise regressors on nongated and gated diffusion tensor imaging data, and compared it to an established data-driven robust fitting method. In the brainstem and cerebellum the extended tensor models reduced the noise in the tensor-fit by up to 23% in accordance with previous studies on physiological noise. The extended tensor model addresses both large-amplitude outliers and small-amplitude signal-changes. The framework of the extended tensor model also facilitates further investigation into physiological noise in diffusion tensor imaging. The proposed extended tensor model can be readily combined with other artefact correction methods such as robust fitting and eddy current correction. PMID:22936599

Photoaligning and photopatterning technology: applications in displays and photonics

NASA Astrophysics Data System (ADS)

Chigrinov, Vladimir

2016-03-01

The advantages of LC photoalignment technology in comparison with common "rubbing" alignment methods tend to the continuation of the research in this field. Almost all the criteria of perfect LC alignment are met in case of azo-dye layers. Nowadays azo-dye alignment materials can be already used in LCD manufacturing, e.g. for the alignment of monomers in LCP films for new generations of photonics and optics devices. Recently the new application of photoaligned technology for the tunable LC lenses with a variable focal distance was proposed. New optically rewritable (ORW) liquid crystal display and photonics devices with a light controllable structure may include LC E-paper screens, LC lenses with a variable focal distance etc. Fast ferroelectric liquid crystal devices (FLCD) are achieved through the application of nano-scale photo aligning (PA) layers in FLC cells. The novel photoaligned FLC devices may include field sequential color (FSC) FLC with a high resolution, high brightness, low power consumption and extended color gamut to be used for PCs, PDAs, switchable goggles, and new generation of switchable 2D/3D LCD TVs, as well as photonics elements.

Large longitudinal spin alignment generated in inelastic nuclear reactions

NASA Astrophysics Data System (ADS)

Hoff, D. E. M.; Potel, G.; Brown, K. W.; Charity, R. J.; Pruitt, C. D.; Sobotka, L. G.; Webb, T. B.; Roeder, B.; Saastamoinen, A.

2018-05-01

Large longitudinal spin alignment of E /A =24 MeV 7Li projectiles inelastically excited by Be, C, and Al targets was observed when the latter remain in their ground state. This alignment is a consequence of an angular-momentum-excitation-energy mismatch, which is well described by a DWBA cluster-model (α +t ). The longitudinal alignment of several other systems is also well described by DWBA calculations, including one where a cluster model is inappropriate, demonstrating that the alignment mechanism is a more general phenomenon. Predictions are made for inelastic excitation of 12C for beam energies above and below the mismatch threshold.

Mapping the nonlinear optical susceptibility by noncollinear second-harmonic generation.

PubMed

Larciprete, M C; Bovino, F A; Giardina, M; Belardini, A; Centini, M; Sibilia, C; Bertolotti, M; Passaseo, A; Tasco, V

2009-07-15

We present a method, based on noncollinear second-harmonic generation, to evaluate the nonzero elements of the nonlinear optical susceptibility. At a fixed incidence angle, the generated signal is investigated by varying the polarization state of both fundamental beams. The resulting polarization charts allows us to verify if Kleinman's symmetry rules can be applied to a given material or to retrieve the absolute value of the nonlinear optical tensor terms, from a reference measurement. Experimental measurements obtained from gallium nitride layers are reported. The proposed method does not require an angular scan and thus is useful when the generated signal is strongly affected by sample rotation.

[An Improved Spectral Quaternion Interpolation Method of Diffusion Tensor Imaging].

PubMed

Xu, Yonghong; Gao, Shangce; Hao, Xiaofei

2016-04-01

Diffusion tensor imaging(DTI)is a rapid development technology in recent years of magnetic resonance imaging.The diffusion tensor interpolation is a very important procedure in DTI image processing.The traditional spectral quaternion interpolation method revises the direction of the interpolation tensor and can preserve tensors anisotropy,but the method does not revise the size of tensors.The present study puts forward an improved spectral quaternion interpolation method on the basis of traditional spectral quaternion interpolation.Firstly,we decomposed diffusion tensors with the direction of tensors being represented by quaternion.Then we revised the size and direction of the tensor respectively according to different situations.Finally,we acquired the tensor of interpolation point by calculating the weighted average.We compared the improved method with the spectral quaternion method and the Log-Euclidean method by the simulation data and the real data.The results showed that the improved method could not only keep the monotonicity of the fractional anisotropy(FA)and the determinant of tensors,but also preserve the tensor anisotropy at the same time.In conclusion,the improved method provides a kind of important interpolation method for diffusion tensor image processing.

CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping.

PubMed

Nguyen, Tung; Shi, Weisong; Ruden, Douglas

2011-06-06

Research in genetics has developed rapidly recently due to the aid of next generation sequencing (NGS). However, massively-parallel NGS produces enormous amounts of data, which leads to storage, compatibility, scalability, and performance issues. The Cloud Computing and MapReduce framework, which utilizes hundreds or thousands of shared computers to map sequencing reads quickly and efficiently to reference genome sequences, appears to be a very promising solution for these issues. Consequently, it has been adopted by many organizations recently, and the initial results are very promising. However, since these are only initial steps toward this trend, the developed software does not provide adequate primary functions like bisulfite, pair-end mapping, etc., in on-site software such as RMAP or BS Seeker. In addition, existing MapReduce-based applications were not designed to process the long reads produced by the most recent second-generation and third-generation NGS instruments and, therefore, are inefficient. Last, it is difficult for a majority of biologists untrained in programming skills to use these tools because most were developed on Linux with a command line interface. To urge the trend of using Cloud technologies in genomics and prepare for advances in second- and third-generation DNA sequencing, we have built a Hadoop MapReduce-based application, CloudAligner, which achieves higher performance, covers most primary features, is more accurate, and has a user-friendly interface. It was also designed to be able to deal with long sequences. The performance gain of CloudAligner over Cloud-based counterparts (35 to 80%) mainly comes from the omission of the reduce phase. In comparison to local-based approaches, the performance gain of CloudAligner is from the partition and parallel processing of the huge reference genome as well as the reads. The source code of CloudAligner is available at http://cloudaligner.sourceforge.net/ and its web version is at http://mine.cs.wayne.edu:8080/CloudAligner/. Our results show that CloudAligner is faster than CloudBurst, provides more accurate results than RMAP, and supports various input as well as output formats. In addition, with the web-based interface, it is easier to use than its counterparts.

Effect of spatially and temporally variable recharge on subsurface reactive transport of contaminants at Oak Ridge Integrated Field Research Challenge site

NASA Astrophysics Data System (ADS)

Kumar, J.; Lichtner, P. C.; Mills, R. T.; Hammond, G. E.; Svyatskiy, D.; Tang, G.; Brooks, S. C.; Watson, D. B.; Parker, J.

2011-12-01

Recharge is one of the most fundamental components of groundwater systems which drives both flow and transport in the subsurface and plays an important role in the migration of contaminants at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site. The area receives an average of 137 cm of precipitation per year, most of it during winter. About 50% of the precipitation is lost to evapotranspiration, 40% runs off directly to surface water, and less than 10% recharges to ground water. The migration of the reactive contaminant plume at the site is modeled using the massively parallel flow and reactive transport model PFLOTRAN. The geology at the site consists of dipping beds of limestone, shale and sandstone with strike N 55° E and dip 45° SE, over which is superimposed a highly porous, horizontally oriented, saprolite weathering profile. To model this system in 3-D a grid was constructed with x-axis aligned with the strike of the geologic formation and z-axis vertical. This formulation requires a full permeability tensor with off-diagonal components obtained by rotation of the principal axes tensor through the formation dip angle. A full tensor capability was implemented in PFLOTRAN using the mimetic finite difference (MFD) method, a mass conserving, second-order accurate scheme with auxiliary pressure degrees of freedom at grid cell faces. A complex geochemical fluid with 17 primary reactive species and a number of minerals was implemented to model the contaminant discharged from the S-3 ponds at the ORIFRC site. A 50-year history of observed rainfall at the site was used as input to the model to estimate transient recharge conditions and to study the effect of spatially and temporally varied recharge. Results from the investigations of impact of spatio-temporal variation in recharge on the migration of contaminant plume will be presented.

Structural modeling of carbonaceous mesophase amphotropic mixtures under uniaxial extensional flow.

PubMed

Golmohammadi, Mojdeh; Rey, Alejandro D

2010-07-21

The extended Maier-Saupe model for binary mixtures of model carbonaceous mesophases (uniaxial discotic nematogens) under externally imposed flow, formulated in previous studies [M. Golmohammadi and A. D. Rey, Liquid Crystals 36, 75 (2009); M. Golmohammadi and A. D. Rey, Entropy 10, 183 (2008)], is used to characterize the effect of uniaxial extensional flow and concentration on phase behavior and structure of these mesogenic blends. The generic thermorheological phase diagram of the single-phase binary mixture, given in terms of temperature (T) and Deborah (De) number, shows the existence of four T-De transition lines that define regions that correspond to the following quadrupolar tensor order parameter structures: (i) oblate (perpendicular, parallel), (ii) prolate (perpendicular, parallel), (iii) scalene O(perpendicular, parallel), and (iv) scalene P(perpendicular, parallel), where the symbols (perpendicular, parallel) indicate alignment of the tensor order ellipsoid with respect to the extension axis. It is found that with increasing T the dominant component of the mixture exhibits weak deviations from the well-known pure species response to uniaxial extensional flow (uniaxial perpendicular nematic-->biaxial nematic-->uniaxial parallel paranematic). In contrast, the slaved component shows a strong deviation from the pure species response. This deviation is dictated by the asymmetric viscoelastic coupling effects emanating from the dominant component. Changes in conformation (oblate <==> prolate) and orientation (perpendicular <==> parallel) are effected through changes in pairs of eigenvalues of the quadrupolar tensor order parameter. The complexity of the structural sensitivity to temperature and extensional flow is a reflection of the dual lyotropic/thermotropic nature (amphotropic nature) of the mixture and their cooperation/competition. The analysis demonstrates that the simple structures (biaxial nematic and uniaxial paranematic) observed in pure discotic mesogens under uniaxial extensional flow are significantly enriched by the interaction of the lyotropic/thermotropic competition with the binary molecular architectures and with the quadrupolar nature of the flow.

TU-AB-BRA-02: An Efficient Atlas-Based Synthetic CT Generation Method

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

Han, X

2016-06-15

Purpose: A major obstacle for MR-only radiotherapy is the need to generate an accurate synthetic CT (sCT) from MR image(s) of a patient for the purposes of dose calculation and DRR generation. We propose here an accurate and efficient atlas-based sCT generation method, which has a computation speed largely independent of the number of atlases used. Methods: Atlas-based sCT generation requires a set of atlases with co-registered CT and MR images. Unlike existing methods that align each atlas to the new patient independently, we first create an average atlas and pre-align every atlas to the average atlas space. When amore » new patient arrives, we compute only one deformable image registration to align the patient MR image to the average atlas, which indirectly aligns the patient to all pre-aligned atlases. A patch-based non-local weighted fusion is performed in the average atlas space to generate the sCT for the patient, which is then warped back to the original patient space. We further adapt a PatchMatch algorithm that can quickly find top matches between patches of the patient image and all atlas images, which makes the patch fusion step also independent of the number of atlases used. Results: Nineteen brain tumour patients with both CT and T1-weighted MR images are used as testing data and a leave-one-out validation is performed. Each sCT generated is compared against the original CT image of the same patient on a voxel-by-voxel basis. The proposed method produces a mean absolute error (MAE) of 98.6±26.9 HU overall. The accuracy is comparable with a conventional implementation scheme, but the computation time is reduced from over an hour to four minutes. Conclusion: An average atlas space patch fusion approach can produce highly accurate sCT estimations very efficiently. Further validation on dose computation accuracy and using a larger patient cohort is warranted. The author is a full time employee of Elekta, Inc.« less

COSMIC VORTICITY AND THE ORIGIN HALO SPINS

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

Libeskind, Noam I.; Steinmetz, Matthias; Gottloeber, Stefan

2013-04-01

In the standard model of cosmology, structure emerges out of a non-rotational flow and the angular momentum of collapsing halos is induced by tidal torques. The growth of angular momentum in the linear and quasi-linear phases is associated with a shear, curl-free, flow and it is well described within the linear framework of tidal torque theory (TTT). However, TTT ceases to be applicable as halos approach turnaround when their ambient flow field becomes rotational. Subsequently, halos become embedded in a vortical flow field and the growth of their angular momentum is affected by the vorticity of their ambient velocity field.more » Using a cosmological simulation, we have examined the importance of the curl of the velocity field in determining halo spin, finding a significant alignment between the two: the vorticity tends to be perpendicular to the axis of the fastest collapse of the velocity shear tensor (e{sub 1}). This is independent of halo masses and cosmic web environment. Our results agree with previous findings on the tendency of halo spin to be perpendicular to e{sub 1}, and of the spin of (simulated) halos and (observed) galaxies to be aligned with the large-scale structure. It follows that angular momentum growth proceeds in two distinct phases. First, the angular momentum emerges out of a shear, curl-free, potential flow, as described by TTT. In the second phase, in which halos approach virialization, the angular momentum emerges out of a vortical flow and halo spin becomes partially aligned with the vorticity of the ambient flow field.« less

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

Calva-tildeo, M.O.; Reboucas, M.J.; Teixeira, A.F.F.

The breakdown of causality in homogeneous Goedel-type space-time manifolds is examined. An extension of Reboucas--Tiomno (RT) and Accioly--Goncalves studies is made. The existence of noncausal curves is also investigated under two different conditions on the energy-momentum tensor. An integral representation of the infinitesimal generators of isometries is obtained, extending previous works on the RT geometry.

Cut and join operator ring in tensor models

NASA Astrophysics Data System (ADS)

Itoyama, H.; Mironov, A.; Morozov, A.

2018-07-01

Recent advancement of rainbow tensor models based on their superintegrability (manifesting itself as the existence of an explicit expression for a generic Gaussian correlator) has allowed us to bypass the long-standing problem seen as the lack of eigenvalue/determinant representation needed to establish the KP/Toda integrability. As the mandatory next step, we discuss in this paper how to provide an adequate designation to each of the connected gauge-invariant operators that form a double coset, which is required to cleverly formulate a tree-algebra generalization of the Virasoro constraints. This problem goes beyond the enumeration problem per se tied to the permutation group, forcing us to introduce a few gauge fixing procedures to the coset. We point out that the permutation-based labeling, which has proven to be relevant for the Gaussian averages is, via interesting complexity, related to the one based on the keystone trees, whose algebra will provide the tensor counterpart of the Virasoro algebra for matrix models. Moreover, our simple analysis reveals the existence of nontrivial kernels and co-kernels for the cut operation and for the join operation respectively that prevent a straightforward construction of the non-perturbative RG-complete partition function and the identification of truly independent time variables. We demonstrate these problems by the simplest non-trivial Aristotelian RGB model with one complex rank-3 tensor, studying its ring of gauge-invariant operators, generated by the keystone triple with the help of four operations: addition, multiplication, cut and join.

Inner Core Anisotropy: Can Seismic Observations be Reconciled with Ab Initio Calculations of Elasticity?

NASA Astrophysics Data System (ADS)

Song, X.; Jordan, T. H.

2016-12-01

Body-wave and normal-mode observations have revealed an inner-core structure that is radially layered, axially anisotropic, and hemispherically asymmetric. Previous theoretical studies have examined the consistency of these features with the elasticity of iron crystals thought to dominate inner-core composition, but a fully consistent model has been elusive. Here we compare the seismic observation with effective-medium models derived from ab initio calculations of the elasticity tensors for hcp-Fe and bcc-Fe. Our estimates are based on Jordan's (GJI, 2015) effective medium theory, which is derived from a self-consistent, second-order Born approximation. The theory provides closed-form expressions for the effective elastic parameters of 3D anisotropic, heterogeneous media in which the local anisotropy is a constant hexagonal stiffness tensor C stochastically oriented about a constant symmetry axis \\hat{s} and the statistics of the small-scale heterogeneities are transversely isotropic in the plane perpendicular to \\hat{s}. The stochastic model is then described by a dimensionless "aspect ratio of the heterogeneity", 0 ≤ η < ∞, and a dimensionless "orientation ratio of the anisotropy", 0 ≤ ξ < ∞. The latter determines the degree to which the axis of C is aligned with \\hat{s}. We compute the loci of models with \\hat{s} oriented along the Earth's rotational axis ( \\hat{s} = north) by varying ξ and η for various ab initio estimates of C. We show that a lot of widely used estimates of C are inconsistent with most published normal-mode models of inner-core anisotropy. In particular, if the P-wave fast axis aligns with the rotational axis, which is required to satisfy the body-wave observations, then these hcp-Fe models predict that the fast polarization of the S waves is in the plane perpendicular to \\hat{s}, which disagrees with most normal-mode models. We have attempted to resolve this discrepancy by examining alternative hcp-Fe models, including radially anisotropic distributions of stochastic anisotropy and heterogeneity (i.e., where \\hat{s} = \\hat{r}), as well as bcc-Fe models. Our calculations constrain the form of C needed to satisfy the seismological inferences.

C%2B%2B tensor toolbox user manual.

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

Plantenga, Todd D.; Kolda, Tamara Gibson

2012-04-01

The C++ Tensor Toolbox is a software package for computing tensor decompositions. It is based on the Matlab Tensor Toolbox, and is particularly optimized for sparse data sets. This user manual briefly overviews tensor decomposition mathematics, software capabilities, and installation of the package. Tensors (also known as multidimensional arrays or N-way arrays) are used in a variety of applications ranging from chemometrics to network analysis. The Tensor Toolbox provides classes for manipulating dense, sparse, and structured tensors in C++. The Toolbox compiles into libraries and is intended for use with custom applications written by users.

Moment Tensor Descriptions for Simulated Explosions of the Source Physics Experiment (SPE)

NASA Astrophysics Data System (ADS)

Yang, X.; Rougier, E.; Knight, E. E.; Patton, H. J.

2014-12-01

In this research we seek to understand damage mechanisms governing the behavior of geo-materials in the explosion source region, and the role they play in seismic-wave generation. Numerical modeling tools can be used to describe these mechanisms through the development and implementation of appropriate material models. Researchers at Los Alamos National Laboratory (LANL) have been working on a novel continuum-based-viscoplastic strain-rate-dependent fracture material model, AZ_Frac, in an effort to improve the description of these damage sources. AZ_Frac has the ability to describe continuum fracture processes, and at the same time, to handle pre-existing anisotropic material characteristics. The introduction of fractures within the material generates further anisotropic behavior that is also accounted for within the model. The material model has been calibrated to a granitic medium and has been applied in a number of modeling efforts under the SPE project. In our modeling, we use a 2D, axisymmetric layered earth model of the SPE site consisting of a weathered layer on top of a half-space. We couple the hydrodynamic simulation code with a seismic simulation code and propagate the signals to distances of up to 2 km. The signals are inverted for time-dependent moment tensors using a modified inversion scheme that accounts for multiple sources at different depths. The inversion scheme is evaluated for its resolving power to determine a centroid depth and a moment tensor description of the damage source. The capabilities of the inversion method to retrieve such information from waveforms recorded on three SPE tests conducted to date are also being assessed.

Experimental validation of the influence of white matter anisotropy on the intracranial EEG forward solution.

