Initial Grid Research Articles

Relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data.

Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis.Availability and implementation: The software relax is written in Python with C modules and is released under the GPLv3+ license. Source code and precompiled binaries for all major operating systems are available from http://www.nmr-relax.com.Contact: edward@nmr-relax.com

Cellular Automata Supportingn-Connectivity

We propose a new algorithm based on cellular automation (CA) for preservingn-connectivity,n>1. The CA algorithm transforms an initial grid configuration in a grid with same number of holes but without 1-connected components. Also, maximal thinning ofn-connected components,n>1, is achieved. The grid can be used as initial for investigating properties of initial grid. Computational performances are evaluated and measured on real cases. The obtained results indicate that the proposed approach achieves comparable complexity as standard approaches; however, the speed-up and scalability of the proposed algorithm are not limited by the number of processing nodes.

Surface Modernities: Open-Air Markets, Containment and Verticality in Two Border Towns of Russia and China

This article focuses on the contrasting urbanisms that characterize the two cities of Heihe and Blagoveshchensk on the Sino-Russian border. Since 1990, with the bulk of international trade taking place on the Chinese side, Heihe has rapidly developed into a modern town; by contrast, Blagoveshchensk appears sedate and almost stagnant. Another stark contrast between the two cities is in the ways in which ideas of modernity are spatialized through their urban practices, with Blagoveshchensk demonstrating a preference for horizontal functionalism while Heihe largely follows the iconic and vertical model found in the megacities of the Chinese south.Foregrounding this very spatial imbalance, the paper argues that the Russian association between horizontality and modernity unwittingly collapses Heihe’s riverfront skyline into a smooth surface lacking depth, and renders invisible those economic drivers that operate below this surface as well as along a vertical axis. As a result of this, spatiality provides an initial cultural grid through which the development, success and modernity of the Other is assessed.The methodology followed in this article is primarily anthropological. The research was carried out in October and November2011. A dozen semi-structured and open-ended interviews were conducted with informants of diverse ages and social backgrounds, including businessmen and women, academics, young professionals and students. This research was funded through a grant by the Newton Trust (Cambridge, UK).

Managing the Global Dataset in Block-index based on ESSG

Abstract. Earth observation system, which can realize global coverage in three dimensions, has provided massive data from earth observations at global scale for Earth System Science (ESS) and global change researches. It is named SDOG-based ESSG that the Spheroid Degenerated Octree Grid (SDOG) was chosen as an initial grid to develop an Earth System Spatial Grid (ESSG), which provides storage strategy and management framework based on triple (C, T, A) and SDOG grid coding for massive data. The objection of this paper is to provide an effective spatial data organization and indexing method, which organizes triple units into block and encodes for each triples block and converts multi-source global scale datasets into triples block so as to manage massive raster data at global scale.

Co-registration of laser altimeter tracks with digital terrain models and applications in planetary science

We have derived algorithms and techniques to precisely co-register laser altimeter profiles with gridded Digital Terrain Models (DTMs), typically derived from stereo images. The algorithm consists of an initial grid search followed by a least-squares matching and yields the translation parameters at sub-pixel level needed to align the DTM and the laser profiles in 3D space. This software tool was primarily developed and tested for co-registration of laser profiles from the Lunar Orbiter Laser Altimeter (LOLA) with DTMs derived from the Lunar Reconnaissance Orbiter (LRO) Narrow Angle Camera (NAC) stereo images. Data sets can be co-registered with positional accuracy between 0.13m and several meters depending on the pixel resolution and amount of laser shots, where rough surfaces typically result in more accurate co-registrations. Residual heights of the data sets are as small as 0.18m. The software can be used to identify instrument misalignment, orbit errors, pointing jitter, or problems associated with reference frames being used. Also, assessments of DTM effective resolutions can be obtained. From the correct position between the two data sets, comparisons of surface morphology and roughness can be made at laser footprint- or DTM pixel-level. The precise co-registration allows us to carry out joint analysis of the data sets and ultimately to derive merged high-quality data products. Examples of matching other planetary data sets, like LOLA with LRO Wide Angle Camera (WAC) DTMs or Mars Orbiter Laser Altimeter (MOLA) with stereo models from the High Resolution Stereo Camera (HRSC) as well as Mercury Laser Altimeter (MLA) with Mercury Dual Imaging System (MDIS) are shown to demonstrate the broad science applications of the software tool.

