Grid File Research Articles

Stereological assessment of extracellular polymeric substances, exo-enzymes, and specific bacterial strains in bioaggregates using fluorescence experiments

This review addresses the introduction of fluorescent molecular tags into exo-enzymes and extra polymeric substances of bioaggregates and the use of confocal laser scanning microscopy (CLSM) to map their role, purpose and quantitative description of the biological processes they undertake. Multiple color staining coupled with CLSM and fluorescent in situ hybridisation (FISH) and flow cytometry have identified the individual polymeric substances, whether they are proteins, lipids, polysaccharides, nucleic acids or antibodies, as well as the microorganisms in the bioaggregate. Procedures are presented for simultaneous multicolor staining with seven different fluorochromes - SYTOX Blue for nucleic acids; Nile red for lipids; Calcofluor white [CW] for beta-polysaccharides; concanavalin A [Con A] for alpha-poly-saccharides; fluorescein-isothiocyanate [FITC] for proteins; SYTO 63 for live microbial cells and Calcium Green for monitoring calcium levels in the microbial cells. For the distribution of certain microbial strains, metabolic enzymes and extrapolymeric substances to be quantitatively described the generated colored images are converted into digital forms under specific predefined criteria. Procedures and computer software programs (Amira; MATLAB) are presented in order to quantitatively establish grid patterns from the CLSM images. The image is digitized using a threshholding algorithm followed by a reconstruction of the image as a volumetric grid for finite element simulation. The original color image is first converted to a grey followed by resizing, detection and modification of bilevel images and finally a total reversal of the image colors. The grid file is then used by specific computer software (Gambit, Fluent) for further numerical studies incorporating chemical reactions, transport processes and computational fluid dynamics including intra-bioaggregate fluid flow, and heat and mass transfer within the bioaggregate matrix.

Grid and Cloud Computing and their Application

Grid and Cloud Computing and their Application

A Dynamic Grid File for High-Dimensional Data Cube Storage and Range-Sum Querying

In this article; the authors propose to use the grid file to store multi-dimensional data cubes and answer angesum queries. The grid file is enhanced with a dynamic splitting mechanism to accommodate insertions of data. It overcomes the drawback of the traditional grid file in storing uneven data while enjoying its advantages of simplicity and efficiency. The space requirement grows linearly with the dimension of the data cube; compared with the exponential growth of conventional methods that store pre-computed aggregate values for range-sum queries. The update cost is O (1); much faster than the pre-computed data cube approaches; which generally have exponential update cost. The grid file structure can also respond to range queries quickly. They compare it with an approach that uses the R*-tree structure to store the data cube. The experimental results show that the proposed method performs favorably in file size; update speed; construction time; and query response time for both evenly and unevenly distributed data.

CheckDen, a program to compute quantum molecular properties on spatial grids

CheckDen, a program to compute quantum molecular properties on a variety of spatial grids is presented. The program reads as unique input wavefunction files written by standard quantum packages and calculates the electron density ρ( r), promolecule and density difference function, gradient of ρ( r), Laplacian of ρ( r), information entropy, electrostatic potential, kinetic energy densities G( r) and K( r), electron localization function (ELF), and localized orbital locator (LOL) function. These properties can be calculated on a wide range of one-, two-, and three-dimensional grids that can be processed by widely used graphics programs to render high-resolution images. CheckDen offers also other options as extracting separate atom contributions to the property computed, converting grid output data into CUBE and OpenDX volumetric data formats, and perform arithmetic combinations with grid files in all the recognized formats.

Crustal structure beneath the Iberian Peninsula and surrounding waters: A new compilation of deep seismic sounding results

We present here an updated compilation of crustal parameters beneath the Iberian Peninsula and surrounding waters, inferred from extensive deep seismic exploration performed in the last three decades. Firstly, the more relevant experiments developed in both terrestrial and marine domains are revisited, together with the corresponding seismic velocity–depth models published that reveal the characteristics of the different tectonic domains sampled, including oceanic zones, continental margins, orogenic and rift belts. The results are summarized in three crustal transects sketched along representative directions. Secondly, we compiled the Moho depths along all the available seismic profiles to produce a geo-referred database. This database has then been interpolated using kriging algorithms to obtain a continuous Moho depth model, in the form of a regular grid file. This integrative Moho map for a key area in the Western Mediterranean documenting the interaction between European and African plates can contribute to constrain further regional studies, either at crustal, lithospheric or mantle scales.