PubMed

Bangera, Nitin B; Schomer, Donald L; Dehghani, Nima; Ulbert, Istvan; Cash, Sydney; Papavasiliou, Steve; Eisenberg, Solomon R; Dale, Anders M; Halgren, Eric

2010-12-01

Forward solutions with different levels of complexity are employed for localization of current generators, which are responsible for the electric and magnetic fields measured from the human brain. The influence of brain anisotropy on the forward solution is poorly understood. The goal of this study is to validate an anisotropic model for the intracranial electric forward solution by comparing with the directly measured 'gold standard'. Dipolar sources are created at known locations in the brain and intracranial electroencephalogram (EEG) is recorded simultaneously. Isotropic models with increasing level of complexity are generated along with anisotropic models based on Diffusion tensor imaging (DTI). A Finite Element Method based forward solution is calculated and validated using the measured data. Major findings are (1) An anisotropic model with a linear scaling between the eigenvalues of the electrical conductivity tensor and water self-diffusion tensor in brain tissue is validated. The greatest improvement was obtained when the stimulation site is close to a region of high anisotropy. The model with a global anisotropic ratio of 10:1 between the eigenvalues (parallel: tangential to the fiber direction) has the worst performance of all the anisotropic models. (2) Inclusion of cerebrospinal fluid as well as brain anisotropy in the forward model is necessary for an accurate description of the electric field inside the skull. The results indicate that an anisotropic model based on the DTI can be constructed non-invasively and shows an improved performance when compared to the isotropic models for the calculation of the intracranial EEG forward solution.

Tensor Factorization for Low-Rank Tensor Completion.

PubMed

Zhou, Pan; Lu, Canyi; Lin, Zhouchen; Zhang, Chao

2018-03-01

Recently, a tensor nuclear norm (TNN) based method was proposed to solve the tensor completion problem, which has achieved state-of-the-art performance on image and video inpainting tasks. However, it requires computing tensor singular value decomposition (t-SVD), which costs much computation and thus cannot efficiently handle tensor data, due to its natural large scale. Motivated by TNN, we propose a novel low-rank tensor factorization method for efficiently solving the 3-way tensor completion problem. Our method preserves the low-rank structure of a tensor by factorizing it into the product of two tensors of smaller sizes. In the optimization process, our method only needs to update two smaller tensors, which can be more efficiently conducted than computing t-SVD. Furthermore, we prove that the proposed alternating minimization algorithm can converge to a Karush-Kuhn-Tucker point. Experimental results on the synthetic data recovery, image and video inpainting tasks clearly demonstrate the superior performance and efficiency of our developed method over state-of-the-arts including the TNN and matricization methods.

Similar Tensor Arrays - A Framework for Storage of Tensor Array Data

NASA Astrophysics Data System (ADS)

Brun, Anders; Martin-Fernandez, Marcos; Acar, Burak; Munoz-Moreno, Emma; Cammoun, Leila; Sigfridsson, Andreas; Sosa-Cabrera, Dario; Svensson, Björn; Herberthson, Magnus; Knutsson, Hans

This chapter describes a framework for storage of tensor array data, useful to describe regularly sampled tensor fields. The main component of the framework, called Similar Tensor Array Core (STAC), is the result of a collaboration between research groups within the SIMILAR network of excellence. It aims to capture the essence of regularly sampled tensor fields using a minimal set of attributes and can therefore be used as a “greatest common divisor” and interface between tensor array processing algorithms. This is potentially useful in applied fields like medical image analysis, in particular in Diffusion Tensor MRI, where misinterpretation of tensor array data is a common source of errors. By promoting a strictly geometric perspective on tensor arrays, with a close resemblance to the terminology used in differential geometry, (STAC) removes ambiguities and guides the user to define all necessary information. In contrast to existing tensor array file formats, it is minimalistic and based on an intrinsic and geometric interpretation of the array itself, without references to other coordinate systems.

Electromagnetic stress tensor for an amorphous metamaterial medium

NASA Astrophysics Data System (ADS)

Wang, Neng; Wang, Shubo; Ng, Jack

2018-03-01

We analytically and numerically investigated the internal optical forces exerted by an electromagnetic wave inside an amorphous metamaterial medium. We derived, by using the principle of virtual work, the Helmholtz stress tensor, which takes into account the electrostriction effect. Several examples of amorphous media are considered, and different electromagnetic stress tensors, such as the Einstein-Laub tensor and Minkowski tensor, are also compared. It is concluded that the Helmholtz stress tensor is the appropriate tensor for such systems.

Achromatic shearing phase sensor for generating images indicative of measure(s) of alignment between segments of a segmented telescope's mirrors

NASA Technical Reports Server (NTRS)

Stahl, H. Philip (Inventor); Walker, Chanda Bartlett (Inventor)

2006-01-01

An achromatic shearing phase sensor generates an image indicative of at least one measure of alignment between two segments of a segmented telescope's mirrors. An optical grating receives at least a portion of irradiance originating at the segmented telescope in the form of a collimated beam and the collimated beam into a plurality of diffraction orders. Focusing optics separate and focus the diffraction orders. Filtering optics then filter the diffraction orders to generate a resultant set of diffraction orders that are modified. Imaging optics combine portions of the resultant set of diffraction orders to generate an interference pattern that is ultimately imaged by an imager.

Generating Models of Surgical Procedures using UMLS Concepts and Multiple Sequence Alignment

PubMed Central

Meng, Frank; D’Avolio, Leonard W.; Chen, Andrew A.; Taira, Ricky K.; Kangarloo, Hooshang

2005-01-01

Surgical procedures can be viewed as a process composed of a sequence of steps performed on, by, or with the patient’s anatomy. This sequence is typically the pattern followed by surgeons when generating surgical report narratives for documenting surgical procedures. This paper describes a methodology for semi-automatically deriving a model of conducted surgeries, utilizing a sequence of derived Unified Medical Language System (UMLS) concepts for representing surgical procedures. A multiple sequence alignment was computed from a collection of such sequences and was used for generating the model. These models have the potential of being useful in a variety of informatics applications such as information retrieval and automatic document generation. PMID:16779094

Tensor Toolbox for MATLAB v. 3.0

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

Kola, Tamara; Bader, Brett W.; Acar Ataman, Evrim NMN

Tensors (also known as multidimensional arrays or N-way arrays) are used in a variety of applications ranging from chemometrics to network analysis. The Tensor Toolbox provides classes for manipulating dense, sparse, and structured tensors using MATLAB's object-oriented features. It also provides algorithms for tensor decomposition and factorization, algorithms for computing tensor eigenvalues, and methods for visualization of results.

Switchable radioactive neutron source device

DOEpatents

Stanford, G.S.; Rhodes, E.A.; Devolpi, A.; Boyar, R.E.

1987-11-06

This invention is a switchable neutron generating apparatus comprised of a pair of plates, the first plate having an alpha emitter section on it and the second plate having a target material portion on it which generates neutrons when its nuclei absorb an alpha particle. In operation, the alpha portion of the first plate is aligned with the neutron portion of the second plate to produce neutrons and brought out of alignment to cease production of neutrons. 3 figs.

Diffusion Tensor Image Registration Using Hybrid Connectivity and Tensor Features

PubMed Central

Wang, Qian; Yap, Pew-Thian; Wu, Guorong; Shen, Dinggang

2014-01-01

Most existing diffusion tensor imaging (DTI) registration methods estimate structural correspondences based on voxelwise matching of tensors. The rich connectivity information that is given by DTI, however, is often neglected. In this article, we propose to integrate complementary information given by connectivity features and tensor features for improved registration accuracy. To utilize connectivity information, we place multiple anchors representing different brain anatomies in the image space, and define the connectivity features for each voxel as the geodesic distances from all anchors to the voxel under consideration. The geodesic distance, which is computed in relation to the tensor field, encapsulates information of brain connectivity. We also extract tensor features for every voxel to reflect the local statistics of tensors in its neighborhood. We then combine both connectivity features and tensor features for registration of tensor images. From the images, landmarks are selected automatically and their correspondences are determined based on their connectivity and tensor feature vectors. The deformation field that deforms one tensor image to the other is iteratively estimated and optimized according to the landmarks and their associated correspondences. Experimental results show that, by using connectivity features and tensor features simultaneously, registration accuracy is increased substantially compared with the cases using either type of features alone. PMID:24293159

Spherical Tensor Calculus for Local Adaptive Filtering

NASA Astrophysics Data System (ADS)

Reisert, Marco; Burkhardt, Hans

In 3D image processing tensors play an important role. While rank-1 and rank-2 tensors are well understood and commonly used, higher rank tensors are rare. This is probably due to their cumbersome rotation behavior which prevents a computationally efficient use. In this chapter we want to introduce the notion of a spherical tensor which is based on the irreducible representations of the 3D rotation group. In fact, any ordinary cartesian tensor can be decomposed into a sum of spherical tensors, while each spherical tensor has a quite simple rotation behavior. We introduce so called tensorial harmonics that provide an orthogonal basis for spherical tensor fields of any rank. It is just a generalization of the well known spherical harmonics. Additionally we propose a spherical derivative which connects spherical tensor fields of different degree by differentiation. Based on the proposed theory we present two applications. We propose an efficient algorithm for dense tensor voting in 3D, which makes use of tensorial harmonics decomposition of the tensor-valued voting field. In this way it is possible to perform tensor voting by linear-combinations of convolutions in an efficient way. Secondly, we propose an anisotropic smoothing filter that uses a local shape and orientation adaptive filter kernel which can be computed efficiently by the use spherical derivatives.

BRST Exactness of Stress-Energy Tensors

NASA Astrophysics Data System (ADS)

Miyata, Hideo; Sugimoto, Hiroshi

BRST commutators in the topological conformal field theories obtained by twisting N=2 theories are evaluated explicitly. By our systematic calculations of the multiple integrals which contain screening operators, the BRST exactness of the twisted stress-energy tensors is deduced for classical simple Lie algebras and general level k. We can see that the paths of integrations do not affect the result, and further, the N=2 coset theories are obtained by deleting two simple roots with Kac-label 1 from the extended Dynkin diagram; in other words, by not performing the integrations over the variables corresponding to the two simple roots of Kac-Moody algebras. It is also shown that a series of N=1 theories are generated in the same way by deleting one simple root with Kac-label 2.

Clustering fossils in solid inflation

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

Akhshik, Mohammad, E-mail: m.akhshik@ipm.ir

In solid inflation the single field non-Gaussianity consistency condition is violated. As a result, the long tenor perturbation induces observable clustering fossils in the form of quadrupole anisotropy in large scale structure power spectrum. In this work we revisit the bispectrum analysis for the scalar-scalar-scalar and tensor-scalar-scalar bispectrum for the general parameter space of solid. We consider the parameter space of the model in which the level of non-Gaussianity generated is consistent with the Planck constraints. Specializing to this allowed range of model parameter we calculate the quadrupole anisotropy induced from the long tensor perturbations on the power spectrum ofmore » the scalar perturbations. We argue that the imprints of clustering fossil from primordial gravitational waves on large scale structures can be detected from the future galaxy surveys.« less

Ergodic actions of SμU(2) on C∗-algebras from II1 subfactors

NASA Astrophysics Data System (ADS)

Pinzari, Claudia; Roberts, John E.

2010-03-01

To a proper inclusion N⊂M of II factors of finite Jones index [M:N], we associate an ergodic C∗-action of the quantum group SμU(2) (or more generally of certain groups Ao(F)). The higher relative commutant N'∩M can be identified with the spectral space of the rth tensor power u of the defining representation of the quantum group. The index and the deformation parameter are related by -1≤μ<0 and [M:N]=|μ+μ-1|. This ergodic action may be thought of as a virtual subgroup of SμU(2) in the sense of Mackey arising from the tensor category generated by the N-bimodule NMN. μ is negative as NMN is a real bimodule.

HIA: a genome mapper using hybrid index-based sequence alignment.

PubMed

Choi, Jongpill; Park, Kiejung; Cho, Seong Beom; Chung, Myungguen

2015-01-01

A number of alignment tools have been developed to align sequencing reads to the human reference genome. The scale of information from next-generation sequencing (NGS) experiments, however, is increasing rapidly. Recent studies based on NGS technology have routinely produced exome or whole-genome sequences from several hundreds or thousands of samples. To accommodate the increasing need of analyzing very large NGS data sets, it is necessary to develop faster, more sensitive and accurate mapping tools. HIA uses two indices, a hash table index and a suffix array index. The hash table performs direct lookup of a q-gram, and the suffix array performs very fast lookup of variable-length strings by exploiting binary search. We observed that combining hash table and suffix array (hybrid index) is much faster than the suffix array method for finding a substring in the reference sequence. Here, we defined the matching region (MR) is a longest common substring between a reference and a read. And, we also defined the candidate alignment regions (CARs) as a list of MRs that is close to each other. The hybrid index is used to find candidate alignment regions (CARs) between a reference and a read. We found that aligning only the unmatched regions in the CAR is much faster than aligning the whole CAR. In benchmark analysis, HIA outperformed in mapping speed compared with the other aligners, without significant loss of mapping accuracy. Our experiments show that the hybrid of hash table and suffix array is useful in terms of speed for mapping NGS sequencing reads to the human reference genome sequence. In conclusion, our tool is appropriate for aligning massive data sets generated by NGS sequencing.

On the evolution of the invariants of the velocity gradient tensor in single-square-grid-generated turbulence

NASA Astrophysics Data System (ADS)

Zhou, Yi; Nagata, Koji; Sakai, Yasuhiko; Ito, Yasumasa; Hayase, Toshiyuki

2015-07-01

Direct numerical simulations were performed to investigate the topological evolution of turbulence generated by a single square grid. Immediately behind the single square grid (i.e., in the irrotational dissipation region), the conditional mean trajectories (CMTs) of R and Q are distinctly different from those in homogeneous isotropic turbulence (HIT), where R and Q are the third and second invariants, respectively, of the velocity gradient tensor. In this region, the non-local influence of the pressure Hessian is dominant, which causes irrotational viscous dissipation. The anisotropic part of the pressure Hessian may be responsible for the irrotational viscous dissipation found at the turbulent/nonturbulent interface in turbulent jets [C. B. da Silva and J. C. F. Pereira, "Invariants of the velocity-gradient, rate-of-strain, and rate-of-rotation tensors across the turbulent/nonturbulent interface in jets," Phys. Fluids 20, 055101 (2008) and Watanabe et al., "Vortex stretching and compression near the turbulent/non-turbulent interface in a planar jet," J. Fluid Mech. 758, 754 (2014)]. In the transition region, the CMTs of R and Q gradually acquire an evolution pattern similar to that in HIT. The expansion of the (R, Q) map at Q > 0 is associated with the effects of the restricted Euler term. Finally, in the fully turbulent region, the CMTs of R and Q demonstrate a clockwise evolution toward a point close to the origin. However, the cyclic spiraling seen in HIT is not found. The lack of the cyclic evolution may be attributed to the considerably large effect of the viscous term owing to the relatively small local Reynolds number. On average, the combined influences of the restricted Euler term and anisotropic part of the pressure Hessian contribute to the generation of small-scale motions, and the viscous term tends to remove small-scale motions.

Desktop aligner for fabrication of multilayer microfluidic devices.

PubMed

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-07-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm(-1). To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices.

Desktop aligner for fabrication of multilayer microfluidic devices

PubMed Central

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-01-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm−1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices. PMID:26233409

Application of discrete Fourier inter-coefficient difference for assessing genetic sequence similarity.

PubMed

King, Brian R; Aburdene, Maurice; Thompson, Alex; Warres, Zach

2014-01-01

Digital signal processing (DSP) techniques for biological sequence analysis continue to grow in popularity due to the inherent digital nature of these sequences. DSP methods have demonstrated early success for detection of coding regions in a gene. Recently, these methods are being used to establish DNA gene similarity. We present the inter-coefficient difference (ICD) transformation, a novel extension of the discrete Fourier transformation, which can be applied to any DNA sequence. The ICD method is a mathematical, alignment-free DNA comparison method that generates a genetic signature for any DNA sequence that is used to generate relative measures of similarity among DNA sequences. We demonstrate our method on a set of insulin genes obtained from an evolutionarily wide range of species, and on a set of avian influenza viral sequences, which represents a set of highly similar sequences. We compare phylogenetic trees generated using our technique against trees generated using traditional alignment techniques for similarity and demonstrate that the ICD method produces a highly accurate tree without requiring an alignment prior to establishing sequence similarity.

Precision alignment and calibration of optical systems using computer generated holograms

NASA Astrophysics Data System (ADS)

Coyle, Laura Elizabeth

As techniques for manufacturing and metrology advance, optical systems are being designed with more complexity than ever before. Given these prescriptions, alignment and calibration can be a limiting factor in their final performance. Computer generated holograms (CGHs) have several unique properties that make them powerful tools for meeting these demanding tolerances. This work will present three novel methods for alignment and calibration of optical systems using computer generated holograms. Alignment methods using CGHs require that the optical wavefront created by the CGH be related to a mechanical datum to locate it space. An overview of existing methods is provided as background, then two new alignment methods are discussed in detail. In the first method, the CGH contact Ball Alignment Tool (CBAT) is used to align a ball or sphere mounted retroreflector (SMR) to a Fresnel zone plate pattern with micron level accuracy. The ball is bonded directly onto the CGH substrate and provides permanent, accurate registration between the optical wavefront and a mechanical reference to locate the CGH in space. A prototype CBAT was built and used to align and bond an SMR to a CGH. In the second method, CGH references are used to align axi-symmetric optics in four degrees of freedom with low uncertainty and real time feedback. The CGHs create simultaneous 3D optical references where the zero order reflection sets tilt and the first diffracted order sets centration. The flexibility of the CGH design can be used to accommodate a wide variety of optical systems and maximize sensitivity to misalignments. A 2-CGH prototype system was aligned multiplied times and the alignment uncertainty was quantified and compared to an error model. Finally, an enhanced calibration method is presented. It uses multiple perturbed measurements of a master sphere to improve the calibration of CGH-based Fizeau interferometers ultimately measuring aspheric test surfaces. The improvement in the calibration is a function of the interferometer error and the aspheric departure of the desired test surface. This calibration is most effective at reducing coma and trefoil from figure error or misalignments of the interferometer components. The enhanced calibration can reduce overall measurement uncertainty or allow the budgeted error contribution from another source to be increased. A single set of sphere measurements can be used to calculate calibration maps for closely related aspheres, including segmented primary mirrors for telescopes. A parametric model is developed and compared to the simulated calibration of a case study interferometer.

Molecular design for nonpolar chiral-axial quadratic nonlinear optics

NASA Astrophysics Data System (ADS)

Wiggers, Gregory A.

In this thesis the hyperpolarizability of various multi-dimensional molecules is studied theoretically/computationally, with particular focus on the second-rank Kleinman-disallowed (KD) component of the hyperpolarizability. This component, which transforms as a second-rank traceless symmetric tensor, could be utilized in certain chiral-axial molecular alignment schemes to produce a bulk response. Nonpolar chiral-axial systems have been proposed in contrast to polar media, which utilize the vector component of the molecular hyperpolarizability and require parallel alignment of the molecular dipoles. Such parallel alignment of dipoles must be "frozen in" in order to overcome the natural tendency for dipoles to align anti-parallel. This limits the density of chromophores that can be loaded into a polar material. Nonpolar materials do not have such limits in theory. The two geometric classes of molecules that can most easily be incorporated into nonpolar chiral-uniaxial materials are propeller-shaped (C3 or D3 symmetry) and Λ-shaped (C2v symmetry). This work describes efforts to design molecules within these classes that would be suitable for bulk NLO materials. The sum-over-states (SOS) expression is used to model the molecular hyperpolarizability, and quantum chemical calculations, along with linear absorption data (when available) provide the necessary parameters to evaluate truncated forms of the SOS expression. A host of chemical and geometric modifications will be considered in order to elucidate important structure/function relationships. Also, the SOS model will be tested in some cases when experimental measurements (via Kleinman-disallowed hyper-Rayleigh scattering) are available. While a majority of this work focuses on multi-dimensional molecules, a small section deals with the question of optimizing the hyperpolarizability of a one-dimensional system. It is suggested that the recently-proposed idea of "modulated conjugation" as a means for improving intrinsic molecular hyperpolarizability is based on subtle misinterpretations of computational results. Even so, the concept of modulated conjugation may lead to improved hyperpolarizabilities and possible reasons are discussed.

Nondestructive Complete Mechanical Characterization of Zinc Blende and Wurtzite GaAs Nanowires Using Time-Resolved Pump-Probe Spectroscopy.