Fitting Polynomial Volumes to Surface Meshes with Voronoï Squared Distance Minimization

AbstractWe propose a method for mapping polynomial volumes. Given a closed surface and an initial template volume grid, our method deforms the template grid by fitting its boundary to the input surface while minimizing a volume distortion criterion. The result is a point‐to‐point map distorting linear cells into curved ones. Our method is based on several extensions of Voronoi Squared Distance Minimization (VSDM) combined with a higher‐order finite element formulation of the deformation energy. This allows us to globally optimize the mapping without prior parameterization. The anisotropic VSDM formulation allows for sharp and semi‐sharp features to be implicitly preserved without tagging. We use a hierarchical finite element function basis that selectively adapts to the geometric details. This makes both the method more efficient and the representation more compact. We apply our method to geometric modeling applications in computer‐aided design and computer graphics, including mixed‐element meshing, mesh optimization, subdivision volume fitting, and shell meshing.

A new method for gridding DNA microarrays

In this paper, a new methodological scheme for the gridding of DNA microarrays is proposed. The scheme composes of a series of processes applied sequentially. Each DNA microarray image is pre-processed to remove any noise and the center of each spot is detected using a template matching algorithm. Then, an initial gridding is automatically placed on the DNA microarray image by ‘building’ rectangular pyramids around the detected spots' centers. The gridlines “move” between the pyramids, horizontally and vertically, forming this initial grid. Furthermore, a refinement process is applied composing of a five-step approach in order to correct gridding imperfections caused by its initial placement, both in non-spot cases and in more than one spot enclosure cases. The proposed gridding scheme is applied on DNA microarray images under known transformations and on real-world DNA data. Its performance is compared against the projection pursuit method, which is often used due to its speed and simplicity, as well as against a state-of-the-art method, the Optimal Multi-level Thresholding Gridding (OMTG). According to the obtained results, the proposed gridding scheme outperforms both methods, qualitatively and quantitatively.

New Methods in Modeling of Hot Stellar Atmospheres

Abstract In the present study we had three main aims. First to study the possibility of reducing the initial model atmosphere data to short analytical polynomials. The second was to use as the depth variable the logarithm of the local gas pressure instead the Rosseland mean. The third aim was to check the applicability of the derived formulae and proposed computation methods to obtain high precision self-consistent results in modeling hot plane-parallel stellar atmospheres. Introducing the dimensionless (reduced) local quantities θ = T/T eff and β = P/P(T eff) it has been shown that for hot convection-free stellar atmospheres the curves log θ versus log β reduce an initial grid of models to simple polynomials and bring forth some general features of the model stellar atmospheres. Even for stellar atmospheres having the convective zones in the deeper atmospheric layers, the outer part of the atmosphere (up to T = T eff and for T eff > 5000 K) can be described in the same manner by curves log θ versus log β as for the hotter stars. Iterative modeling of any hot stellar atmosphere can be started from these formulae (obtained for solar abundances), using rational polynomial ratios for P(T eff), obtaining from these data the needed T versus P dependence. To check suitability of the formulae, the iterative correction of the model stellar atmospheres has been carried out by the traditional Unsöld-Lucy method and by the novel least squares optimization based on Levenberg-Marquardt method, followed by Broyden correction loop. It has been shown that the flux constancy obtained by it is almost 2 dex higher than obtained by the Unsöld-Lucy method. The precision estimators as criteria of the modeling algorithms self-consistency and of the computational precision level have been proposed and used.

3D line-support grid flattening for more accurate geostatistical reservoir population with petrophysical properties

Reservoir models are essential if we need to clearly understand the fossil resources and, hence, to make better use of them. Feeding these models with physical properties on the basis of wells data is a key step in their construction. Line-support (LS) grid is the most popular grid in reservoir engineering, it is massively used for reservoir simulations. In the current methods used to populate with properties the LS grid of a reservoir unit, a Cartesian grid of equivalent size (in each direction), obtained by averaging the edge lengths, is first of all completed. The properties calculated in this way are then transferred as they are into the initial LS grid, because there is cell-for-cell correspondence. This leads to distortion of the Cartesian grid, making it fit the shape of the LS grid. This has the effect of altering calculations of correlation distances between well markers in geostatistical population simulations. Consequently, this primarily induces distortions on the simulated bodies. To resolve this problem, in this paper, we propose innovative methods for a "smooth" conversion from the LS grid of the structural space to the Cartesian grid of the geostatistical population space. The basic principle is to calculate the correlation distances between wells on the basis of "quasi-isometric" flattening of the stratigraphic unit LS grid in the population space. This same flattening technique is then used for inverse transfer of the properties from the population space to the structural space.