RGLite, an interface between ROOT and gLite—proof on the grid

Using the gLitePROOF package it is possible to perform PROOF-based distributed data analysis on the gLite Grid. The LHC experiments managed to run globally distributed Monte Carlo productions on the Grid, now the development of tools for data analysis is in the foreground. To grant access interfaces must be provided. The ROOT/PROOF framework is used as a starting point. Using abstract ROOT classes (TGrid, …) interfaces can be implemented, via which Grid access from ROOT can be accomplished. A concrete implementation exists for the ALICE Grid environment AliEn. Within the D-Grid project an interface to the common Grid middleware of all LHC experiments, gLite, has been created. Therefore it is possible to query Grid File Catalogues from ROOT for the location of the data to be analysed. Grid jobs can be submitted into a gLite based Grid. The status of the jobs can be asked for, and their results can be obtained.

Análise Estatística da Concentração de Potássio Obtida por Aerolevantamentos Geofísicos em Diferentes Formações Geológicas na Região de Santa Maria (RS)

The present work was developed in outcrops of Santa Maria region, southern Brazil, Rio Grande do Sul State. Statistic evaluations were applied in different rock types. The possibility to distinguish different geologic units, sedimentary and volcanic (acid and basic types) by means of the statistic analyses from the use of airborne gamma-ray spectrometry integrating potash radiation emissions data with geological and geochemistry data is discussed. This Project was carried out at 1973 by Geological Survey of Brazil/Companhia de Pesquisas de Recursos Minerais. The Camaquã Project evaluated the behavior of potash concentrations generating XYZ Geosof 1997 format, one grid, thematic map and digital thematic map files from this total area. Using these data base, the integration of statistics analyses in sedimentary formations which belong to the Depressão Central do Rio Grande do Sul and/or to volcanic rocks from Planalto da Serra Geral at the border of Paraná Basin was tested. Univariate statistics model was used: the media, the standard media error, and the trust limits were estimated. The Tukey’s Test was used in order to compare mean values. The results allowed to create criteria to distinguish geological formations based on their potash content. The back-calibration technique was employed to transform K radiation to percentage. Inside this context it was possible to define characteristic values from radioactive potash emissions and their trust ranges in relation to geologic formations. The potash variable when evaluated in relation to geographic Universal Transverse Mercator coordinates system showed a spatial relation following one polynomial model of second order, with one determination coefficient. The statística 7.1 software Generalist Linear Models produced by Statistics Department of Federal University of Santa Maria/Brazil was used.

Qualification and refinement of the gravity database based on cross-validation approach — A case study of Iran

In this article, we propose a technique for the precise cleaning of the gravity anomaly database based on the cross validation approach. The terrestrial gravity anomalies were compared versus a global geopotential model and take into account the effect of topography in this comparison. The efficiency of the cross-validation technique is illustrated in outlier detection as well as in choosing the proper gridding technique as a case study in construction of the Iranian new gravity database. In order to reduce the effect of topography and the discretisation error, a special interpolation scheme is used for gridding of the free-air gravity anomalies. The final grid file was created based on the Kriging method with 80″ × 90″ block resolution. The overall accuracy for the new Iranian gravity database is estimated in the order of 10 mGal.

A kinematic‐wave‐based distributed watershed model using FEM, GIS and remotely sensed data

AbstractFor the appropriate management of water resources in a watershed, it is essential to calculate the time distribution of runoff for the given rainfall event. In this paper, a kinematic‐wave‐based distributed watershed model using finite element method (FEM), geographical information systems (GIS) and remote‐sensing‐based approach is presented for the runoff simulation of small watersheds. The kinematic wave equations are solved using FEM for overland and channel flow to generate runoff at the outlet of the watershed concerned. The interception loss is calculated by an empirical model based on leaf area index (LAI). The Green‐Ampt Mein Larson (GAML) model is used for the estimation of infiltration. Remotely sensed data has been used to extract land use (LU)/land cover (LC). GIS have been used to prepare finite element grid and input files such as Manning's roughness and slope. The developed overland flow model has been checked with an analytical solution for a hypothetical watershed. The model has been applied to a gauged watershed and an ungauged watershed. From the results, it is seen that the model is able to simulate the hydrographs reasonably well. A sensitivity analysis of the model is carried out with the calibrated infiltration parameters, overland flow Manning's roughness, channel flow Manning's roughness, time step and grid size. The present model is useful in predicting the hydrograph in small, ungauged watersheds. Copyright © 2007 John Wiley & Sons, Ltd.