PubMed

Mante, Pierre-Adrien; Lehmann, Sebastian; Anttu, Nicklas; Dick, Kimberly A; Yartsev, Arkady

2016-08-10

We have developed and demonstrated an experimental method, based on the picosecond acoustics technique, to perform nondestructive complete mechanical characterization of nanowires, that is, the determination of the complete elasticity tensor. By means of femtosecond pump-probe spectroscopy, coherent acoustic phonons were generated in an ensemble of nanowires and their dynamics was resolved. Specific phonon modes were identified and the detection mechanism was addressed via wavelength dependent experiments. We calculated the exact phonon dispersion relation of the nanowires by fitting the experimentally observed frequencies, thus allowing the extraction of the complete elasticity tensor. The elasticity tensor and the nanowire diameter were determined for zinc blende GaAs nanowires and were found to be in a good agreement with literature data and independent measurements. Finally, we have applied this technique to characterize wurtzite GaAs nanowires, a metastable phase in bulk, for which no experimental values of elastic constants are currently available. Our results agree well with previous first principle calculations. The proposed approach to the complete and nondestructive mechanical characterization of nanowires will allow the efficient mechanical study of new crystal phases emerging in nanostructures, as well as size-dependent properties of nanostructured materials.

Accurate estimation of short read mapping quality for next-generation genome sequencing

PubMed Central

Ruffalo, Matthew; Koyutürk, Mehmet; Ray, Soumya; LaFramboise, Thomas

2012-01-01

Motivation: Several software tools specialize in the alignment of short next-generation sequencing reads to a reference sequence. Some of these tools report a mapping quality score for each alignment—in principle, this quality score tells researchers the likelihood that the alignment is correct. However, the reported mapping quality often correlates weakly with actual accuracy and the qualities of many mappings are underestimated, encouraging the researchers to discard correct mappings. Further, these low-quality mappings tend to correlate with variations in the genome (both single nucleotide and structural), and such mappings are important in accurately identifying genomic variants. Approach: We develop a machine learning tool, LoQuM (LOgistic regression tool for calibrating the Quality of short read mappings, to assign reliable mapping quality scores to mappings of Illumina reads returned by any alignment tool. LoQuM uses statistics on the read (base quality scores reported by the sequencer) and the alignment (number of matches, mismatches and deletions, mapping quality score returned by the alignment tool, if available, and number of mappings) as features for classification and uses simulated reads to learn a logistic regression model that relates these features to actual mapping quality. Results: We test the predictions of LoQuM on an independent dataset generated by the ART short read simulation software and observe that LoQuM can ‘resurrect’ many mappings that are assigned zero quality scores by the alignment tools and are therefore likely to be discarded by researchers. We also observe that the recalibration of mapping quality scores greatly enhances the precision of called single nucleotide polymorphisms. Availability: LoQuM is available as open source at http://compbio.case.edu/loqum/. Contact: matthew.ruffalo@case.edu. PMID:22962451

Alternatives for jet engine control

NASA Technical Reports Server (NTRS)

Sain, M. K.

1983-01-01

Tensor model order reduction, recursive tensor model identification, input design for tensor model identification, software development for nonlinear feedback control laws based upon tensors, and development of the CATNAP software package for tensor modeling, identification and simulation were studied. The last of these are discussed.

Patient-tailored multimodal neuroimaging, visualization and quantification of human intra-cerebral hemorrhage

NASA Astrophysics Data System (ADS)

Goh, Sheng-Yang M.; Irimia, Andrei; Vespa, Paul M.; Van Horn, John D.

2016-03-01

In traumatic brain injury (TBI) and intracerebral hemorrhage (ICH), the heterogeneity of lesion sizes and types necessitates a variety of imaging modalities to acquire a comprehensive perspective on injury extent. Although it is advantageous to combine imaging modalities and to leverage their complementary benefits, there are difficulties in integrating information across imaging types. Thus, it is important that efforts be dedicated to the creation and sustained refinement of resources for multimodal data integration. Here, we propose a novel approach to the integration of neuroimaging data acquired from human patients with TBI/ICH using various modalities; we also demonstrate the integrated use of multimodal magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI) data for TBI analysis based on both visual observations and quantitative metrics. 3D models of healthy-appearing tissues and TBIrelated pathology are generated, both of which are derived from multimodal imaging data. MRI volumes acquired using FLAIR, SWI, and T2 GRE are used to segment pathology. Healthy tissues are segmented using user-supervised tools, and results are visualized using a novel graphical approach called a `connectogram', where brain connectivity information is depicted within a circle of radially aligned elements. Inter-region connectivity and its strength are represented by links of variable opacities drawn between regions, where opacity reflects the percentage longitudinal change in brain connectivity density. Our method for integrating, analyzing and visualizing structural brain changes due to TBI and ICH can promote knowledge extraction and enhance the understanding of mechanisms underlying recovery.

Induced Seismicity at the UK "Hot Dry Rock" Test Site for Geothermal Energy Production

NASA Astrophysics Data System (ADS)

Li, Xun; Main, Ian; Jupe, Andrew

2018-03-01

In enhanced geothermal systems (EGS), fluid is injected at high pressure in order to stimulate fracturing and/or fluid flow through otherwise relatively impermeable underlying hot rocks to generate power and/or heat. The stimulation induces micro-earthquakes whose precise triggering mechanism and relationship to new and pre-existing fracture networks are still the subject of some debate. Here we analyse the dataset for induced micro-earthquakes at the UK "hot dry rock" experimental geothermal site (Rosemanowes, Cornwall). We quantify the evolution of several metrics used to characterise induced seismicity, including the seismic strain partition factor and the "seismogenic index". The results show a low strain partition factor of 0.01% and a low seismogenenic index indicating that aseismic processes dominate. We also analyse the spatio-temporal distribution of hypocentres, using simple models for the evolution of hydraulic diffusivity by (a) isotropic and (b) anisotropic pore-pressure relaxation. The principal axes of the diffusivity or permeability tensor inferred from the spatial distribution of earthquake foci are aligned parallel to the present-day stress field, although the maximum permeability is vertical, whereas the maximum principal stress is horizontal. Our results are consistent with a triggering mechanism that involves (a) seismic shear slip along optimally-oriented pre-existing fractures, (b) a large component of aseismic slip with creep (c) activation of tensile fractures as hydraulic conduits created by both the present-day stress field and by the induced shear slip, both exploiting pre-existing joint sets exposed in borehole data.

Pair creation, motion, and annihilation of topological defects in two-dimensional nematic liquid crystals

NASA Astrophysics Data System (ADS)

Cortese, Dario; Eggers, Jens; Liverpool, Tanniemola B.

2018-02-01

We present a framework for the study of disclinations in two-dimensional active nematic liquid crystals and topological defects in general. The order tensor formalism is used to calculate exact multiparticle solutions of the linearized static equations inside a planar uniformly aligned state so that the total charge has to vanish. Topological charge conservation then requires that there is always an equal number of q =1 /2 and q =-1 /2 charges. Starting from a set of hydrodynamic equations, we derive a low-dimensional dynamical system for the parameters of the static solutions, which describes the motion of a half-disclination pair or of several pairs. Within this formalism, we model defect production and annihilation, as observed in experiments. Our dynamics also provide an estimate for the critical density at which production and annihilation rates are balanced.

Three-dimensional smoothed particle hydrodynamics simulation for injection molding flow of short fiber-reinforced polymer composites

NASA Astrophysics Data System (ADS)

He, Liping; Lu, Gang; Chen, Dachuan; Li, Wenjun; Lu, Chunsheng

2017-07-01

This paper investigates the three-dimensional (3D) injection molding flow of short fiber-reinforced polymer composites using a smoothed particle hydrodynamics (SPH) simulation method. The polymer melt was modeled as a power law fluid and the fibers were considered as rigid cylindrical bodies. The filling details and fiber orientation in the injection-molding process were studied. The results indicated that the SPH method could effectively predict the order of filling, fiber accumulation, and heterogeneous distribution of fibers. The SPH simulation also showed that fibers were mainly aligned to the flow direction in the skin layer and inclined to the flow direction in the core layer. Additionally, the fiber-orientation state in the simulation was quantitatively analyzed and found to be consistent with the results calculated by conventional tensor methods.

Video repairing under variable illumination using cyclic motions.

PubMed

Jia, Jiaya; Tai, Yu-Wing; Wu, Tai-Pang; Tang, Chi-Keung

2006-05-01

This paper presents a complete system capable of synthesizing a large number of pixels that are missing due to occlusion or damage in an uncalibrated input video. These missing pixels may correspond to the static background or cyclic motions of the captured scene. Our system employs user-assisted video layer segmentation, while the main processing in video repair is fully automatic. The input video is first decomposed into the color and illumination videos. The necessary temporal consistency is maintained by tensor voting in the spatio-temporal domain. Missing colors and illumination of the background are synthesized by applying image repairing. Finally, the occluded motions are inferred by spatio-temporal alignment of collected samples at multiple scales. We experimented on our system with some difficult examples with variable illumination, where the capturing camera can be stationary or in motion.

Multiple sequence alignment in HTML: colored, possibly hyperlinked, compact representations.

PubMed

Campagne, F; Maigret, B

1998-02-01

Protein sequence alignments are widely used in protein structure prediction, protein engineering, modeling of proteins, etc. This type of representation is useful at different stages of scientific activity: looking at previous results, working on a research project, and presenting the results. There is a need to make it available through a network (intranet or WWW), in a way that allows biologists, chemists, and noncomputer specialists to look at the data and carry on research--possibly in a collaborative research. Previous methods (text-based, Java-based) are reported and their advantages are discussed. We have developed two novel approaches to represent the alignments as colored, hyper-linked HTML pages. The first method creates an HTML page that uses efficiently the image cache mechanism of a WWW browser, thereby allowing the user to browse different alignments without waiting for the images to be loaded through the network, but only for the first viewed alignment. The generated pages can be browsed with any HTML2.0-compliant browser. The second method that we propose uses W3C-CSS1-style sheets to render alignments. This new method generates pages that require recent browsers to be viewed. We implemented these methods in the Viseur program and made a WWW service available that allows a user to convert an MSF alignment file in HTML for WWW publishing. The latter service is available at http:@www.lctn.u-nancy.fr/viseur/services.htm l.

GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D

NASA Astrophysics Data System (ADS)

Richmond, Nicola J.; Abrams, Charlene A.; Wolohan, Philippa R. N.; Abrahamian, Edmond; Willett, Peter; Clark, Robert D.

2006-09-01

Alignment of multiple ligands based on shared pharmacophoric and pharmacosteric features is a long-recognized challenge in drug discovery and development. This is particularly true when the spatial overlap between structures is incomplete, in which case no good template molecule is likely to exist. Pair-wise rigid ligand alignment based on linear assignment (the LAMDA algorithm) has the potential to address this problem (Richmond et al. in J Mol Graph Model 23:199-209, 2004). Here we present the version of LAMDA embodied in the GALAHAD program, which carries out multi-way alignments by iterative construction of hypermolecules that retain the aggregate as well as the individual attributes of the ligands. We have also generalized the cost function from being purely atom-based to being one that operates on ionic, hydrogen bonding, hydrophobic and steric features. Finally, we have added the ability to generate useful partial-match 3D search queries from the hypermolecules obtained. By running frozen conformations through the GALAHAD program, one can utilize the extended version of LAMDA to generate pharmacophores and pharmacosteres that agree well with crystal structure alignments for a range of literature datasets, with minor adjustments of the default parameters generating even better models. Allowing for inclusion of partial match constraints in the queries yields pharmacophores that are consistently a superset of full-match pharmacophores identified in previous analyses, with the additional features representing points of potentially beneficial interaction with the target.

Visualizing second order tensor fields with hyperstreamlines

NASA Technical Reports Server (NTRS)

Delmarcelle, Thierry; Hesselink, Lambertus

1993-01-01

Hyperstreamlines are a generalization to second order tensor fields of the conventional streamlines used in vector field visualization. As opposed to point icons commonly used in visualizing tensor fields, hyperstreamlines form a continuous representation of the complete tensor information along a three-dimensional path. This technique is useful in visulaizing both symmetric and unsymmetric three-dimensional tensor data. Several examples of tensor field visualization in solid materials and fluid flows are provided.

Rapid Quantification of 3D Collagen Fiber Alignment and Fiber Intersection Correlations with High Sensitivity

PubMed Central

Sun, Meng; Bloom, Alexander B.; Zaman, Muhammad H.

2015-01-01

Metastatic cancers aggressively reorganize collagen in their microenvironment. For example, radially orientated collagen fibers have been observed surrounding tumor cell clusters in vivo. The degree of fiber alignment, as a consequence of this remodeling, has often been difficult to quantify. In this paper, we present an easy to implement algorithm for accurate detection of collagen fiber orientation in a rapid pixel-wise manner. This algorithm quantifies the alignment of both computer generated and actual collagen fiber networks of varying degrees of alignment within 5°°. We also present an alternative easy method to calculate the alignment index directly from the standard deviation of fiber orientation. Using this quantitative method for determining collagen alignment, we demonstrate that the number of collagen fiber intersections has a negative correlation with the degree of fiber alignment. This decrease in intersections of aligned fibers could explain why cells move more rapidly along aligned fibers than unaligned fibers, as previously reported. Overall, our paper provides an easier, more quantitative and quicker way to quantify fiber orientation and alignment, and presents a platform in studying effects of matrix and cellular properties on fiber alignment in complex 3D environments. PMID:26158674

ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos.

PubMed

Roca, Alberto I

2014-01-01

The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family. The JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images. The ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org.

Magnetospheric discontinuities and interfaces as roots of discrete auroral arcs: modeling and comparison with in-situ data

NASA Astrophysics Data System (ADS)

Echim, M.; Maggiolo, R.; de Keyser, J. M.; Roth, M. A.

2009-12-01

We discuss the quasi-stationary coupling between magnetospheric sharp plasma interfaces and discrete auroral arcs. The magnetospheric generator is described by a Vlasov equilibrium similar to the kinetic models of tangential discontinuities. It provides the self-consistent profile of the magnetospheric convergent electric field, Φm. A kinetic current-voltage relationship gives the field-aligned current density flowing into and out of the ionosphere as a function of the potential difference between the magnetospheric generator and the ionospheric load. The electric potential in the ionosphere, Φi, is computed from the current continuity equation taking into account the variation of the Pedersen conductance, ΣP, with the energy flux of the precipitating magnetospheric electrons (ɛem). We discuss results obtained for the interface between the Plasma Sheet Boundary Layer (PSBL) and the lobes and respectively for the inner edge of the Low Latitude Boundary Layer (LLBL). This type of interfaces provides a field-aligned potential drop, ΔΦ=Φi-Φm, of the order of several kilovolts and field-aligned current densities, j||, of the order of tens of μA/m2 . The precipitating particles are confined in thin regions whose thickness is of the order of several kilometers at 200 km altitude. We show that visible auroral arcs form when the velocity shear across the generator magnetospheric plasma interface is above a threshold depending also on the kinetic properties of the generator. Brighter arcs forms for larger velocity shear in the magnetospheric generator. The field-aligned potential drop tends to decrease when the density gradient across the interface increases. Conjugated observations on April 28, 2001 by Cluster and DMSP-F14 give us the opportunity to validate the model with data gathered simultaneously below and above the acceleration region. The magnetospheric module of the coupling model provides a good estimation of the plasma parameters measured by Cluster across the magnetospheric interface: the electric potential, the plasma density and the parallel flux of downgoing electrons and upgoing Oxygen ions. The results of the ionospheric module of the model are in good agreement with the DMSP-F14 measurements of the field-aligned current density, the flux of precipitating energy and the accelerating field-aligned potential drop. A synthetic electron energy spectrum derived from the computed field-aligned potential drop retrieves the spatial scale and spectral width of the inverted-V event observed by DMSP-F14.

Cortico-Cortical, Cortico-Striatal, and Cortico-Thalamic White Matter Fiber Tracts Generated in the Macaque Brain via Dynamic Programming

PubMed Central

Lal, Rakesh M.; An, Michael; Poynton, Clare B.; Li, Muwei; Jiang, Hangyi; Oishi, Kenichi; Selemon, Lynn D.; Mori, Susumu; Miller, Michael I.

2013-01-01

Abstract Probabilistic methods have the potential to generate multiple and complex white matter fiber tracts in diffusion tensor imaging (DTI). Here, a method based on dynamic programming (DP) is introduced to reconstruct fibers pathways whose complex anatomical structures cannot be resolved beyond the resolution of standard DTI data. DP is based on optimizing a sequentially additive cost function derived from a Gaussian diffusion model whose covariance is defined by the diffusion tensor. DP is used to determine the optimal path between initial and terminal nodes by efficiently searching over all paths, connecting the nodes, and choosing the path in which the total probability is maximized. An ex vivo high-resolution scan of a macaque hemi-brain is used to demonstrate the advantages and limitations of DP. DP can generate fiber bundles between distant cortical areas (superior longitudinal fasciculi, arcuate fasciculus, uncinate fasciculus, and fronto-occipital fasciculus), neighboring cortical areas (dorsal and ventral banks of the principal sulcus), as well as cortical projections to the hippocampal formation (cingulum bundle), neostriatum (motor cortical projections to the putamen), thalamus (subcortical bundle), and hippocampal formation projections to the mammillary bodies via the fornix. Validation is established either by comparison with in vivo intracellular transport of horseradish peroxidase in another macaque monkey or by comparison with atlases. DP is able to generate known pathways, including crossing and kissing tracts. Thus, DP has the potential to enhance neuroimaging studies of cortical connectivity. PMID:23879573

Specialized CFD Grid Generation Methods for Near-Field Sonic Boom Prediction

NASA Technical Reports Server (NTRS)

Park, Michael A.; Campbell, Richard L.; Elmiligui, Alaa; Cliff, Susan E.; Nayani, Sudheer N.

2014-01-01

Ongoing interest in analysis and design of low sonic boom supersonic transports re- quires accurate and ecient Computational Fluid Dynamics (CFD) tools. Specialized grid generation techniques are employed to predict near- eld acoustic signatures of these con- gurations. A fundamental examination of grid properties is performed including grid alignment with ow characteristics and element type. The issues a ecting the robustness of cylindrical surface extrusion are illustrated. This study will compare three methods in the extrusion family of grid generation methods that produce grids aligned with the freestream Mach angle. These methods are applied to con gurations from the First AIAA Sonic Boom Prediction Workshop.

Centroid stabilization in alignment of FOA corner cube: designing of a matched filter

NASA Astrophysics Data System (ADS)

Awwal, Abdul; Wilhelmsen, Karl; Roberts, Randy; Leach, Richard; Miller Kamm, Victoria; Ngo, Tony; Lowe-Webb, Roger

2015-02-01

The current automation of image-based alignment of NIF high energy laser beams is providing the capability of executing multiple target shots per day. An important aspect of performing multiple shots in a day is to reduce additional time spent aligning specific beams due to perturbations in those beam images. One such alignment is beam centration through the second and third harmonic generating crystals in the final optics assembly (FOA), which employs two retro-reflecting corner cubes to represent the beam center. The FOA houses the frequency conversion crystals for third harmonic generation as the beams enters the target chamber. Beam-to-beam variations and systematic beam changes over time in the FOA corner-cube images can lead to a reduction in accuracy as well as increased convergence durations for the template based centroid detector. This work presents a systematic approach of maintaining FOA corner cube centroid templates so that stable position estimation is applied thereby leading to fast convergence of alignment control loops. In the matched filtering approach, a template is designed based on most recent images taken in the last 60 days. The results show that new filter reduces the divergence of the position estimation of FOA images.