An automatic unstructured grid generation method for viscous flow simulations

High aspect-ratio grids are required for accurate solution of boundary layer and wake flow. An approach for the efficient generation of isotropic and stretched viscous unstructured grids is introduced in this paper. The proposed grid generation algorithm starts with a very coarse initial grid. In far field regions, isotropic cells of excellent quality are produced using a combination of point insertion and cell subdivision techniques. Simultaneously, a directional grid refinement strategy is used to construct highly stretched triangular cells in viscous dominated regions. First, anisotropic unstructured grids are produced in the stream-wise direction. Then, cells close to the solid surface are refined to highly stretched layer of triangles suitable for boundary layer region. The accuracy of the current grid generation approach is assessed by laminar and turbulent compressible flow solutions around NACA0012, RAE2822, and NHLP multi-element airfoils. Numerical flow simulation results are compared with published data. Comparisons point to accuracy of the proposed unstructured viscous grid generation procedure.

Fuzzy Fractal Interpolation Surface and its Applications

Tackling of uncertain data is a major problem in analysis, modeling and simulation. Fractal interpolation surface and fuzzy set method are employed to solve the issue of uncertainty in modeling irregular surface. Initial interpolation data grid point is used as the kernel of Gaussian fuzzy membership function and its fuzzy numbers can be calculated by specifying λ of λ-cut set. These fuzzy numbers are used as uncertain data, which are the boundaries of the fluctuation of initial grid, and defined as a new kind of fuzzy interpolation grids. With these interpolation grids fractal interpolation surface algorithm is applied to act on. By these definitions, experimental data for modeling rock surface is illustrated to show that how the interpolation scheme proposed in this paper enhances the controllability for manipulating uncertain data.

Effect of Initial Grid's Size in Thermal Diffusion Simulation

The thermal diffusion similitude should be well considered during the numerical simulating of its distribution in power plants or nuclear power stations. The distribution near the waterspout is well related to the initial grid’s size. The bigger the initial grid is, the faster the thermal diffusion. Reasonable initial grid should be related to thermal discharge and flow velocity. Five different grid’s sizes are adopted to simulate the constant diffusion phenomenon in a rectangle water channel, the currents near the waterspout, the thermal diffusion near or away from the waterspout are discussed in this paper, and a rational size of initial grid is proposed to relative researchers.

Mesh Generation for Arch Dam Abutment Slip Block Based on Virtual Grid

Abstract. In order to generate mesh for arch dam abutment slip block automatically, virtual grid method is proposed based on grid-based automatic generation algorithm. The proposed algorithm avoids generating initial grid in one time, but intersects the model with a series of plane sections firstly. Then form initial grid by using vector intersection method for adjacent sections. By modifying initial grid, a layer of mesh is formed. The algorithm proposed can better adapt to complex topography and generates hexahedral meshes for the block of arch dam abutment automatically. The method can present data for limit equilibrium analysis and numerical calculation method such as finite element method. Based on original topography and structural plane data, the automatic identification, generation and meshing of arch dam abutment block is accomplished.

TURBULENT MAGNETIC FIELD AMPLIFICATION FROM SPIRAL SASI MODES: IMPLICATIONS FOR CORE-COLLAPSE SUPERNOVAE AND PROTO-NEUTRON STAR MAGNETIZATION

We extend our investigation of magnetic field evolution in three-dimensional flows driven by the stationary accretion shock instability (SASI) with a suite of higher-resolution idealized models of the post-bounce core-collapse supernova environment. Our magnetohydrodynamic simulations vary in initial magnetic field strength, rotation rate, and grid resolution. Vigorous SASI-driven turbulence inside the shock amplifies magnetic fields exponentially; but while the amplified fields reduce the kinetic energy of small-scale flows, they do not seem to affect the global shock dynamics. The growth rate and final magnitude of the magnetic energy are very sensitive to grid resolution, and both are underestimated by the simulations. Nevertheless our simulations suggest that neutron star magnetic fields exceeding $10^{14}$ G can result from dynamics driven by the SASI, \emph{even for non-rotating progenitors}.

Improvement on Spherical Symmetry in Two-Dimensional Cylindrical Coordinates for a Class of Control Volume Lagrangian Schemes

AbstractIn, Maire developed a class of cell-centered Lagrangian schemes for solving Euler equations of compressible gas dynamics in cylindrical coordinates. These schemes use a node-based discretization of the numerical fluxes. The control volume version has several distinguished properties, including the conservation of mass, momentum and total energy and compatibility with the geometric conservation law (GCL). However it also has a limitation in that it cannot preserve spherical symmetry for one-dimensional spherical flow. An alternative is also given to use the first order area-weighted approach which can ensure spherical symmetry, at the price of sacrificing conservation of momentum. In this paper, we apply the methodology proposed in our recent work to the first order control volume scheme of Maire in to obtain the spherical symmetry property. The modified scheme can preserve one-dimensional spherical symmetry in a two-dimensional cylindrical geometry when computed on an equal-angle-zoned initial grid, and meanwhile it maintains its original good properties such as conservation and GCL. Several two-dimensional numerical examples in cylindrical coordinates are presented to demonstrate the good performance of the scheme in terms of symmetry, non-oscillation and robustness properties.