Design and implementation of index structures for fuzzy spatial databases

Over the years database management systems have evolved to include spatially referenced data. Because spatial data are complex and have a number of unique constraints (i.e., spatial components and uncertain properties), spatial database systems can be effective only if the spatial data are properly handled at the physical level. Therefore, it is important to develop an effective spatial and aspatial indexing technique to facilitate flexible spatial and/or aspatial querying for such databases. For this purpose we introduce an indexing approach to use (fuzzy) spatial and (fuzzy) aspatial data. We use a number of spatial index structures, such as Multilevel Grid File (MLGF), G-tree, R-tree, and R*-tree, for fuzzy spatial databases and compare the performances of these structures for various flexible queries. © 2007 Wiley Periodicals, Inc. Int J Int Syst 22: 805–826, 2007.

Lessons learned through driving science applications in the PRAGMA grid

This paper describes the coordination, design and implementation of the PRAGMA Grid. Applications in genomics, quantum mechanics, climate simulation, organic chemistry and molecular simulation have driven the middleware requirements, and the PRAGMA Grid provides a mechanism for science and technology teams to collaborate, for grids to interoperate and for international users to share software beyond the essential, de facto standard Globus core. Several middleware tools developed by researchers within PRAGMA have been deployed in the PRAGMA grid and this has enabled significant insights, improvements and new collaborations to flourish. In this paper, we describe how human factors, resource availability and performance issues have affected the middleware, applications and the grid design. We also describe how middleware components in grid monitoring, grid accounting and grid file systems have dealt with some of the major characteristics of our grid. We also briefly describe a number of mechanisms that we have employed to make software easily available to PRAGMA and global grid communities.

Efficient indexing data structures for flash-based sensor devices

Flash memory is the most prevalent storage medium found on modern wireless sensor devices (WSDs) . In this article we present two external memory index structures for the efficient retrieval of records stored on the local flash memory of a WSD. Our index structures, MicroHash and MicroGF (micro grid files) , exploit the asymmetric read/write and wear characteristics of flash memory in order to offer high-performance indexing and searching capabilities in the presence of a low-energy budget, which is typical for the devices under discussion. Both structures organize data and index pages on the flash media using a sorted by timestamp file organization. A key idea behind these index structures is that expensive random access deletions are completely eliminated. MicroHash enables equality searches by value in constant time and equality searches by timestamp in logarithmic time at a small cost of storing index pages on the flash media. Similarly, MicroGF enables spatial equality and proximity searches in constant time. We have implemented these index structures in nesC, the programming language of the TinyOS operating system. Our trace-driven experimentation with several real datasets reveals that our index structures offer excellent search performance at a small cost of constructing and maintaining the index.

An upgraded version of the generator BCVEGPY2.0 for hadronic production of [formula omitted] meson and its excited states

An upgraded version of the package BCVEGPY2.0: [C.-H. Chang, J.-X. Wang, X.-G. Wu, Comput. Phys. Common. 174 (2006) 241] is presented, which works under LINUX system and is named as BCVEGPY2.1. With the version and a GNU C compiler additionally, users may simulate the B-c-events in various experimental environments very conveniently. It has been manipulated in better modularity and code reusability (less cross communication among various modules) than BCVEGPY2.0 has. Furthermore, in the upgraded version a special execution is arranged as that the GNU command make compiles a requested code with the help of a master makefile in main code directory, and then builds an executable file with the default name run. Finally, this paper may also be considered as an erratum, i.e., typo errors in BCVEGPY2.0 and corrections accordingly have been listed.