Generation of Stable Co-Cultures of Vascular Cells in a Honeycomb Alginate Scaffold

PubMed Central

Yamamoto, Masaya; James, Daylon; Li, Hui; Butler, Jason; Rafii, Shahin

2010-01-01

Scaffold-guided vascular tissue engineering has been investigated as a means to generate functional and transplantable vascular tissue grafts that increase the efficacy of cell-based therapeutic strategies in regenerative medicine. In this study, we employed confocal microscopy and three-dimensional reconstruction to assess the engraftment and growth potential of vascular cells within an alginate scaffold with aligned pores. We fabricated honeycomb alginate scaffolds with aligned pores, whose surface was immobilized with fibronectin and subsequently coated with matrigel. Endothelial cells were seeded into aligned pore scaffolds in the presence and absence of human smooth muscle cells. We showed that endothelial cells seeded into alginate scaffolds attach on the surface of aligned pores in vitro, giving rise to stable co-cultures of vascular cells. Moreover, the three-dimensional alginate depots containing the cells were exposed to laminar flow in order to recapitulate physiological shear stress found in the vasculature in vivo. After the flow exposure, the scaffold remained intact and some cells remained adherent to the scaffold and aligned in the flow direction. These studies demonstrate that alginate scaffolds provide a suitable matrix for establishing durable angiogenic modules that may ultimately enhance organ revascularization. PMID:19705957

Ordered rate constitutive theories for thermoviscoelastic solids with memory in Lagrangian description using Gibbs potential

NASA Astrophysics Data System (ADS)

Surana, K. S.; Reddy, J. N.; Nunez, Daniel

2015-11-01

This paper presents ordered rate constitutive theories of orders m and n, i.e., ( m, n) for finite deformation of homogeneous, isotropic, compressible and incompressible thermoviscoelastic solids with memory in Lagrangian description using entropy inequality in Gibbs potential Ψ as an alternate approach of deriving constitutive theories using entropy inequality in terms of Helmholtz free energy density Φ. Second Piola-Kirchhoff stress σ [0] and Green's strain tensor ɛ [0] are used as conjugate pair. We consider Ψ, heat vector q, entropy density η and rates of upto orders m and n of σ [0] and ɛ [0], i.e., σ [ i]; i = 0, 1, . . . , m and ɛ [ j]; j = 0, 1, . . . , n. We choose Ψ, ɛ [ n], q and η as dependent variables in the constitutive theories with ɛ [ j]; j = 0, 1, . . . , n - 1, σ [ i]; i = 0, 1, . . . , m, temperature gradient g and temperature θ as their argument tensors. Rationale for this choice is explained in the paper. Entropy inequality, decomposition of σ [0] into equilibrium and deviatoric stresses, the conditions resulting from entropy inequality and the theory of generators and invariants are used in the derivations of ordered rate constitutive theories of orders m and n in stress and strain tensors. Constitutive theories for the heat vector q (of up to orders m and n - 1) that are consistent (in terms of the argument tensors) with the constitutive theories for ɛ [ n] (of up to orders m and n) are also derived. Many simplified forms of the rate theories of orders ( m, n) are presented. Material coefficients are derived by considering Taylor series expansions of the coefficients in the linear combinations representing ɛ [ n] and q using the combined generators of the argument tensors about a known configuration {{\\underline{\\varOmega}}} in the combined invariants of the argument tensors and temperature. It is shown that the rate constitutive theories of order one ( m = 1, n = 1) when further simplified result in constitutive theories that resemble currently used theories but are in fact different. The solid continua characterized by these theories have mechanisms of elasticity, dissipation and memory, i.e., relaxation behavior or rheology. Fourier heat conduction law is shown to be an over simplified case of the rate theory of order one ( m = 1, n = 1) for q. The paper establishes when there is equivalence between the constitutive theories derived here using Ψ and those presented in reference Surana et al. (Acta Mech. doi:10.1007/s00707-014-1173-6, 2014) that are derived using Helmholtz free energy density Φ. The fundamental differences between the two constitutive theories in terms of physics and their explicit forms using Φ and Ψ are difficult to distinguish from the ordered theories of orders ( m, n) due to complexity of expressions. However, by choosing lower ordered theories, the difference between the two approaches can be clearly seen.

Periodically poled potassium niobate for second-harmonic generation at 463 nm.

PubMed

Meyn, J P; Klein, M E; Woll, D; Wallenstein, R; Rytz, D

1999-08-15

We report on the fabrication and characterization of quasi-phase-matched potassium niobate crystals for second-harmonic generation. Periodic 30-mum -pitch antiparallel ferroelectric domains are fabricated by means of poling in an electrical field. Both birefrigence and periodic phase shift of the generated second harmonic contribute to phase matching when the d(31) nonlinear optical tensor element is used. 3.8 mW of second-harmonic radiation at 463 nm is generated by frequency doubling of the output of master-oscillator power-amplifier diode laser in a 5-mm-long crystal. The measured effective nonlinear coefficient is 3.7pm/V. The measured spectral acceptance bandwidth of 0.25 nm corresponds to the theoretical value.

Antisymmetric tensor generalizations of affine vector fields.

PubMed

Houri, Tsuyoshi; Morisawa, Yoshiyuki; Tomoda, Kentaro

2016-02-01

Tensor generalizations of affine vector fields called symmetric and antisymmetric affine tensor fields are discussed as symmetry of spacetimes. We review the properties of the symmetric ones, which have been studied in earlier works, and investigate the properties of the antisymmetric ones, which are the main theme in this paper. It is shown that antisymmetric affine tensor fields are closely related to one-lower-rank antisymmetric tensor fields which are parallelly transported along geodesics. It is also shown that the number of linear independent rank- p antisymmetric affine tensor fields in n -dimensions is bounded by ( n + 1)!/ p !( n - p )!. We also derive the integrability conditions for antisymmetric affine tensor fields. Using the integrability conditions, we discuss the existence of antisymmetric affine tensor fields on various spacetimes.

Real-time object recognition in multidimensional images based on joined extended structural tensor and higher-order tensor decomposition methods

NASA Astrophysics Data System (ADS)

Cyganek, Boguslaw; Smolka, Bogdan

2015-02-01

In this paper a system for real-time recognition of objects in multidimensional video signals is proposed. Object recognition is done by pattern projection into the tensor subspaces obtained from the factorization of the signal tensors representing the input signal. However, instead of taking only the intensity signal the novelty of this paper is first to build the Extended Structural Tensor representation from the intensity signal that conveys information on signal intensities, as well as on higher-order statistics of the input signals. This way the higher-order input pattern tensors are built from the training samples. Then, the tensor subspaces are built based on the Higher-Order Singular Value Decomposition of the prototype pattern tensors. Finally, recognition relies on measurements of the distance of a test pattern projected into the tensor subspaces obtained from the training tensors. Due to high-dimensionality of the input data, tensor based methods require high memory and computational resources. However, recent achievements in the technology of the multi-core microprocessors and graphic cards allows real-time operation of the multidimensional methods as is shown and analyzed in this paper based on real examples of object detection in digital images.

Isovector and isoscalar tensor charges of the nucleon from lattice QCD

DOE PAGES

Bhattacharya, Tanmoy; Cirigliano, Vincenzo; Cohen, Saul D.; ...

2015-11-01

Here, we present results for the isovector and flavor diagonal tensor charges g u–d T, g u T, g d T, and g s T needed to probe novel tensor interactions at the TeV scale in neutron and nuclear β-decays and the contribution of the quark electric dipole moment (EDM) to the neutron EDM. The lattice QCD calculations were done using nine ensembles of gauge configurations generated by the MILC collaboration using the HISQ action with 2+1+1 dynamical flavors. These ensembles span three lattice spacings a ≈ 0.06, 0.09 and 0.12 fm and three quark masses corresponding to the pionmore » masses M π ≈ 130, 220 and 310 MeV. Using estimates from these ensembles, we quantify all systematic uncertainties and perform a simultaneous extrapolation in the lattice spacing, volume and light quark masses for the connected contributions. The final estimates of the connected nucleon (proton) tensor charge for the isovector combination is g u–d T = 1.020(76) in the MS¯ scheme at 2 GeV. The additional disconnected quark loop contributions needed for the flavor-diagonal matrix elements are calculated using a stochastic estimator employing the truncated solver method with the all-mode-averaging technique. We find that the size of the disconnected contribution is smaller than the statistical error in the connected contribution. This allows us to bound the disconnected contribution and include it as an additional uncertainty in the flavor-diagonal charges. After a continuum extrapolation, we find g u T = 0.774(66), g d T = –0.233(28) and g u+d T = 0.541(67). The strangeness tensor charge, that can make a significant contribution to the neutron EDM due to the large ratio m s/m u,d, is g s T = 0.008(9) in the continuum limit.« less

From Pixels to Response Maps: Discriminative Image Filtering for Face Alignment in the Wild.

PubMed

Asthana, Akshay; Zafeiriou, Stefanos; Tzimiropoulos, Georgios; Cheng, Shiyang; Pantic, Maja

2015-06-01

We propose a face alignment framework that relies on the texture model generated by the responses of discriminatively trained part-based filters. Unlike standard texture models built from pixel intensities or responses generated by generic filters (e.g. Gabor), our framework has two important advantages. First, by virtue of discriminative training, invariance to external variations (like identity, pose, illumination and expression) is achieved. Second, we show that the responses generated by discriminatively trained filters (or patch-experts) are sparse and can be modeled using a very small number of parameters. As a result, the optimization methods based on the proposed texture model can better cope with unseen variations. We illustrate this point by formulating both part-based and holistic approaches for generic face alignment and show that our framework outperforms the state-of-the-art on multiple "wild" databases. The code and dataset annotations are available for research purposes from http://ibug.doc.ic.ac.uk/resources.

Regional Seismic Methods of Identifying Explosions

NASA Astrophysics Data System (ADS)

Walter, W. R.; Ford, S. R.; Pasyanos, M.; Pyle, M. L.; Hauk, T. F.

2013-12-01

A lesson from the 2006, 2009 and 2013 DPRK declared nuclear explosion Ms:mb observations is that our historic collection of data may not be representative of future nuclear test signatures (e.g. Selby et al., 2012). To have confidence in identifying future explosions amongst the background of other seismic signals, we need to put our empirical methods on a firmer physical footing. Here we review the two of the main identification methods: 1) P/S ratios and 2) Moment Tensor techniques, which can be applied at the regional distance (200-1600 km) to very small events, improving nuclear explosion monitoring and confidence in verifying compliance with the Comprehensive Nuclear-Test-Ban Treaty (CTBT). Amplitude ratios of seismic P-to-S waves at sufficiently high frequencies (~>2 Hz) can identify explosions among a background of natural earthquakes (e.g. Walter et al., 1995). However the physical basis for the generation of explosion S-waves, and therefore the predictability of this P/S technique as a function of event properties such as size, depth, geology and path, remains incompletely understood. Calculated intermediate period (10-100s) waveforms from regional 1-D models can match data and provide moment tensor results that separate explosions from earthquakes and cavity collapses (e.g. Ford et al. 2009). However it has long been observed that some nuclear tests produce large Love waves and reversed Rayleigh waves that complicate moment tensor modeling. Again the physical basis for the generation of these effects from explosions remains incompletely understood. We are re-examining regional seismic data from a variety of nuclear test sites including the DPRK and the former Nevada Test Site (now the Nevada National Security Site (NNSS)). Newer relative amplitude techniques can be employed to better quantify differences between explosions and used to understand those differences in term of depth, media and other properties. We are also making use of the Source Physics Experiments (SPE) at NNSS. The SPE chemical explosions are explicitly designed to improve our understanding of emplacement and source material effects on the generation of shear and surface waves (e.g. Snelson et al., 2013). Our goal is to improve our explosion models and our ability to understand and predict where P/S and moment tensor methods of identifying explosions work, and any circumstances where they may not. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

MICA: Multiple interval-based curve alignment

NASA Astrophysics Data System (ADS)

Mann, Martin; Kahle, Hans-Peter; Beck, Matthias; Bender, Bela Johannes; Spiecker, Heinrich; Backofen, Rolf

2018-01-01

MICA enables the automatic synchronization of discrete data curves. To this end, characteristic points of the curves' shapes are identified. These landmarks are used within a heuristic curve registration approach to align profile pairs by mapping similar characteristics onto each other. In combination with a progressive alignment scheme, this enables the computation of multiple curve alignments. Multiple curve alignments are needed to derive meaningful representative consensus data of measured time or data series. MICA was already successfully applied to generate representative profiles of tree growth data based on intra-annual wood density profiles or cell formation data. The MICA package provides a command-line and graphical user interface. The R interface enables the direct embedding of multiple curve alignment computation into larger analyses pipelines. Source code, binaries and documentation are freely available at https://github.com/BackofenLab/MICA

D-GENIES: dot plot large genomes in an interactive, efficient and simple way.

PubMed

Cabanettes, Floréal; Klopp, Christophe

2018-01-01

Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited in the input sequence size. D-GENIES is a standalone and web application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference, zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.

XUV ionization of aligned molecules

NASA Astrophysics Data System (ADS)

Kelkensberg, F.; Rouzée, A.; Siu, W.; Gademann, G.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.; Vrakking, M. J. J.

2011-11-01

New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO2 molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

On the orientation of the backbone dipoles in native folds

PubMed Central

Ripoll, Daniel R.; Vila, Jorge A.; Scheraga, Harold A.

2005-01-01

The role of electrostatic interactions in determining the native fold of proteins has been investigated by analyzing the alignment of peptide bond dipole moments with the local electrostatic field generated by the rest of the molecule with and without solvent effects. This alignment was calculated for a set of 112 native proteins by using charges from a gas phase potential. Most of the peptide dipoles in this set of proteins are on average aligned with the electrostatic field. The dipole moments associated with α-helical conformations show the best alignment with the electrostatic field, followed by residues in β-strand conformations. The dipole moments associated with other secondary structure elements are on average better aligned than in randomly generated conformations. The alignment of a dipole with the local electrostatic field depends on both the topology of the native fold and the charge distribution assumed for all of the residues. The influences of (i) solvent effects, (ii) different sets of charges, and (iii) the charge distribution assumed for the whole molecule were examined with a subset of 22 proteins each of which contains <30 ionizable groups. The results show that alternative charge distribution models lead to significant differences among the associated electrostatic fields, whereas the electrostatic field is less sensitive to the particular set of the adopted charges themselves (empirical conformational energy program for peptides or parameters for solvation energy). PMID:15894608

Voxel-Wise Comparisons of the Morphology of Diffusion Tensors Across Groups of Experimental Subjects

PubMed Central

Bansal, Ravi; Staib, Lawrence H.; Plessen, Kerstin J.; Xu, Dongrong; Royal, Jason; Peterson, Bradley S.

2007-01-01

Water molecules in the brain diffuse preferentially along the fiber tracts within white matter, which form the anatomical connections across spatially distant brain regions. A diffusion tensor (DT) is a probabilistic ellipsoid composed of 3 orthogonal vectors, each having a direction and an associated scalar magnitude, that represent the probability of water molecules diffusing in each of those directions. The 3D morphologies of DTs can be compared across groups of subjects to reveal disruptions in structural organization and neuroanatomical connectivity of the brains of persons with various neuropsychiatric illnesses. Comparisons of tensor morphology across groups have typically been performed on scalar measures of diffusivity, such as Fractional Anisotropy (FA), rather than directly on the complex 3D morphologies of DTs. Scalar measures, however, are related in nonlinear ways to the eigenvalues and eigenvectors that create the 3D morphologies of DTs. We present a mathematical framework that permits the direct comparison across groups of mean eigenvalues and eigenvectors of individual DTs. We show that group-mean eigenvalues and eigenvectors are multivariate Gaussian distributed, and we use the Delta method to compute their approximate covariance matrices. Our results show that the theoretically computed Mean Tensor (MT) eigenvectors and eigenvalues match well with their respective true values. Furthermore, a comparison of synthetically generated groups of DTs highlights the limitations of using FA to detect group differences. Finally, analyses of in vivo DT data using our method reveal significant between-group differences in diffusivity along fiber tracts within white matter, whereas analyses based on FA values failed to detect some of these differences. PMID:18006284

Multiple Echo Diffusion Tensor Acquisition Technique (MEDITATE) on a 3T clinical scanner

PubMed Central

Baete, Steven H.; Cho, Gene; Sigmund, Eric E.

2013-01-01

This paper describes the concepts and implementation of an MRI method, Multiple Echo Diffusion Tensor Acquisition Technique (MEDITATE), which is capable of acquiring apparent diffusion tensor maps in two scans on a 3T clinical scanner. In each MEDITATE scan, a set of RF-pulses generates multiple echoes whose amplitudes are diffusion-weighted in both magnitude and direction by a pattern of diffusion gradients. As a result, two scans acquired with different diffusion weighting strengths suffice for accurate estimation of diffusion tensor imaging (DTI)-parameters. The MEDITATE variation presented here expands previous MEDITATE approaches to adapt to the clinical scanner platform, such as exploiting longitudinal magnetization storage to reduce T2-weighting. Fully segmented multi-shot Cartesian encoding is used for image encoding. MEDITATE was tested on isotropic (agar gel), anisotropic diffusion phantoms (asparagus), and in vivo skeletal muscle in healthy volunteers with cardiac-gating. Comparisons of accuracy were performed with standard twice-refocused spin echo (TRSE) DTI in each case and good quantitative agreement was found between diffusion eigenvalues, mean diffusivity, and fractional anisotropy derived from TRSE-DTI and from the MEDITATE sequence. Orientation patterns were correctly reproduced in both isotropic and anisotropic phantoms, and approximately so for in vivo imaging. This illustrates that the MEDITATE method of compressed diffusion encoding is feasible on the clinical scanner platform. With future development and employment of appropriate view-sharing image encoding this technique may be used in clinical applications requiring time-sensitive acquisition of DTI parameters such as dynamical DTI in muscle. PMID:23828606

Minkowski Tensors in Two Dimensions: Probing the Morphology and Isotropy of the Matter and Galaxy Density Fields

NASA Astrophysics Data System (ADS)

Appleby, Stephen; Chingangbam, Pravabati; Park, Changbom; Hong, Sungwook E.; Kim, Juhan; Ganesan, Vidhya

2018-05-01

We apply the Minkowski tensor statistics to two-dimensional slices of the three-dimensional matter density field. The Minkowski tensors are a set of functions that are sensitive to directionally dependent signals in the data and, furthermore, can be used to quantify the mean shape of density fields. We begin by reviewing the definition of Minkowski tensors and introducing a method of calculating them from a discretely sampled field. Focusing on the statistic {W}21,1—a 2 × 2 matrix—we calculate its value for both the entire excursion set and individual connected regions and holes within the set. To study the morphology of structures within the excursion set, we calculate the eigenvalues λ 1, λ 2 for the matrix {W}21,1 of each distinct connected region and hole and measure their mean shape using the ratio β \\equiv < {λ }2/{λ }1> . We compare both {W}21,1 and β for a Gaussian field and a smoothed density field generated from the latest Horizon Run 4 cosmological simulation to study the effect of gravitational collapse on these functions. The global statistic {W}21,1 is essentially independent of gravitational collapse, as the process maintains statistical isotropy. However, β is modified significantly, with overdensities becoming relatively more circular compared to underdensities at low redshifts. When applying the statistics to a redshift-space distorted density field, the matrix {W}21,1 is no longer proportional to the identity matrix, and measurements of its diagonal elements can be used to probe the large-scale velocity field.

Seamless, axially aligned, fiber tubes, meshes, microbundles and gradient biomaterial constructs

PubMed Central

Elia, Roberto; Firpo, Matthew A.; Kaplan, David L.; Peattie, Robert A.