Numerical Study and Performance Evaluation for a Pulse Detonation Engine with an Exhaust Nozzle (1st Report: Estimation on Performance using a Detailed Reaction Model)

This paper presents a propulsive performance evaluation for a H2/Air pulse detonation engine (PDE) equipped with a converging-diverging exhaust nozzle. The evaluation was conducted using system-level modeling and multi-cycle numerical simulations. This study discusses two-dimensional and axisymmetric compressible Euler equations with a detailed chemical reaction model. First, the single-shot propulsive performance of a simplified-PDE (i.e., no exhaust nozzle) is evaluated to show the validity of the numerical and performance evaluation method. The influences of the initial conditions, ignition energy, grid resolution and scale effects on the propulsive performance are studied using multi-cycle simulations. The present results are compared with the results calculated by Ma et al. and Harris et al. The differences between their results and the present simulations are approximately 2–3% because their chemical reactions use a one-step model with a single-γ model. The effects of the specific heat ratio should be estimated for various nozzle configurations and flight conditions.

A dynamic hybrid Reynolds-averaged Navier Stokes–Large eddy simulation modeling framework

A dynamic framework for hybrid Reynolds-averaged Navier-Stokes (RANS)—large eddy simulation (LES) modeling is proposed, wherein the RANS-to-LES transition parameter is adjusted to maintain continuity in turbulence production. The model is applied for temporally developing plane channel flow at varying Reynolds numbers with different initial turbulence intensity and grid resolution. On sufficiently fine grids, dynamic hybrid RANS-LES model (DHRL) yields similar results to LES simulations. On coarse grids, DHRL activates RANS mode in the log layer, thus improving the mean flow predictions. The model framework addresses grid sensitivity issues observed in other hybrid RANS-LES approaches and may be used with any desired combination of LES and RANS basis models.

L-system specification of knot-insertion rules for non-uniform B-spline subdivision

Subdivision schemes are based on a hierarchy of knot grids in parameter space. A univariate grid hierarchy is regular if all knots are equidistant on each level, and irregular otherwise. We use L-systems to design a wide class of systematically described irregular grid hierarchies. Furthermore, we give sufficient conditions on the L-system which guarantee that the subdivision scheme, based on the non-uniform B-spline of degree d defined on the initial knot grid, is uniformly convergent. If n is the number of symbols in the alphabet of the L-system, this subdivision scheme is defined with a finite set of masks (at most n d + 1 ) which does not depend on the subdivision step. We provide an implementation of such schemes which is available as a worksheet for Sage software.

Multimodal Likelihoods in Educational Assessment

It has been known for some time that item response theory (IRT) models may exhibit a likelihood function of a respondent’s ability which may have multiple modes, flat modes, or both. These conditions, often associated with guessing of multiple-choice (MC) questions, can introduce uncertainty and bias to ability estimation by maximum likelihood (ML) when standard Newton solutions are used. This article evaluates the performance of several maximization methods, including initial (grid) searches probing the function slopes, simulated annealing, exhaustive likelihood evaluation, and the standard Newton algorithm. In extensive studies, involving several million records of both generated and real data, the algorithms were evaluated with respect to precision and speed. Two methods, exhaustive search and grid search, followed by Newton steps, all yielded ML estimates at the required precision. At today’s computer speeds, either of these algorithms may be considered for high-volume response pattern scoring.

Digital image correlation of metal nanofilms on SU-8 for flexible electronics and MEMS

This paper presents strain measurements using digital image correlation of common microelectronic metal nanofilms deposited onto a polymer substrate (SU-8), which has applications in flexible electronics and nano/microsystems reliability analysis. The novel experimental method is based on digital image correlation coupled with microtensile test apparatus for the in situ investigation of the deformation behaviour of the deposited thin films under uniaxial tensile loading. One of the key features of the method is the real-time two-dimensional strain field measurements on a bare thin film surface, during the deformation process, without any initial speckle or grid deposition. The outstanding performances of the method, having a spatial resolution of 0.7 µm, allow one to envisage further studies related to the understanding of the mechanical behaviour of such thin films and, in particular, the damage localization process.