2012-01-01

A new electrospinning apparatus was developed to generate nanofibrous materials with improved organizational control. The system functions by oscillating the deposition signal (ODS) of multiple collectors, allowing significantly improved nanofiber control by manipulating the electric field which drives the electrospinning process. Other electrospinning techniques designed to impart deposited fiber organizational control, such as rotating mandrels or parallel collector systems, do not generate seamless constructs with high quality alignment in sizes large enough for medical devices. In contrast, the ODS collection system produces deposited fiber networks with highly pure alignment in a variety of forms and sizes, including flat (8 × 8 cm2), tubular (1.3 cm diameter), or rope-like microbundle (45 μm diameter) samples. Additionally, the mechanism of our technique allows for scale-up beyond these dimensions. The ODS collection system produced 81.6 % of fibers aligned within 5° of the axial direction, nearly a four-fold improvement over the rotating mandrel technique. The meshes produced from the 9 % (w/v) fibroin/PEO blend demonstrated significant mechanical anisotropy due to the fiber alignment. In 37 °C PBS, aligned samples produced an ultimate tensile strength of 16.47 ± 1.18 MPa, a Young's modulus of 37.33 MPa, and a yield strength of 7.79 ± 1.13 MPa. The material was 300 % stiffer when extended in the direction of fiber alignment and required 20 times the amount of force to be deformed, compared to aligned meshes extended perpendicular to the fiber direction. The ODS technique could be applied to any electrospinnable polymer to overcome the more limited uniformity and induced mechanical strain of rotating mandrel techniques, and greatly surpasses the limited length of standard parallel collector techniques. PMID:22890517

A Workflow to Improve the Alignment of Prostate Imaging with Whole-mount Histopathology.

PubMed

Yamamoto, Hidekazu; Nir, Dror; Vyas, Lona; Chang, Richard T; Popert, Rick; Cahill, Declan; Challacombe, Ben; Dasgupta, Prokar; Chandra, Ashish

2014-08-01

Evaluation of prostate imaging tests against whole-mount histology specimens requires accurate alignment between radiologic and histologic data sets. Misalignment results in false-positive and -negative zones as assessed by imaging. We describe a workflow for three-dimensional alignment of prostate imaging data against whole-mount prostatectomy reference specimens and assess its performance against a standard workflow. Ethical approval was granted. Patients underwent motorized transrectal ultrasound (Prostate Histoscanning) to generate a three-dimensional image of the prostate before radical prostatectomy. The test workflow incorporated steps for axial alignment between imaging and histology, size adjustments following formalin fixation, and use of custom-made parallel cutters and digital caliper instruments. The control workflow comprised freehand cutting and assumed homogeneous block thicknesses at the same relative angles between pathology and imaging sections. Thirty radical prostatectomy specimens were histologically and radiologically processed, either by an alignment-optimized workflow (n = 20) or a control workflow (n = 10). The optimized workflow generated tissue blocks of heterogeneous thicknesses but with no significant drifting in the cutting plane. The control workflow resulted in significantly nonparallel blocks, accurately matching only one out of four histology blocks to their respective imaging data. The image-to-histology alignment accuracy was 20% greater in the optimized workflow (P < .0001), with higher sensitivity (85% vs. 69%) and specificity (94% vs. 73%) for margin prediction in a 5 × 5-mm grid analysis. A significantly better alignment was observed in the optimized workflow. Evaluation of prostate imaging biomarkers using whole-mount histology references should include a test-to-reference spatial alignment workflow. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

RF Jitter Modulation Alignment Sensing

NASA Astrophysics Data System (ADS)

Ortega, L. F.; Fulda, P.; Diaz-Ortiz, M.; Perez Sanchez, G.; Ciani, G.; Voss, D.; Mueller, G.; Tanner, D. B.

2017-01-01

We will present the numerical and experimental results of a new alignment sensing scheme which can reduce the complexity of alignment sensing systems currently used, while maintaining the same shot noise limited sensitivity. This scheme relies on the ability of electro-optic beam deflectors to create angular modulation sidebands in radio frequency, and needs only a single-element photodiode and IQ demodulation to generate error signals for tilt and translation degrees of freedom in one dimension. It distances itself from current techniques by eliminating the need for beam centering servo systems, quadrant photodetectors and Gouy phase telescopes. RF Jitter alignment sensing can be used to reduce the complexity in the alignment systems of many laser optical experiments, including LIGO and the ALPS experiment.

Higher symmetries of the Schrödinger operator in Newton-Cartan geometry

NASA Astrophysics Data System (ADS)

Gundry, James

2017-03-01

We establish several relationships between the non-relativistic conformal symmetries of Newton-Cartan geometry and the Schrödinger equation. In particular we discuss the algebra sch(d) of vector fields conformally-preserving a flat Newton-Cartan spacetime, and we prove that its curved generalisation generates the symmetry group of the covariant Schrödinger equation coupled to a Newtonian potential and generalised Coriolis force. We provide intrinsic Newton-Cartan definitions of Killing tensors and conformal Schrödinger-Killing tensors, and we discuss their respective links to conserved quantities and to the higher symmetries of the Schrödinger equation. Finally we consider the role of conformal symmetries in Newtonian twistor theory, where the infinite-dimensional algebra of holomorphic vector fields on twistor space corresponds to the symmetry algebra cnc(3) on the Newton-Cartan spacetime.

Multivariate statistics of the Jacobian matrices in tensor based morphometry and their application to HIV/AIDS.

PubMed

Lepore, Natasha; Brun, Caroline A; Chiang, Ming-Chang; Chou, Yi-Yu; Dutton, Rebecca A; Hayashi, Kiralee M; Lopez, Oscar L; Aizenstein, Howard J; Toga, Arthur W; Becker, James T; Thompson, Paul M

2006-01-01

Tensor-based morphometry (TBM) is widely used in computational anatomy as a means to understand shape variation between structural brain images. A 3D nonlinear registration technique is typically used to align all brain images to a common neuroanatomical template, and the deformation fields are analyzed statistically to identify group differences in anatomy. However, the differences are usually computed solely from the determinants of the Jacobian matrices that are associated with the deformation fields computed by the registration procedure. Thus, much of the information contained within those matrices gets thrown out in the process. Only the magnitude of the expansions or contractions is examined, while the anisotropy and directional components of the changes are ignored. Here we remedy this problem by computing multivariate shape change statistics using the strain matrices. As the latter do not form a vector space, means and covariances are computed on the manifold of positive-definite matrices to which they belong. We study the brain morphology of 26 HIV/AIDS patients and 14 matched healthy control subjects using our method. The images are registered using a high-dimensional 3D fluid registration algorithm, which optimizes the Jensen-Rényi divergence, an information-theoretic measure of image correspondence. The anisotropy of the deformation is then computed. We apply a manifold version of Hotelling's T2 test to the strain matrices. Our results complement those found from the determinants of the Jacobians alone and provide greater power in detecting group differences in brain structure.

Improving Functional MRI Registration Using Whole-Brain Functional Correlation Tensors.

PubMed

Zhou, Yujia; Yap, Pew-Thian; Zhang, Han; Zhang, Lichi; Feng, Qianjin; Shen, Dinggang

2017-09-01

Population studies of brain function with resting-state functional magnetic resonance imaging (rs-fMRI) largely rely on the accurate inter-subject registration of functional areas. This is typically achieved through registration of the corresponding T1-weighted MR images with more structural details. However, accumulating evidence has suggested that such strategy cannot well-align functional regions which are not necessarily confined by the anatomical boundaries defined by the T1-weighted MR images. To mitigate this problem, various registration algorithms based directly on rs-fMRI data have been developed, most of which have utilized functional connectivity (FC) as features for registration. However, most of the FC-based registration methods usually extract the functional features only from the thin and highly curved cortical grey matter (GM), posing a great challenge in accurately estimating the whole-brain deformation field. In this paper, we demonstrate that the additional useful functional features can be extracted from brain regions beyond the GM, particularly, white-matter (WM) based on rs-fMRI, for improving the overall functional registration. Specifically, we quantify the local anisotropic correlation patterns of the blood oxygenation level-dependent (BOLD) signals, modeled by functional correlation tensors (FCTs), in both GM and WM. Functional registration is then performed based on multiple components of the whole-brain FCTs using a multichannel Large Deformation Diffeomorphic Metric Mapping (mLDDMM) algorithm. Experimental results show that our proposed method achieves superior functional registration performance, compared with other conventional registration methods.

Nuclear structure research at the Triangle Universities Nuclear Laboratory

NASA Astrophysics Data System (ADS)

Mitchell, G. E.

1992-10-01

Studies of fundamental symmetries by the TRIPLE collaboration using the unique capabilities at LAMTF have found unexpected systematics in the parity-violating amplitudes for epithermal-neutron scattering. Tests to lower the present limits on time-reversal-invariance violation in the strong interaction are being made at in experiments on the scattering of polarized fast neutrons from aligned holmium targets. Studies of few-nucleon systems have received increasing emphasis over the past year, involving a broad program for testing the low- to medium-energy internucleon interactions, from the tensor component in n-p scattering and the n-n scattering lengths, through three-nucleon systems and the alpha particle, on up to Be-8. Of particular interest are three-nucleon systems, both in elastic scattering and in three-body breakup. Beam requirements range from production of intense and highly-polarized neutron beams to tensor-polarized beams for measurements at both very low energies (25-80 keV) and at tandem energies for definitive measurements of D-state components of the triton, He-3, and He-4 obtained from transfer reactions. The program in nuclear astrophysics expanded during 1991-1992. Several facets of the nuclear many-body problem and of excitation mechanisms of the nucleus are being elucidated, including measurements and analyses to elucidate the neutron-nucleus elastic-scattering interaction over a wide range of nuclei and energies. Several projects involved developments in electronuclear physics, instrumentation, RF-transition units, and low-temperature bolometric particle detectors.

Automatic deformable diffusion tensor registration for fiber population analysis.

PubMed

Irfanoglu, M O; Machiraju, R; Sammet, S; Pierpaoli, C; Knopp, M V

2008-01-01

In this work, we propose a novel method for deformable tensor-to-tensor registration of Diffusion Tensor Images. Our registration method models the distances in between the tensors with Geode-sic-Loxodromes and employs a version of Multi-Dimensional Scaling (MDS) algorithm to unfold the manifold described with this metric. Defining the same shape properties as tensors, the vector images obtained through MDS are fed into a multi-step vector-image registration scheme and the resulting deformation fields are used to reorient the tensor fields. Results on brain DTI indicate that the proposed method is very suitable for deformable fiber-to-fiber correspondence and DTI-atlas construction.

Brain tumor classification using the diffusion tensor image segmentation (D-SEG) technique.

PubMed

Jones, Timothy L; Byrnes, Tiernan J; Yang, Guang; Howe, Franklyn A; Bell, B Anthony; Barrick, Thomas R

2015-03-01

There is an increasing demand for noninvasive brain tumor biomarkers to guide surgery and subsequent oncotherapy. We present a novel whole-brain diffusion tensor imaging (DTI) segmentation (D-SEG) to delineate tumor volumes of interest (VOIs) for subsequent classification of tumor type. D-SEG uses isotropic (p) and anisotropic (q) components of the diffusion tensor to segment regions with similar diffusion characteristics. DTI scans were acquired from 95 patients with low- and high-grade glioma, metastases, and meningioma and from 29 healthy subjects. D-SEG uses k-means clustering of the 2D (p,q) space to generate segments with different isotropic and anisotropic diffusion characteristics. Our results are visualized using a novel RGB color scheme incorporating p, q and T2-weighted information within each segment. The volumetric contribution of each segment to gray matter, white matter, and cerebrospinal fluid spaces was used to generate healthy tissue D-SEG spectra. Tumor VOIs were extracted using a semiautomated flood-filling technique and D-SEG spectra were computed within the VOI. Classification of tumor type using D-SEG spectra was performed using support vector machines. D-SEG was computationally fast and stable and delineated regions of healthy tissue from tumor and edema. D-SEG spectra were consistent for each tumor type, with constituent diffusion characteristics potentially reflecting regional differences in tissue microstructure. Support vector machines classified tumor type with an overall accuracy of 94.7%, providing better classification than previously reported. D-SEG presents a user-friendly, semiautomated biomarker that may provide a valuable adjunct in noninvasive brain tumor diagnosis and treatment planning. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Neuro-Oncology.

Experimental validation of the influence of white matter anisotropy on the intracranial EEG forward solution

PubMed Central

Schomer, Donald L.; Dehghani, Nima; Ulbert, Istvan; Cash, Sydney; Papavasiliou, Steve; Eisenberg, Solomon R.; Dale, Anders M.; Halgren, Eric

2010-01-01

Forward solutions with different levels of complexity are employed for localization of current generators, which are responsible for the electric and magnetic fields measured from the human brain. The influence of brain anisotropy on the forward solution is poorly understood. The goal of this study is to validate an anisotropic model for the intracranial electric forward solution by comparing with the directly measured ‘gold standard’. Dipolar sources are created at known locations in the brain and intracranial electroencephalogram (EEG) is recorded simultaneously. Isotropic models with increasing level of complexity are generated along with anisotropic models based on Diffusion tensor imaging (DTI). A Finite Element Method based forward solution is calculated and validated using the measured data. Major findings are (1) An anisotropic model with a linear scaling between the eigenvalues of the electrical conductivity tensor and water self-diffusion tensor in brain tissue is validated. The greatest improvement was obtained when the stimulation site is close to a region of high anisotropy. The model with a global anisotropic ratio of 10:1 between the eigenvalues (parallel: tangential to the fiber direction) has the worst performance of all the anisotropic models. (2) Inclusion of cerebrospinal fluid as well as brain anisotropy in the forward model is necessary for an accurate description of the electric field inside the skull. The results indicate that an anisotropic model based on the DTI can be constructed non-invasively and shows an improved performance when compared to the isotropic models for the calculation of the intracranial EEG forward solution. Electronic supplementary material The online version of this article (doi:10.1007/s10827-009-0205-z) contains supplementary material, which is available to authorized users. PMID:20063051

Tensor-GMRES method for large sparse systems of nonlinear equations

NASA Technical Reports Server (NTRS)

Feng, Dan; Pulliam, Thomas H.

1994-01-01

This paper introduces a tensor-Krylov method, the tensor-GMRES method, for large sparse systems of nonlinear equations. This method is a coupling of tensor model formation and solution techniques for nonlinear equations with Krylov subspace projection techniques for unsymmetric systems of linear equations. Traditional tensor methods for nonlinear equations are based on a quadratic model of the nonlinear function, a standard linear model augmented by a simple second order term. These methods are shown to be significantly more efficient than standard methods both on nonsingular problems and on problems where the Jacobian matrix at the solution is singular. A major disadvantage of the traditional tensor methods is that the solution of the tensor model requires the factorization of the Jacobian matrix, which may not be suitable for problems where the Jacobian matrix is large and has a 'bad' sparsity structure for an efficient factorization. We overcome this difficulty by forming and solving the tensor model using an extension of a Newton-GMRES scheme. Like traditional tensor methods, we show that the new tensor method has significant computational advantages over the analogous Newton counterpart. Consistent with Krylov subspace based methods, the new tensor method does not depend on the factorization of the Jacobian matrix. As a matter of fact, the Jacobian matrix is never needed explicitly.

Generation of various partially coherent beams and their propagation properties in turbulent atmosphere: a review

NASA Astrophysics Data System (ADS)

Cai, Yangjian

2011-03-01

Partially coherent beams, such as Gaussian Schell-model beam, partially coherent dark hollow beam, partially coherent flat-topped beam and electromagnetic Gaussian Schell-model beam, have important applications in free space optical communications, optical imaging, optical trapping, inertial confinement fusion and nonlinear optics. In this paper, experimental generations of various partially coherent beams are introduced. Furthermore, with the help of a tensor method, analytical formulae for such beams propagating in turbulent atmosphere are derived, and the propagation properties of such beams in turbulent atmosphere are reviewed.

DBI in the Sky

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

Alishahiha, M

2004-04-19

We analyze the spectrum of density perturbations generated in models of the recently discovered ''D-cceleration'' mechanism of inflation. In this scenario, strong coupling quantum field theoretic effects sum to provide a DBI-like action for the inflaton. We show that the model has a strict lower bound on the non-Gaussianity of the CMBR power spectrum at an observable level, and is thus falsifiable. This in particular observationally distinguishes this mechanism from traditional slow roll inflation generated by weakly interacting scalar fields. The model also favors a large observable tensor component to the CMBR spectrum.

The 2016 south Alboran earthquake (Mw = 6.4): A reactivation of the Ibero-Maghrebian region?

NASA Astrophysics Data System (ADS)

Buforn, E.; Pro, C.; Sanz de Galdeano, C.; Cantavella, J. V.; Cesca, S.; Caldeira, B.; Udías, A.; Mattesini, M.

2017-08-01

On 25 January 2016, an earthquake of magnitude Mw = 6.4 occurred at the southern part of the Alboran Sea, between southern Spain and northern Morocco. This shock was preceded by a foreshock (Mw = 5.1) and followed by a long aftershock sequence. Focal mechanism of main shock has been estimated from slip inversion of body waves at teleseismic distances. Solution corresponds to left-lateral strike-slip motion, showing a complex bilateral rupture, formed by two sub-events, with most energy propagating along a plane oriented N30°E plane dipping to the NW. Relocation of larger events of the aftershock series, show two alignments of epicentres in NE-SW and NNE-SSW direction that intersect at the epicentre of the main shock. We have estimated the focal mechanisms of the largest aftershocks from moment tensor inversion at regional distances. We have obtained two families of focal mechanisms corresponding to strike slip for the NNE-SSW alignment and thrusting motion for the NE-SW alignment. Among the faults present in the area the Al Idrisi fault (or fault zone) may be a good candidate for the source of this earthquake. The study of Coulomb Failure Stress shows that it is possible that the 2016 earthquake was triggered by the previous nearby earthquakes of 1994 (Mw = 5.8) and 2004 (Mw = 6.3). The possible seismic reactivation of the central part of the Ibero-Maghrebian region is an open question, but it is clear that the occurrence of the 2016 earthquake confirms that from 1994 the seismicity of central part of IMR is increasing and that focal mechanism of largest earthquakes in this central part correspond to complex ruptures (or zone of fault).

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.

Formation of the Sun-aligned arc region and the void (polar slot) under the null-separator structure

NASA Astrophysics Data System (ADS)

Tanaka, T.; Obara, T.; Watanabe, M.; Fujita, S.; Ebihara, Y.; Kataoka, R.

2017-04-01

From the global magnetosphere-ionosphere coupling simulation, we examined the formation of the Sun-aligned arc region and the void (polar slot) under the northward interplanetary magnetic field (IMF) with negative By condition. In the magnetospheric null-separator structure, the separatrices generated from two null points and two separators divide the entire space into four types of magnetic region, i.e., the IMF, the northern open magnetic field, the southern open magnetic field, and the closed magnetic field. In the ionosphere, the Sun-aligned arc region and the void are reproduced in the distributions of simulated plasma pressure and field-aligned current. The outermost closed magnetic field lines on the boundary (separatrix) between the northern open magnetic field and the closed magnetic field are projected to the northern ionosphere at the boundary between the Sun-aligned arc region and the void, both on the morning and evening sides. The magnetic field lines at the plasma sheet inner edge are projected to the equatorward boundary of the oval. Therefore, the Sun-aligned arc region is on the closed magnetic field lines of the plasma sheet. In the plasma sheet, an inflated structure (bulge) is generated at the junction of the tilted plasma sheet in the far-to-middle tail and nontilted plasma sheet in the ring current region. In the Northern Hemisphere, the bulge is on the evening side wrapped by the outermost closed magnetic field lines that are connected to the northern evening ionosphere. This inflated structure (bulge) is associated with shear flows that cause the Sun-aligned arc.

Aligning Where to See and What to Tell: Image Captioning with Region-Based Attention and Scene-Specific Contexts.

PubMed

Fu, Kun; Jin, Junqi; Cui, Runpeng; Sha, Fei; Zhang, Changshui

2017-12-01

Recent progress on automatic generation of image captions has shown that it is possible to describe the most salient information conveyed by images with accurate and meaningful sentences. In this paper, we propose an image captioning system that exploits the parallel structures between images and sentences. In our model, the process of generating the next word, given the previously generated ones, is aligned with the visual perception experience where the attention shifts among the visual regions-such transitions impose a thread of ordering in visual perception. This alignment characterizes the flow of latent meaning, which encodes what is semantically shared by both the visual scene and the text description. Our system also makes another novel modeling contribution by introducing scene-specific contexts that capture higher-level semantic information encoded in an image. The contexts adapt language models for word generation to specific scene types. We benchmark our system and contrast to published results on several popular datasets, using both automatic evaluation metrics and human evaluation. We show that either region-based attention or scene-specific contexts improves systems without those components. Furthermore, combining these two modeling ingredients attains the state-of-the-art performance.

Turbulent fluid motion 2: Scalars, vectors, and tensors

NASA Technical Reports Server (NTRS)

Deissler, Robert G.

1991-01-01

The author shows that the sum or difference of two vectors is a vector. Similarly the sum of any two tensors of the same order is a tensor of that order. No meaning is attached to the sum of tensors of different orders, say u(sub i) + u(sub ij); that is not a tensor. In general, an equation containing tensors has meaning only if all the terms in the equation are tensors of the same order, and if the same unrepeated subscripts appear in all the terms. These facts will be used in obtaining appropriate equations for fluid turbulence. With the foregoing background, the derivation of appropriate continuum equations for turbulence should be straightforward.

Simple and robust generation of ultrafast laser pulse trains using polarization-independent parallel-aligned thin films

NASA Astrophysics Data System (ADS)

Wang, Andong; Jiang, Lan; Li, Xiaowei; Wang, Zhi; Du, Kun; Lu, Yongfeng

2018-05-01

Ultrafast laser pulse temporal shaping has been widely applied in various important applications such as laser materials processing, coherent control of chemical reactions, and ultrafast imaging. However, temporal pulse shaping has been limited to only-in-lab technique due to the high cost, low damage threshold, and polarization dependence. Herein we propose a novel design of ultrafast laser pulse train generation device, which consists of multiple polarization-independent parallel-aligned thin films. Various pulse trains with controllable temporal profile can be generated flexibly by multi-reflections within the splitting films. Compared with other pulse train generation techniques, this method has advantages of compact structure, low cost, high damage threshold and polarization independence. These advantages endow it with high potential for broad utilization in ultrafast applications.

XUV ionization of aligned molecules

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

Kelkensberg, F.; Siu, W.; Gademann, G.

2011-11-15

New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

Energy level alignment and sub-bandgap charge generation in polymer:fullerene bulk heterojunction solar cells.

PubMed

Tsang, Sai-Wing; Chen, Song; So, Franky

2013-05-07

Using charge modulated electroabsorption spectroscopy (CMEAS), for the first time, the energy level alignment of a polymer:fullerene bulk heterojunction photovoltaic cell is directly measured. The charge-transfer excitons generated by the sub-bandgap optical pumping are coupled with the modulating electric field and introduce subtle changes in optical absorption in the sub-bandgap region. This minimum required energy for sub-bandgap charge genreation is defined as the effective bandgap. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Next generation data harmonization

NASA Astrophysics Data System (ADS)

Armstrong, Chandler; Brown, Ryan M.; Chaves, Jillian; Czerniejewski, Adam; Del Vecchio, Justin; Perkins, Timothy K.; Rudnicki, Ron; Tauer, Greg

2015-05-01

Analysts are presented with a never ending stream of data sources. Often, subsets of data sources to solve problems are easily identified but the process to align data sets is time consuming. However, many semantic technologies do allow for fast harmonization of data to overcome these problems. These include ontologies that serve as alignment targets, visual tools and natural language processing that generate semantic graphs in terms of the ontologies, and analytics that leverage these graphs. This research reviews a developed prototype that employs all these approaches to perform analysis across disparate data sources documenting violent, extremist events.

Generalized Higher Order Orthogonal Iteration for Tensor Learning and Decomposition.

PubMed

Liu, Yuanyuan; Shang, Fanhua; Fan, Wei; Cheng, James; Cheng, Hong

2016-12-01

Low-rank tensor completion (LRTC) has successfully been applied to a wide range of real-world problems. Despite the broad, successful applications, existing LRTC methods may become very slow or even not applicable for large-scale problems. To address this issue, a novel core tensor trace-norm minimization (CTNM) method is proposed for simultaneous tensor learning and decomposition, and has a much lower computational complexity. In our solution, first, the equivalence relation of trace norm of a low-rank tensor and its core tensor is induced. Second, the trace norm of the core tensor is used to replace that of the whole tensor, which leads to two much smaller scale matrix TNM problems. Finally, an efficient alternating direction augmented Lagrangian method is developed to solve our problems. Our CTNM formulation needs only O((R N +NRI)log(√{I N })) observations to reliably recover an N th-order I×I×…×I tensor of n -rank (r,r,…,r) , compared with O(rI N-1 ) observations required by those tensor TNM methods ( I > R ≥ r ). Extensive experimental results show that CTNM is usually more accurate than them, and is orders of magnitude faster.

Tensor gauge condition and tensor field decomposition

NASA Astrophysics Data System (ADS)

Zhu, Ben-Chao; Chen, Xiang-Song

2015-10-01

We discuss various proposals of separating a tensor field into pure-gauge and gauge-invariant components. Such tensor field decomposition is intimately related to the effort of identifying the real gravitational degrees of freedom out of the metric tensor in Einstein’s general relativity. We show that as for a vector field, the tensor field decomposition has exact correspondence to and can be derived from the gauge-fixing approach. The complication for the tensor field, however, is that there are infinitely many complete gauge conditions in contrast to the uniqueness of Coulomb gauge for a vector field. The cause of such complication, as we reveal, is the emergence of a peculiar gauge-invariant pure-gauge construction for any gauge field of spin ≥ 2. We make an extensive exploration of the complete tensor gauge conditions and their corresponding tensor field decompositions, regarding mathematical structures, equations of motion for the fields and nonlinear properties. Apparently, no single choice is superior in all aspects, due to an awkward fact that no gauge-fixing can reduce a tensor field to be purely dynamical (i.e. transverse and traceless), as can the Coulomb gauge in a vector case.

Adaptive Multilinear Tensor Product Wavelets

DOE PAGES

Weiss, Kenneth; Lindstrom, Peter

2015-08-12

Many foundational visualization techniques including isosurfacing, direct volume rendering and texture mapping rely on piecewise multilinear interpolation over the cells of a mesh. However, there has not been much focus within the visualization community on techniques that efficiently generate and encode globally continuous functions defined by the union of multilinear cells. Wavelets provide a rich context for analyzing and processing complicated datasets. In this paper, we exploit adaptive regular refinement as a means of representing and evaluating functions described by a subset of their nonzero wavelet coefficients. We analyze the dependencies involved in the wavelet transform and describe how tomore » generate and represent the coarsest adaptive mesh with nodal function values such that the inverse wavelet transform is exactly reproduced via simple interpolation (subdivision) over the mesh elements. This allows for an adaptive, sparse representation of the function with on-demand evaluation at any point in the domain. In conclusion, we focus on the popular wavelets formed by tensor products of linear B-splines, resulting in an adaptive, nonconforming but crack-free quadtree (2D) or octree (3D) mesh that allows reproducing globally continuous functions via multilinear interpolation over its cells.« less

The Topology of Symmetric Tensor Fields

NASA Technical Reports Server (NTRS)

Levin, Yingmei; Batra, Rajesh; Hesselink, Lambertus; Levy, Yuval

1997-01-01

Combinatorial topology, also known as "rubber sheet geometry", has extensive applications in geometry and analysis, many of which result from connections with the theory of differential equations. A link between topology and differential equations is vector fields. Recent developments in scientific visualization have shown that vector fields also play an important role in the analysis of second-order tensor fields. A second-order tensor field can be transformed into its eigensystem, namely, eigenvalues and their associated eigenvectors without loss of information content. Eigenvectors behave in a similar fashion to ordinary vectors with even simpler topological structures due to their sign indeterminacy. Incorporating information about eigenvectors and eigenvalues in a display technique known as hyperstreamlines reveals the structure of a tensor field. The simplify and often complex tensor field and to capture its important features, the tensor is decomposed into an isotopic tensor and a deviator. A tensor field and its deviator share the same set of eigenvectors, and therefore they have a similar topological structure. A a deviator determines the properties of a tensor field, while the isotopic part provides a uniform bias. Degenerate points are basic constituents of tensor fields. In 2-D tensor fields, there are only two types of degenerate points; while in 3-D, the degenerate points can be characterized in a Q'-R' plane. Compressible and incompressible flows share similar topological feature due to the similarity of their deviators. In the case of the deformation tensor, the singularities of its deviator represent the area of vortex core in the field. In turbulent flows, the similarities and differences of the topology of the deformation and the Reynolds stress tensors reveal that the basic addie-viscosity assuptions have their validity in turbulence modeling under certain conditions.

Phasic action of the tensor muscle modulates the calling song in cicadas

PubMed

Fonseca; Hennig

1996-01-01

The effect of tensor muscle contraction on sound production by the tymbal was investigated in three species of cicadas (Tettigetta josei, Tettigetta argentata and Tympanistalna gastrica). All species showed a strict time correlation between the activity of the tymbal motoneurone and the discharge of motor units in the tensor nerve during the calling song. Lesion of the tensor nerve abolished the amplitude modulation of the calling song, but this modulation was restored by electrical stimulation of the tensor nerve or by mechanically pushing the tensor sclerite. Electrical stimulation of the tensor nerve at frequencies higher than 30­40 Hz changed the sound amplitude. In Tett. josei and Tett. argentata there was a gradual increase in sound amplitude with increasing frequency of tensor nerve stimulation, while in Tymp. gastrica there was a sudden reduction in sound amplitude at stimulation frequencies higher than 30 Hz. This contrasting effect in Tymp. gastrica was due to a bistable tymbal frame. Changes in sound pulse amplitude were positively correlated with changes in the time lag measured from tymbal motoneurone stimulation to the sound pulse. The tensor muscle acted phasically because electrical stimulation of the tensor nerve during a time window (0­10 ms) before electrical stimulation of the tymbal motoneurone was most effective in eliciting amplitude modulations. In all species, the tensor muscle action visibly changed the shape of the tymbal. Despite the opposite effects of the tensor muscle on sound pulse amplitude observed between Tettigetta and Tympanistalna species, the tensor muscle of both acts by modulating the shape of the tymbal, which changes the force required for the tymbal muscle to buckle the tymbal.

Gauge and Non-Gauge Tensor Multiplets in 5D Conformal Supergravity

NASA Astrophysics Data System (ADS)

Kugo, T.; Ohashi, K.

2002-12-01

An off-shell formulation of two distinct tensor multiplets, a massive tensor multiplet and a tensor gauge multiplet, is presented in superconformal tensor calculus in five-dimensional space-time. Both contain a rank 2 antisymmetric tensor field, but there is no gauge symmetry in the former, while it is a gauge field in the latter. Both multiplets have 4 bosonic and 4 fermionic on-shell modes, but the former consists of 16 (boson)+16 (fermion) component fields, while the latter consists of 8 (boson)+8 (fermion) component fields.

The energy-momentum tensor(s) in classical gauge theories

DOE PAGES

Blaschke, Daniel N.; Gieres, François; Reboud, Méril; ...

2016-07-12

We give an introduction to, and review of, the energy-momentum tensors in classical gauge field theories in Minkowski space, and to some extent also in curved space-time. For the canonical energy-momentum tensor of non-Abelian gauge fields and of matter fields coupled to such fields, we present a new and simple improvement procedure based on gauge invariance for constructing a gauge invariant, symmetric energy-momentum tensor. In conclusion, the relationship with the Einstein-Hilbert tensor following from the coupling to a gravitational field is also discussed.

Local alignment vectors reveal cancer cell-induced ECM fiber remodeling dynamics

PubMed Central

Lee, Byoungkoo; Konen, Jessica; Wilkinson, Scott; Marcus, Adam I.; Jiang, Yi

2017-01-01

Invasive cancer cells interact with the surrounding extracellular matrix (ECM), remodeling ECM fiber network structure by condensing, degrading, and aligning these fibers. We developed a novel local alignment vector analysis method to quantitatively measure collagen fiber alignment as a vector field using Circular Statistics. This method was applied to human non-small cell lung carcinoma (NSCLC) cell lines, embedded as spheroids in a collagen gel. Collagen remodeling was monitored using second harmonic generation imaging under normal conditions and when the LKB1-MARK1 pathway was disrupted through RNAi-based approaches. The results showed that inhibiting LKB1 or MARK1 in NSCLC increases the collagen fiber alignment and captures outward alignment vectors from the tumor spheroid, corresponding to high invasiveness of LKB1 mutant cancer cells. With time-lapse imaging of ECM micro-fiber morphology, the local alignment vector can measure the dynamic signature of invasive cancer cell activity and cell-migration-induced ECM and collagen remodeling and realigning dynamics. PMID:28045069

Axial, scalar, and tensor charges of the nucleon from 2 + 1 + 1 -flavor lattice QCD

DOE PAGES

Bhattacharya, Tanmoy; Cirigliano, Vincenzo; Cohen, Saul D.; ...

2016-09-19

Here, we present results for the isovector axial, scalar, and tensor charges g u–d A, g u–d S, and g u–d T of the nucleon needed to probe the Standard Model and novel physics. The axial charge is a fundamental parameter describing the weak interactions of nucleons. The scalar and tensor charges probe novel interactions at the TeV scale in neutron and nuclear β-decays, and the flavor-diagonal tensor charges g u T, g d T, and g s T are needed to quantify the contribution of the quark electric dipole moment (EDM) to the neutron EDM. The lattice-QCD calculations weremore » done using nine ensembles of gauge configurations generated by the MILC Collaboration using the highly improved staggered quarks action with 2+1+1 dynamical flavors. These ensembles span three lattice spacings a ≈ 0.06,0.09, and 0.12 fm and light-quark masses corresponding to the pion masses M π ≈ 135, 225, and 315 MeV. High-statistics estimates on five ensembles using the all-mode-averaging method allow us to quantify all systematic uncertainties and perform a simultaneous extrapolation in the lattice spacing, lattice volume, and light-quark masses for the connected contributions. Our final estimates, in the ¯MS scheme at 2 GeV, of the isovector charges are g u–d A = 1.195(33)(20), g u–d S = 0.97(12)(6), and g u–d T = 0.987(51)(20). The first error includes statistical and all systematic uncertainties except that due to the extrapolation Ansatz, which is given by the second error estimate. Combining our estimate for gu–dS with the difference of light quarks masses (m d–m u) QCD = 2.67(35) MeV given by the Flavor Lattice Average Group, we obtain (M N – M P) QCD = 2.59(49) MeV. Estimates of the connected part of the flavor-diagonal tensor charges of the proton are g u T = 0.792(42) and g d T = –0.194(14). Combining our new estimates with precision low-energy experiments, we present updated constraints on novel scalar and tensor interactions, ε S,T, at the TeV scale.« less

Killing(-Yano) tensors in string theory

NASA Astrophysics Data System (ADS)

Chervonyi, Yuri; Lunin, Oleg

2015-09-01

We construct the Killing(-Yano) tensors for a large class of charged black holes in higher dimensions and study general properties of such tensors, in particular, their behavior under string dualities. Killing(-Yano) tensors encode the symmetries beyond isometries, which lead to insights into dynamics of particles and fields on a given geometry by providing a set of conserved quantities. By analyzing the eigenvalues of the Killing tensor, we provide a prescription for constructing several conserved quantities starting from a single object, and we demonstrate that Killing tensors in higher dimensions are always associated with ellipsoidal coordinates. We also determine the transformations of the Killing(-Yano) tensors under string dualities, and find the unique modification of the Killing-Yano equation consistent with these symmetries. These results are used to construct the explicit form of the Killing(-Yano) tensors for the Myers-Perry black hole in arbitrary number of dimensions and for its charged version.

ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos

PubMed Central

2014-01-01

Background The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family. Results The JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images. Conclusions The ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org. PMID:25237393

Tensor calculus: unlearning vector calculus

NASA Astrophysics Data System (ADS)

Lee, Wha-Suck; Engelbrecht, Johann; Moller, Rita

2018-02-01

Tensor calculus is critical in the study of the vector calculus of the surface of a body. Indeed, tensor calculus is a natural step-up for vector calculus. This paper presents some pitfalls of a traditional course in vector calculus in transitioning to tensor calculus. We show how a deeper emphasis on traditional topics such as the Jacobian can serve as a bridge for vector calculus into tensor calculus.

Flow-induced voltage generation in non-ionic liquids over monolayer graphene

NASA Astrophysics Data System (ADS)

Ho Lee, Seung; Jung, Yousung; Kim, Soohyun; Han, Chang-Soo

2013-02-01

To clarify the origin of the flow-induced voltage generation in graphene, we prepared a new experimental device whose electrodes were aligned perpendicular to the flow with a non-ionic liquid. We found that significant voltage in our device was generated with increasing flow velocity, thereby confirming that voltage was due to an intrinsic interaction between graphene and the flowing liquid. To understand the mechanism of the observed flow-induced voltage generation, we systematically varied several important experimental parameters: flow velocity, electrode alignment, liquid polarity, and liquid viscosity. Based on these measurements, we suggest that polarity of the fluid is a significant factor in determining the extent of the voltage generated, and the major mechanism can be attributed to instantaneous potential differences induced in the graphene due to an interaction with polar liquids and to the momentum transferred from the flowing liquid to the graphene.

Orientational control of block copolymer microdomains by sub-tesla magnetic fields

NASA Astrophysics Data System (ADS)

Gopinadhan, Manesh; Choo, Youngwoo; Feng, Xunda; Kawabata, Kohsuke; di, Xiaojun; Osuji, Chinedum

Magnetic fields offer a versatile approach to controlling the orientation of block copolymer (BCP) microdomains during self-assembly. To date however, such control has required the imposition of large magnetic fields (>3T), necessitating the use of complex magnet systems - either superconducting or very large conventional resistive magnets. Here we demonstrate the ability to direct BCP self-assembly using considerably smaller fields (<1T) which are accessible using simple rare-earth permanent magnets. The low field alignment is enabled by the presence of small quantities of mesogenic species that are blended into, and co-assemble with the liquid crystalline (LC) mesophase of the side-chain LC BCP under study. In situ SAXS experiments reveal a pronounced dependence of the critical alignment field strength on the stoichiometry of the blend, and the ability to generate aligned microdomains with orientational distribution coefficients exceeding 0.95 at sub-1 T fields for appropriate stoichiometries. The alignment response overall can be rationalized in terms of increased mobility and grain size due to the presence of the mesogenic additive. We use a permanent magnet to fabricate films with aligned nanopores, and the utility of this approach to generate complex BCP microdomain patterns in thin films by local field screening are highlighted. NSF DMR-1410568 and DMR-0847534.

On the Tensorial Nature of Fluxes in Continuous Media.

ERIC Educational Resources Information Center

Stokes, Vijay Kumar; Ramkrishna, Doraiswami

1982-01-01

Argues that mass and energy fluxes in a fluid are vectors. Topics include the stress tensor, theorem for tensor fields, mass flux as a vector, stress as a second order tensor, and energy flux as a tensor. (SK)

Monopole-driven shell evolution below the doubly magic nucleus 132Sn explored with the long-lived isomer in 126Pd.

PubMed

Watanabe, H; Lorusso, G; Nishimura, S; Otsuka, T; Ogawa, K; Xu, Z Y; Sumikama, T; Söderström, P-A; Doornenbal, P; Li, Z; Browne, F; Gey, G; Jung, H S; Taprogge, J; Vajta, Zs; Wu, J; Yagi, A; Baba, H; Benzoni, G; Chae, K Y; Crespi, F C L; Fukuda, N; Gernhäuser, R; Inabe, N; Isobe, T; Jungclaus, A; Kameda, D; Kim, G D; Kim, Y K; Kojouharov, I; Kondev, F G; Kubo, T; Kurz, N; Kwon, Y K; Lane, G J; Moon, C-B; Montaner-Pizá, A; Moschner, K; Naqvi, F; Niikura, M; Nishibata, H; Nishimura, D; Odahara, A; Orlandi, R; Patel, Z; Podolyák, Zs; Sakurai, H; Schaffner, H; Simpson, G S; Steiger, K; Suzuki, H; Takeda, H; Wendt, A; Yoshinaga, K

2014-07-25

A new isomer with a half-life of 23.0(8) ms has been identified at 2406 keV in (126)Pd and is proposed to have a spin and parity of 10(+) with a maximally aligned configuration comprising two neutron holes in the 1h(11/2) orbit. In addition to an internal-decay branch through a hindered electric octupole transition, β decay from the long-lived isomer was observed to populate excited states at high spins in (126)Ag. The smaller energy difference between the 10(+) and 7(-) isomers in (126)Pd than in the heavier N=80 isotones can be interpreted as being ascribed to the monopole shift of the 1h(11/2) neutron orbit. The effects of the monopole interaction on the evolution of single-neutron energies below (132)Sn are discussed in terms of the central and tensor forces.

On the large-scale dynamics of rapidly rotating convection zones. [in solar and stellar interiors

NASA Technical Reports Server (NTRS)

Durney, B. R.

1983-01-01

The fact that the values of the eight basic waves present in turbulent flows in the presence of rotation prohibit a tilt of eddy towards the axis of rotation is incorporated into a formalism for rapidly rotating convection zones. Equations for turbulent velocities are defined in a rotating coordinate system, assuming that gravity and grad delta T act in a radial direction. An expression is derived for the lifetime of a basic wave and then for the average velocity vector. A real convective eddy is formulated and the wave vectors are calculated. The velocity amplitude and the stress tensor amplitude are integrated over the eddy domain. Applied to the solar convective zone, it is found that the convective cells are aligned along the axis of rotation at the poles and at the equator, a model that conflicts with nonrotating mixng length theory predictions.

Rank-Optimized Logistic Matrix Regression toward Improved Matrix Data Classification.

PubMed

Zhang, Jianguang; Jiang, Jianmin

2018-02-01

While existing logistic regression suffers from overfitting and often fails in considering structural information, we propose a novel matrix-based logistic regression to overcome the weakness. In the proposed method, 2D matrices are directly used to learn two groups of parameter vectors along each dimension without vectorization, which allows the proposed method to fully exploit the underlying structural information embedded inside the 2D matrices. Further, we add a joint [Formula: see text]-norm on two parameter matrices, which are organized by aligning each group of parameter vectors in columns. This added co-regularization term has two roles-enhancing the effect of regularization and optimizing the rank during the learning process. With our proposed fast iterative solution, we carried out extensive experiments. The results show that in comparison to both the traditional tensor-based methods and the vector-based regression methods, our proposed solution achieves better performance for matrix data classifications.

Aligned-or Not?

ERIC Educational Resources Information Center

Roseman, Jo Ellen; Koppal, Mary

2015-01-01

When state leaders and national partners in the development of the Next Generation Science Standards met to consider implementation strategies, states and school districts wanted to know which materials were aligned to the new standards. The answer from the developers was short but not sweet: You won't find much now, and it's going to…

Growth Of Oriented Crystals At Polymerized Membranes

DOEpatents

Charych, Deborah H. , Berman, Amir

2000-01-25

The present invention relates to methods and compositions for the growth and alignment of crystals at biopolymeric films. The methods and compositions of the present invention provide means to generate a variety of dense crystalline ceramic films, with totally aligned crystals, at low temperatures and pressures, suitable for use with polymer and plastic substrates.

Log-odds sequence logos

PubMed Central

Yu, Yi-Kuo; Capra, John A.; Stojmirović, Aleksandar; Landsman, David; Altschul, Stephen F.

2015-01-01

Motivation: DNA and protein patterns are usefully represented by sequence logos. However, the methods for logo generation in common use lack a proper statistical basis, and are non-optimal for recognizing functionally relevant alignment columns. Results: We redefine the information at a logo position as a per-observation multiple alignment log-odds score. Such scores are positive or negative, depending on whether a column’s observations are better explained as arising from relatedness or chance. Within this framework, we propose distinct normalized maximum likelihood and Bayesian measures of column information. We illustrate these measures on High Mobility Group B (HMGB) box proteins and a dataset of enzyme alignments. Particularly in the context of protein alignments, our measures improve the discrimination of biologically relevant positions. Availability and implementation: Our new measures are implemented in an open-source Web-based logo generation program, which is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/logoddslogo/index.html. A stand-alone version of the program is also available from this site. Contact: altschul@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25294922

Generation of Alfvenic Double Layers, Formation of Auroral Arcs, and Their Impact on Energy and Momentum Transfer in M-I Coupling System

NASA Astrophysics Data System (ADS)

Song, Y.; Lysak, R. L.

2017-12-01

Parallel electrostatic electric fields provide a powerful mechanism to accelerate auroral particles to high energy in the auroral acceleration region (AAR), creating both quasi-static and Alfvenic discrete aurorae. The total field-aligned current can be written as J||total=J||+J||D, where the displacement current is denoted as J||D=(1/4π)(∂E||/∂t), which describes the E||-generation (Song and Lysak, 2006). The generation of the total field-aligned current is related to spatial gradients of the parallel vorticity caused by the axial torque acting on field-aligned flux tubes in M-I coupling system. It should be noticed that parallel electric fields are not produced by the field-aligned current. In fact, the E||-generation is caused by Alfvenic interaction in the M-I coupling system, and is favored by a low plasma density and the enhanced localized azimuthal magnetic flux. We suggest that the nonlinear interaction of incident and reflected Alfven wave packets in the AAR can create reactive stress concentration, and therefore can generate the parallel electrostatic electric fields together with a seed low density cavity. The generated electric fields will quickly deepen the seed low density cavity, which can effectively create even stronger electrostatic electric fields. The electrostatic electric fields nested in a low density cavity and surrounded by enhanced azimuthal magnetic flux constitute Alfvenic electromagnetic plasma structures, such as Alfvenic Double Layers (DLs). The Poynting flux carried by Alfven waves can continuously supply energy from the generator region to the auroral acceleration region, supporting and sustaining Alfvenic DLs with long-lasting electrostatic electric fields which accelerate auroral particles to high energy. The generation of parallel electric fields and the formation of auroral arcs can redistribute perpendicular mechanical and magnetic stresses in auroral flux tubes, decoupling the magnetosphere from ionosphere drag locally. This may enhance the magnetotail earthward shear flows and rapidly buildup stronger parallel electric fields in the auroral acceleration region, leading to a sudden and violent tail energy release, if there is accumulated free magnetic energy in the tail.

Flapping current sheet with superposed waves seen in space and on the ground

NASA Astrophysics Data System (ADS)

Wang, G. Q.; Volwerk, M.; Nakamura, R.; Boakes, P.; Zhang, T. L.; Yoshikawa, A.; Baishev, D. G.

2014-12-01

A wavy current sheet event observed on 15 October 2004 between 1235 and 1300 UT has been studied by using Cluster and ground-based magnetometer data. Waves propagating from the tail center to the duskside flank with a period ~30 s and wavelength ~1 RE are superimposed on a flapping current sheet, accompanied with a bursty bulk flow. Three Pi2 pulsations, with onset at ~1236, ~1251, and ~1255 UT, respectively, are observed at the Tixie station located near the foot points of Cluster. The mechanism creating the Pi2 (period ~40 s) onset at ~1236 UT is unclear. The second Pi2 (period ~90 s, onset at ~1251 UT) is associated with a strong field-aligned current, which has a strong transverse component of the magnetic field, observed by Cluster with a time delay ~60 s. We suggest that it is caused by bouncing Alfvén waves between the northern and southern ionosphere which transport the field-aligned current. For the third Pi2 (period ~60 s) there is almost no damping at the first three periods. They occur in conjunction with periodic field-aligned currents one-on-one with 72 s delay. We suggest that it is generated by these periodic field-aligned currents. We conclude that the strong field-aligned currents generated in the plasma sheet during flapping with superimposed higher-frequency waves can drive Pi2 pulsations on the ground, and periodic field-aligned currents can even control the period of the Pi2s.

Particle localization, spinor two-valuedness, and Fermi quantization of tensor systems

NASA Technical Reports Server (NTRS)

Reifler, Frank; Morris, Randall

1994-01-01

Recent studies of particle localization shows that square-integrable positive energy bispinor fields in a Minkowski space-time cannot be physically distinguished from constrained tensor fields. In this paper we generalize this result by characterizing all classical tensor systems, which admit Fermi quantization, as those having unitary Lie-Poisson brackets. Examples include Euler's tensor equation for a rigid body and Dirac's equation in tensor form.

Erratum to Surface‐wave green’s tensors in the near field

USGS Publications Warehouse

Haney, Matthew M.; Hisashi Nakahara,

2016-01-01

Haney and Nakahara (2014) derived expressions for surface‐wave Green’s tensors that included near‐field behavior. Building on the result for a force source, Haney and Nakahara (2014) further derived expressions for a general point moment tensor source using the exact Green’s tensors. However, it has come to our attention that, although the Green’s tensors were correct, the resulting expressions for a general point moment tensor source were missing some terms. In this erratum, we provide updated expressions with these missing terms. The inclusion of the missing terms changes the example given in Haney and Nakahara (2014).

Simultaneous inversion of seismic velocity and moment tensor using elastic-waveform inversion of microseismic data: Application to the Aneth CO2-EOR field

NASA Astrophysics Data System (ADS)

Chen, Y.; Huang, L.

2017-12-01

Moment tensors are key parameters for characterizing CO2-injection-induced microseismic events. Elastic-waveform inversion has the potential to providing accurate results of moment tensors. Microseismic waveforms contains information of source moment tensors and the wave propagation velocity along the wavepaths. We develop an elastic-waveform inversion method to jointly invert the seismic velocity model and moment tensor. We first use our adaptive moment-tensor joint inversion method to estimate moment tensors of microseismic events. Our adaptive moment-tensor inversion method jointly inverts multiple microseismic events with similar waveforms within a cluster to reduce inversion uncertainty for microseismic data recorded using a single borehole geophone array. We use this inversion result as the initial model for our elastic-waveform inversion to minimize the cross-correlated-based data misfit between observed data and synthetic data. We verify our method using synthetic microseismic data and obtain improved results of both moment tensors and seismic velocity model. We apply our new inversion method to microseismic data acquired at a CO2-enhanced oil recovery field in Aneth, Utah, using a single borehole geophone array. The results demonstrate that our new inversion method significantly reduces the data misfit compared to the conventional ray-theory-based moment-tensor inversion.

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

PubMed

Zheng, Qi; Grice, Elizabeth A

2016-10-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

Clinical application of diffusion tensor magnetic resonance imaging in skeletal muscle

PubMed Central

Longwei, Xu

2012-01-01

Summary Diffusion tensor magnetic resonance imaging (DTI) is increasingly applied in the detection and characterization of skeletal muscle. This promising technique has aroused much enthusiasm and generated high expectations, because it is able to provide some specific information of skeletal muscle that is not available from other imaging modalities. Compared with conventional MRI, DTI could reconstruct the trajectories of skeletal muscle fibers. It makes it possible to non-invasively detect several physiological values (diffusion values), like fractional anisotropy (FA) and apparent diffusion coefficient (ADC), which have a great association with the muscle physiology and pathology. Furthermore, other advantages of DTI are the capability of investigating the muscle biomechanics and also investigate the pathological condition of skeletal muscle. Finally, several challenges, which limit the wide application of DTI in skeletal muscle, were discussed. It is believed that this review may arouse in-depth studies on the clinical application of DTI in skeletal muscle in future. PMID:23738269

ON THE SPIN CORRELATIONS OF MUONS AND TAU LEPTONS GENERATED IN THE ANNIHILATION PROCESSES e+e- → μ+μ-, e+e- → τ+τ-

NASA Astrophysics Data System (ADS)

Lyuboshitz, Valery V.; Lyuboshitz, Vladimir L.

2014-12-01

Using the technique of helicity amplitudes, the electromagnetic process e+e- → μ+μ-(τ+τ-) is theoretically studied in the one-photon approximation. The structure of the triplet states of the final (μ+μ-) system is analyzed. It is shown that in the case of unpolarized electron and positron the final muons are also unpolarized, but their spins are strongly correlated. Explicit expressions for the components of the correlation tensor of the (μ+μ-) system are derived. The formula for the angular correlation at the decays of final muons μ+ and μ- is obtained. It is demonstrated that spin correlations of muons in the considered process have the purely quantum character, since one of the Bell-type incoherence inequalities for the correlation tensor components is always violated.

General equilibrium second-order hydrodynamic coefficients for free quantum fields

NASA Astrophysics Data System (ADS)

Buzzegoli, M.; Grossi, E.; Becattini, F.

2017-10-01

We present a systematic calculation of the corrections of the stress-energy tensor and currents of the free boson and Dirac fields up to second order in thermal vorticity, which is relevant for relativistic hydrodynamics. These corrections are non-dissipative because they survive at general thermodynamic equilibrium with non vanishing mean values of the conserved generators of the Lorentz group, i.e. angular momenta and boosts. Their equilibrium nature makes it possible to express the relevant coefficients by means of correlators of the angular-momentum and boost operators with stress-energy tensor and current, thus making simpler to determine their so-called "Kubo formulae". We show that, at least for free fields, the corrections are of quantum origin and we study several limiting cases and compare our results with previous calculations. We find that the axial current of the free Dirac field receives corrections proportional to the vorticity independently of the anomalous term.

Multidimensional supersymmetric quantum mechanics: spurious states for the tensor sector two Hamiltonian.

PubMed

Chou, Chia-Chun; Kouri, Donald J

2013-04-25

We show that there exist spurious states for the sector two tensor Hamiltonian in multidimensional supersymmetric quantum mechanics. For one-dimensional supersymmetric quantum mechanics on an infinite domain, the sector one and two Hamiltonians have identical spectra with the exception of the ground state of the sector one. For tensorial multidimensional supersymmetric quantum mechanics, there exist normalizable spurious states for the sector two Hamiltonian with energy equal to the ground state energy of the sector one. These spurious states are annihilated by the adjoint charge operator, and hence, they do not correspond to physical states for the original Hamiltonian. The Hermitian property of the sector two Hamiltonian implies the orthogonality between spurious and physical states. In addition, we develop a method for construction of a specific form of the spurious states for any quantum system and also generate several spurious states for a two-dimensional anharmonic oscillator system and for the hydrogen atom.

A braided monoidal category for free super-bosons

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

Runkel, Ingo, E-mail: ingo.runkel@uni-hamburg.de

The chiral conformal field theory of free super-bosons is generated by weight one currents whose mode algebra is the affinisation of an abelian Lie super-algebra h with non-degenerate super-symmetric pairing. The mode algebras of a single free boson and of a single pair of symplectic fermions arise for even|odd dimension 1|0 and 0|2 of h, respectively. In this paper, the representations of the untwisted mode algebra of free super-bosons are equipped with a tensor product, a braiding, and an associator. In the symplectic fermion case, i.e., if h is purely odd, the braided monoidal structure is extended to representations ofmore » the Z/2Z-twisted mode algebra. The tensor product is obtained by computing spaces of vertex operators. The braiding and associator are determined by explicit calculations from three- and four-point conformal blocks.« less

Pressure gradients fail to predict diffusio-osmosis

NASA Astrophysics Data System (ADS)

Liu, Yawei; Ganti, Raman; Frenkel, Daan

2018-05-01

We present numerical simulations of diffusio-osmotic flow, i.e. the fluid flow generated by a concentration gradient along a solid-fluid interface. In our study, we compare a number of distinct approaches that have been proposed for computing such flows and compare them with a reference calculation based on direct, non-equilibrium molecular dynamics simulations. As alternatives, we consider schemes that compute diffusio-osmotic flow from the gradient of the chemical potentials of the constituent species and from the gradient of the component of the pressure tensor parallel to the interface. We find that the approach based on treating chemical potential gradients as external forces acting on various species agrees with the direct simulations, thereby supporting the approach of Marbach et al (2017 J. Chem. Phys. 146 194701). In contrast, an approach based on computing the gradients of the microscopic pressure tensor does not reproduce the direct non-equilibrium results.

A tensor network approach to many-body localization

NASA Astrophysics Data System (ADS)

Yu, Xiongjie; Pekker, David; Clark, Bryan

Understanding the many-body localized phase requires access to eigenstates in the middle of the many-body spectrum. While exact-diagonalization is able to access these eigenstates, it is restricted to systems sizes of about 22 spins. To overcome this limitation, we develop tensor network algorithms which increase the accessible system size by an order of magnitude. We describe both our new algorithms as well as the additional physics about MBL we can extract from them. For example, we demonstrate the power of these methods by verifying the breakdown of the Eigenstate Thermalization Hypothesis (ETH) in the many-body localized phase of the random field Heisenberg model, and show the saturation of entanglement in the MBL phase and generate eigenstates that differ by local excitations. Work was supported by AFOSR FA9550-10-1-0524 and FA9550-12-1-0057, the Kaufmann foundation, and SciDAC FG02-12ER46875.

A framework for developing a mimetic tensor artificial viscosity for Lagrangian hydrocodes on arbitrary polygonal and polyhedral meshes (u)

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

Lipnikov, Konstantin; Shashkov, Mikhail

2011-01-11

We construct a new mimetic tensor artificial viscosity on general polygonal and polyhedral meshes. The tensor artificial viscosity is based on a mimetic discretization of coordinate invariant operators, divergence of a tensor and gradient of a vector. The focus of this paper is on the symmetric form, div ({mu},{var_epsilon}(u)), of the tensor artificial viscosity where {var_epsilon}(u) is the symmetrized gradient of u and {mu}, is a tensor. The mimetic discretizations of this operator is derived for the case of a full tensor coefficient {mu}, that may reflect a shock direction. We demonstrate performance of the new viscosity for the Nohmore » implosion, Sedov explosion and Saltzman piston problems in both Cartesian and axisymmetric coordinate systems.« less

Tensor-based spatiotemporal saliency detection

NASA Astrophysics Data System (ADS)

Dou, Hao; Li, Bin; Deng, Qianqian; Zhang, LiRui; Pan, Zhihong; Tian, Jinwen

2018-03-01

This paper proposes an effective tensor-based spatiotemporal saliency computation model for saliency detection in videos. First, we construct the tensor representation of video frames. Then, the spatiotemporal saliency can be directly computed by the tensor distance between different tensors, which can preserve the complete temporal and spatial structure information of object in the spatiotemporal domain. Experimental results demonstrate that our method can achieve encouraging performance in comparison with the state-of-the-art methods.

Kinematic Alignment and Bonding of Silicon Mirrors for High-Resolution Astronomical X-Ray Optics

NASA Technical Reports Server (NTRS)

Chan, Kai-Wing; Mazzarella, James R.; Saha, Timo T.; Zhang, William W.; Mcclelland, Ryan S.; Biskack, Michael P.; Riveros, Raul E.; Allgood, Kim D.; Kearney, John D.; Sharpe, Marton V.;

Technique for information retrieval using enhanced latent semantic analysis generating rank approximation matrix by factorizing the weighted morpheme-by-document matrix

DOEpatents

Chew, Peter A; Bader, Brett W

2012-10-16

A technique for information retrieval includes parsing a corpus to identify a number of wordform instances within each document of the corpus. A weighted morpheme-by-document matrix is generated based at least in part on the number of wordform instances within each document of the corpus and based at least in part on a weighting function. The weighted morpheme-by-document matrix separately enumerates instances of stems and affixes. Additionally or alternatively, a term-by-term alignment matrix may be generated based at least in part on the number of wordform instances within each document of the corpus. At least one lower rank approximation matrix is generated by factorizing the weighted morpheme-by-document matrix and/or the term-by-term alignment matrix.

Seismic properties and mineral crystallographic preferred orientations from EBSD data: Results from a crustal-scale detachment system, Aegean region

NASA Astrophysics Data System (ADS)

Cossette, Élise; Schneider, David; Audet, Pascal; Grasemann, Bernhard; Habler, Gerlinde

2015-05-01

The crystallographic preferred orientations (CPOs) were measured on a suite of samples representative of different structural depths along the West Cycladic Detachment System, Greece. Electron backscatter diffraction (EBSD) analyses were conducted on calcitic and mica schists, impure quartzites, and a blueschist, and the average seismic properties of the rocks were calculated with the Voigt-Reuss-Hill average of the single minerals' elastic stiffness tensor. The calcitic and quartzitic rocks have P- and S-wave velocity anisotropies (AVp, AVs) averaging 8.1% and 7.1%, respectively. The anisotropy increases with depth represented by the blueschist, with AVp averaging 20.3% and AVs averaging 14.5%, due to the content of aligned glaucophane and mica, which strongly control the seismic properties of the rocks. Localised anisotropies of very high magnitudes are caused by the presence of mica schists as they possess the strongest anisotropies, with values of ~ 25% for AVp and AVs. The direction of the fast and slow P-wave velocities occurs parallel and perpendicular to the foliation, respectively, for most samples. The fast propagation has the same NE-SW orientation as the lithospheric stretching direction experienced in the Cyclades since the Late Oligocene. The maximum shear wave anisotropy is subhorizontal, similarly concordant with mineral alignment that developed during extension in the Aegean. Radial anisotropy in the Aegean mid-crust is strongly favoured to azimuthal anisotropy by our results.

Beamlike photon pairs entangled by a 2x2 fiber

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

Lo, Hsin-Pin; Department of Electrophysics, National Chiao-Tung University, Hsinchu, 300, Taiwan; Yabushita, Atsushi

Polarization-entangled photon pairs have been widely used as a light source of quantum communication. The polarization-entangled photon pairs are generally obtained at the crossing points of the light cones that are generated from a type-II nonlinear crystal. However, it is hard to pick up the photon pairs coming out from the crossing points because of their invisible wavelength and low intensity. In our previous work, we succeeded in generating polarization-entangled photon pairs by overlapping two light paths for the photon-pair generation. The photon pairs could be entangled in all of the generated photon pairs without clipping the crossing points, evenmore » with some difficulty in its alignment to overlap the two light paths. In this paper, we have developed an optical system which generates polarization-entangled photon pairs using a beamlike photon pair, without the difficulty in alignment. The measured results show that the photon pairs generated in the system are entangled in their polarizations.« less

Tensor network method for reversible classical computation

NASA Astrophysics Data System (ADS)

Yang, Zhi-Cheng; Kourtis, Stefanos; Chamon, Claudio; Mucciolo, Eduardo R.; Ruckenstein, Andrei E.

2018-03-01

We develop a tensor network technique that can solve universal reversible classical computational problems, formulated as vertex models on a square lattice [Nat. Commun. 8, 15303 (2017), 10.1038/ncomms15303]. By encoding the truth table of each vertex constraint in a tensor, the total number of solutions compatible with partial inputs and outputs at the boundary can be represented as the full contraction of a tensor network. We introduce an iterative compression-decimation (ICD) scheme that performs this contraction efficiently. The ICD algorithm first propagates local constraints to longer ranges via repeated contraction-decomposition sweeps over all lattice bonds, thus achieving compression on a given length scale. It then decimates the lattice via coarse-graining tensor contractions. Repeated iterations of these two steps gradually collapse the tensor network and ultimately yield the exact tensor trace for large systems, without the need for manual control of tensor dimensions. Our protocol allows us to obtain the exact number of solutions for computations where a naive enumeration would take astronomically long times.

ARYANA: Aligning Reads by Yet Another Approach

PubMed Central

2014-01-01

Motivation Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. Contribution We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. Availability ARYANA with complete source code can be obtained from http://github.com/aryana-aligner PMID:25252881

ARYANA: Aligning Reads by Yet Another Approach.

PubMed

Gholami, Milad; Arbabi, Aryan; Sharifi-Zarchi, Ali; Chitsaz, Hamidreza; Sadeghi, Mehdi

2014-01-01

Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $10(6) prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. ARYANA with complete source code can be obtained from http://github.com/aryana-aligner.

Polarization-Modulated Second Harmonic Generation Microscopy in Collagen

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

Stoller, P C

Collagen is a key structural protein in the body; several pathological conditions lead to changes in collagen. Among imaging modalities that can be used in vivo, second harmonic generation (SHG) microscopy has a key advantage: it provides {approx}1 {micro}m resolution information about collagen structure as a function of depth. A new technique--polarization-modulated SHG--is presented: it permits simultaneous measurement of collagen orientation, of a lower bound on the magnitude of the second order nonlinear susceptibility tensor, and of the ratio of the two independent elements in this tensor. It is applied to characterizing SHG in collagen and to determining effects ofmore » biologically relevant changes in collagen structure. The magnitude of the second harmonic signal in two dimensional images varies with position even in structurally homogeneous tissue; this phenomenon is due to interference between second harmonic light generated by neighboring fibrils, which are randomly oriented parallel or anti-parallel to each other. Studies in which focal spot size was varied indicated that regions where fibrils are co-oriented are less than {approx}1.5 {micro}m in diameter. A quartz reference was used to determine the spot size as well as a lower limit (d{sub xxx} > 0.3 pm/V) for the magnitude of the second order nonlinear susceptibility. The ratio of the two independent tensor elements ranged between d{sub XYY}/d{sub XXX} = 0.60 and 0.75. SHG magnitude alone was not useful for identifying structural anomalies in collagenous tissue. Instead, changes in the polarization dependence of SHG were used to analyze biologically relevant perturbations in collagen structure. Changes in polarization dependence were observed in dehydrated samples, but not in highly crosslinked samples, despite significant alterations in packing structure. Complete thermal denaturation and collagenase digestion produced samples with no detectable SHG signal. Collagen orientation was measured in thin samples of several different tissues in transmission mode as well as at different depths (up to 200 {micro}m) in thick samples in reflection mode; birefringence had no effect on the measurement. These studies showed that SHG microscopy was capable of detecting pathophysiological changes in collagen structure, suggesting that this technique has potential clinical applications.« less

Modified alignment CGHs for aspheric surface test

NASA Astrophysics Data System (ADS)

Song, Jae-Bong; Yang, Ho-Soon; Rhee, Hyug-Gyo; Lee, Yun-Woo

2009-08-01

Computer Generated Holograms (CGH) for optical test are commonly consisted of one main pattern for testing aspheric surface and some alignment patterns for aligning the interferometer, CGH, and the test optics. To align the CGH plate and the test optics, we designed the alignment CGHs modified from the cat's eye alignment method, which are consisted of a couple of CGH patterns. The incident beam passed through the one part of the alignment CGH pattern is focused onto the one radius position of the test aspheric surface, and is reflected to the other part, and vice versa. This method has several merits compared to the conventional cat's eye alignment method. First, this method can be used in testing optics with a center hole, and the center part of CGH plate can be assigned to the alignment pattern. Second, the alignment pattern becomes a concentric circular arc pattern. The whole CGH patterns including the main pattern and alignment patterns are consisted of only concentric circular fringes. This concentric circular pattern can be easily made by the polar coordinated writer with circular scanning. The required diffraction angle becomes relatively small, so the 1st order diffraction beams instead of the 3rd order diffraction beam can be used as alignment beams, and the visibility can be improved. This alignment method also is more sensitive to the tilt and the lateral shift of the test aspheric surface. Using this alignment pattern, a 200 mm diameter F/0.5 aspheric mirror and a 600 mm diameter F/0.9 mirror were tested.

Genten: Software for Generalized Tensor Decompositions v. 1.0.0

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

Phipps, Eric T.; Kolda, Tamara G.; Dunlavy, Daniel

Tensors, or multidimensional arrays, are a powerful mathematical means of describing multiway data. This software provides computational means for decomposing or approximating a given tensor in terms of smaller tensors of lower dimension, focusing on decomposition of large, sparse tensors. These techniques have applications in many scientific areas, including signal processing, linear algebra, computer vision, numerical analysis, data mining, graph analysis, neuroscience and more. The software is designed to take advantage of parallelism present emerging computer architectures such has multi-core CPUs, many-core accelerators such as the Intel Xeon Phi, and computation-oriented GPUs to enable efficient processing of large tensors.

The Kummer tensor density in electrodynamics and in gravity

NASA Astrophysics Data System (ADS)

Baekler, Peter; Favaro, Alberto; Itin, Yakov; Hehl, Friedrich W.

2014-10-01

Guided by results in the premetric electrodynamics of local and linear media, we introduce on 4-dimensional spacetime the new abstract notion of a Kummer tensor density of rank four, K. This tensor density is, by definition, a cubic algebraic functional of a tensor density of rank four T, which is antisymmetric in its first two and its last two indices: T=-T=-T. Thus, K∼T3, see Eq. (46). (i) If T is identified with the electromagnetic response tensor of local and linear media, the Kummer tensor density encompasses the generalized Fresnel wave surfaces for propagating light. In the reversible case, the wave surfaces turn out to be Kummer surfaces as defined in algebraic geometry (Bateman 1910). (ii) If T is identified with the curvature tensor R of a Riemann-Cartan spacetime, then K∼R3 and, in the special case of general relativity, K reduces to the Kummer tensor of Zund (1969). This K is related to the principal null directions of the curvature. We discuss the properties of the general Kummer tensor density. In particular, we decompose K irreducibly under the 4-dimensional linear group GL(4,R) and, subsequently, under the Lorentz group SO(1,3).

OPERATOR NORM INEQUALITIES BETWEEN TENSOR UNFOLDINGS ON THE PARTITION LATTICE

PubMed Central

Wang, Miaoyan; Duc, Khanh Dao; Fischer, Jonathan; Song, Yun S.

2017-01-01

Interest in higher-order tensors has recently surged in data-intensive fields, with a wide range of applications including image processing, blind source separation, community detection, and feature extraction. A common paradigm in tensor-related algorithms advocates unfolding (or flattening) the tensor into a matrix and applying classical methods developed for matrices. Despite the popularity of such techniques, how the functional properties of a tensor changes upon unfolding is currently not well understood. In contrast to the body of existing work which has focused almost exclusively on matricizations, we here consider all possible unfoldings of an order-k tensor, which are in one-to-one correspondence with the set of partitions of {1, …, k}. We derive general inequalities between the lp-norms of arbitrary unfoldings defined on the partition lattice. In particular, we demonstrate how the spectral norm (p = 2) of a tensor is bounded by that of its unfoldings, and obtain an improved upper bound on the ratio of the Frobenius norm to the spectral norm of an arbitrary tensor. For specially-structured tensors satisfying a generalized definition of orthogonal decomposability, we prove that the spectral norm remains invariant under specific subsets of unfolding operations. PMID:28286347

The Twist Tensor Nuclear Norm for Video Completion.

PubMed

Hu, Wenrui; Tao, Dacheng; Zhang, Wensheng; Xie, Yuan; Yang, Yehui

2017-12-01

In this paper, we propose a new low-rank tensor model based on the circulant algebra, namely, twist tensor nuclear norm (t-TNN). The twist tensor denotes a three-way tensor representation to laterally store 2-D data slices in order. On one hand, t-TNN convexly relaxes the tensor multirank of the twist tensor in the Fourier domain, which allows an efficient computation using fast Fourier transform. On the other, t-TNN is equal to the nuclear norm of block circulant matricization of the twist tensor in the original domain, which extends the traditional matrix nuclear norm in a block circulant way. We test the t-TNN model on a video completion application that aims to fill missing values and the experiment results validate its effectiveness, especially when dealing with video recorded by a nonstationary panning camera. The block circulant matricization of the twist tensor can be transformed into a circulant block representation with nuclear norm invariance. This representation, after transformation, exploits the horizontal translation relationship between the frames in a video, and endows the t-TNN model with a more powerful ability to reconstruct panning videos than the existing state-of-the-art low-rank models.

Relativistic interpretation of the nature of the nuclear tensor force

NASA Astrophysics Data System (ADS)

Zong, Yao-Yao; Sun, Bao-Yuan

2018-02-01

The spin-dependent nature of the nuclear tensor force is studied in detail within the relativistic Hartree-Fock approach. The relativistic formalism for the tensor force is supplemented with an additional Lorentz-invariant tensor formalism in the σ-scalar channel, so as to take into account almost fully the nature of the tensor force brought about by the Fock diagrams in realistic nuclei. Specifically, the tensor sum rules are tested for the spin and pseudo-spin partners with and without nodes, to further understand the nature of the tensor force within the relativistic model. It is shown that the interference between the two components of nucleon spinors causes distinct violations of the tensor sum rules in realistic nuclei, mainly due to the opposite signs on the κ quantities of the upper and lower components, as well as the nodal difference. However, the sum rules can be precisely reproduced if the same radial wave functions are taken for the spin/pseudo-spin partners in addition to neglecting the lower/upper components, revealing clearly the nature of the tensor force. Supported by National Natural Science Foundation of China (11375076, 11675065) and the Fundamental Research Funds for the Central Universities (lzujbky-2016-30)

OPERATOR NORM INEQUALITIES BETWEEN TENSOR UNFOLDINGS ON THE PARTITION LATTICE.

PubMed

Wang, Miaoyan; Duc, Khanh Dao; Fischer, Jonathan; Song, Yun S

2017-05-01

Interest in higher-order tensors has recently surged in data-intensive fields, with a wide range of applications including image processing, blind source separation, community detection, and feature extraction. A common paradigm in tensor-related algorithms advocates unfolding (or flattening) the tensor into a matrix and applying classical methods developed for matrices. Despite the popularity of such techniques, how the functional properties of a tensor changes upon unfolding is currently not well understood. In contrast to the body of existing work which has focused almost exclusively on matricizations, we here consider all possible unfoldings of an order- k tensor, which are in one-to-one correspondence with the set of partitions of {1, …, k }. We derive general inequalities between the l p -norms of arbitrary unfoldings defined on the partition lattice. In particular, we demonstrate how the spectral norm ( p = 2) of a tensor is bounded by that of its unfoldings, and obtain an improved upper bound on the ratio of the Frobenius norm to the spectral norm of an arbitrary tensor. For specially-structured tensors satisfying a generalized definition of orthogonal decomposability, we prove that the spectral norm remains invariant under specific subsets of unfolding operations.

Creating Next Generation Teacher Preparation Programs to Support Implementation of the Next Generation Science Standards and Common Core State Standards in K-12 Schools: An Opportunity for the Earth and Space Sciences

NASA Astrophysics Data System (ADS)

Geary, E. E.; Egger, A. E.; Julin, S.; Ronca, R.; Vokos, S.; Ebert, E.; Clark-Blickenstaff, J.; Nollmeyer, G.

2015-12-01

A consortium of two and four year Washington State Colleges and Universities in partnership with Washington's Office of the Superintendent of Public Instruction (OSPI), the Teachers of Teachers of Science, and Teachers of Teachers of Mathematics, and other key stakeholders, is currently working to improve science and mathematics learning for all Washington State students by creating a new vision for STEM teacher preparation in Washington State aligned with the Next Generation Science Standards (NGSS) and the Common Core State Standards (CCSS) in Mathematics and Language Arts. Specific objectives include: (1) strengthening elementary and secondary STEM Teacher Preparation courses and curricula, (2) alignment of STEM teacher preparation programs across Washington State with the NGSS and CCSS, (3) development of action plans to support implementation of STEM Teacher Preparation program improvement at Higher Education Institutions (HEIs) across the state, (4) stronger collaborations between HEIs, K-12 schools, government agencies, Non-Governmental Organizations, and STEM businesses, involved in the preparation of preservice STEM teachers, (5) new teacher endorsements in Computer Science and Engineering, and (6) development of a proto-type model for rapid, adaptable, and continuous improvement of STEM teacher preparation programs. A 2015 NGSS gap analysis of teacher preparation programs across Washington State indicates relatively good alignment of courses and curricula with NGSS Disciplinary Core Ideas and Scientific practices, but minimal alignment with NGSS Engineering practices and Cross Cutting Concepts. Likewise, Computer Science and Sustainability ideas and practices are not well represented in current courses and curricula. During the coming year teams of STEM faculty, education faculty and administrators will work collaboratively to develop unique action plans for aligning and improving STEM teacher preparation courses and curricula at their institutions.

Shear induced alignment of short nanofibers in 3D printed polymer composites.

PubMed

Yunus, Doruk Erdem; Shi, Wentao; Sohrabi, Salman; Liu, Yaling

2016-12-09

3D printing of composite materials offers an opportunity to combine the desired properties of composite materials with the flexibility of additive manufacturing in geometric shape and complexity. In this paper, the shear-induced alignment of aluminum oxide nanowires during stereolithography printing was utilized to fabricate a nanowire reinforced polymer composite. To align the fibers, a lateral oscillation mechanism was implemented and combined with wall pattern printing technique to generate shear flow in both vertical and horizontal directions. A series of specimens were fabricated for testing the composite material's tensile strength. The results showed that mechanical properties of the composite were improved by reinforcement of nanofibers through shear induced alignment. The improvement of tensile strength was approximately ∼28% by aligning the nanowires at 5 wt% (∼1.5% volume fraction) loading of aluminum oxide nanowires.

Fabrication of overlaid nanopattern arrays for plasmon memory

NASA Astrophysics Data System (ADS)

Okabe, Takao; Wadayama, Hisahiro; Taniguchi, Jun

2018-01-01

Stacking technique of nanopattern array is gathering attention to fabricate next generation data storage such as plasmon memory. This technique provides multi- overlaid nanopatterns which made by nanoimprint lithography. In the structure, several metal nanopatterned layer and resin layer as a spacer are overlaid alternately. The horizontal position of nanopatterns to under nanopatterns and thickness of resin layer as spacer should be controlled accurately, because these parameters affect reading performance and capacity of plasmon memory. In this study, we developed new alignment mark to fabricate multi- overlaid nanopatterns. The alignment accuracy with the order of 300 nm was demonstrated for Ag nanopatterns in 2 layers. The alignment mark can measure the thickness of spacer. The relationship of spacer thickness and position of scale bar on the alignment mark was measured. The usefulness of the alignment mark for highdensity plasmon memory is shown.

Polarization properties of below-threshold harmonics from aligned molecules H2+ in linearly polarized laser fields.

PubMed

Dong, Fulong; Tian, Yiqun; Yu, Shujuan; Wang, Shang; Yang, Shiping; Chen, Yanjun

2015-07-13

We investigate the polarization properties of below-threshold harmonics from aligned molecules in linearly polarized laser fields numerically and analytically. We focus on lower-order harmonics (LOHs). Our simulations show that the ellipticity of below-threshold LOHs depends strongly on the orientation angle and differs significantly for different harmonic orders. Our analysis reveals that this LOH ellipticity is closely associated with resonance effects and the axis symmetry of the molecule. These results shed light on the complex generation mechanism of below-threshold harmonics from aligned molecules.

Experimental image alignment system

NASA Technical Reports Server (NTRS)

Moyer, A. L.; Kowel, S. T.; Kornreich, P. G.

1980-01-01

A microcomputer-based instrument for image alignment with respect to a reference image is described which uses the DEFT sensor (Direct Electronic Fourier Transform) for image sensing and preprocessing. The instrument alignment algorithm which uses the two-dimensional Fourier transform as input is also described. It generates signals used to steer the stage carrying the test image into the correct orientation. This algorithm has computational advantages over algorithms which use image intensity data as input and is suitable for a microcomputer-based instrument since the two-dimensional Fourier transform is provided by the DEFT sensor.

Vorticity equation for MHD fast waves in geospace environment

NASA Technical Reports Server (NTRS)

Yamauchi, M.; Lundin, R.; Lui, A. T. Y.

1993-01-01

The MHD vorticity equation is modified in order to apply it to nonlinear MHD fast waves or shocks when their extent along the magnetic field is limited. Field-aligned current (FAC) generation is also discussed on the basis of this modified vorticity equation. When the wave normal is not aligned to the finite velocity convection and the source region is spatially limited, a longitudinal polarization causes a pair of plus and minus charges inside the compressional plane waves or shocks, generating a pair of FACs. This polarization is not related to the separation between the electrons and ions caused by their difference in mass, a separation which is inherent to compressional waves. The resultant double field-aligned current structure exists both with and without the contributions from curvature drift, which is questionable in terms of its contribution to vorticity change from the viewpoint of single-particle motion.