Calculation of magnitude magnetic transforms with high centricity and low dependence on the magnetization vector direction

We present a Matlab tool that calculates five magnitude magnetic transforms (MMTs) from an input measured anomalous magnetic field. The MMTs are all based on the total magnitude anomaly (TMA), and consist of the TMA itself, the modulus of the gradient of the TMA, the Laplacian of the TMA, half of the square root of the Laplacian of the square of the TMA, and the square root of the product of the TMA plus the Laplacian of the TMA. These MMTs produce anomalies that are closer to the magnetic source’s true horizontal position and are simpler to interpret than the measured anomalous magnetic field itself. While the conventional magnetic transforms of reduction-to-the-pole (RTP), the pseudogravity field, and the analytic signal (AS) also have these properties, these MMTs have several additional advantages. They require only first-order, horizontal derivatives for their calculation. They are also more stable at low magnetic latitudes than the RTP, and have a pattern that is independent of the geomagnetic-field vector direction, in contrast to the AS. The Matlab tool is designed to deal with big data sets and is compatible with common data formats, GS ASCII grid files, and XYZ data files. A calculation of the MMTs of the total magnetic anomaly of a synthetic example at a low magnetic latitude and with a field example from the Kuju volcanic area, Japan demonstrate the effectiveness of the program.

A global and parallel file system for grids

Data management is one of the most important problems in grid environments. Most of the efforts in data management in grids have been focused on data replication. Data replication is a practical and effective method to achieve efficient data access in grids. However all data replication schemes lack in providing a grid file system. One important challenge facing grid computing is the design of a grid file system. The Global Grid Forum defines a Grid File System as a human-readable resource namespace for management of heterogeneous distributed data resources, that can span across multiple autonomous administrative domains. This paper describes a new Grid File System according to the Global Grid Forum recommendations that integrates heterogeneous data storage resources in grids using standard grid technologies: GridFTP and the Resource Namespace Services, both defined by the Global Grid Forum. To obtain high performance, we apply the parallel I /O techniques used in traditional parallel file systems.

ADVANCED MODELLING OF EPITAXIAL ORDERING OF ORGANIC LAYERS ON CRYSTALLINE SURFACES

A fine balance between weak molecule-molecule interactions and usually only weakly laterally varying molecule-substrate interactions governs the physical structure of organic-inorganic and organic-organic heteroepitaxial thin films. Therefore, it is important to investigate the energetics of realistically large overlayer domains. So far, Potential calculations for large domains of organic overlayers on crystalline substrates were computationally demanding due to the vast number of atoms to be considered. Here, we present a technique which for the first time enables the calculation of both the molecule-substrate interaction potential and the molecule-molecule interaction potential for large molecular domains (up to several thousands of rather large molecules) by utilizing potential energy grid files. This technique does not only allow the investigation of the substrate influence but also full Monte-Carlo based structural optimizations, if applied to 2D crystalline overlayers. Furthermore, it provides an estimate for the energetic gain combined with the differently aligned overlayer domains. In several examples we will discuss the usefulness of this method. As a general result, we will provide evidence that energetically favorable lattice structures in OMBE systems are not restricted to commensurate unit cells or coincident super cells.

Understanding organic–inorganic heteroepitaxial growth of molecules on crystalline substrates: Experiment and theory

The physical structure of organic--inorganic heteroepitaxial thin films is usually governed by a fine balance between weak molecule--molecule interactions and a small lateral variation of the molecule--substrate interaction potential. In order to investigate the energetics of such a layer system, one has to consider large molecular domains [Mannsfeld and Fritz, Phys. Rev. B 69, 75416 (2004)]. So far, layer potential calculations for large domains of organic thin films on crystalline substrates were difficult to perform concerning the computational effort which stems from the huge number of atoms which have to be included. Here, we present a technique which enables the calculation of the molecule--substrate interactions for large molecular domains by utilizing potential energy grid files. As an application example, we discuss the growth of titanylphthalocyanine (TiOPc) on Au(111). TiOPc is found to grow homogeneously in extended domains on top of the alternating domains of the Au(111) surface reconstruction, locally exhibiting a point-on-line coincident epitaxy with the substrate lattice. Here, we demonstrate that the optimal structure and orientation of the TiOPc lattice in such extended overlayer domains can be predicted by potential optimization calculations using the technique described herein.

MULTI-KEY INDEX FOR DISTRIBUTED DATABASE SYSTEM

In this paper we present a multi-key index model that enables us to search a record with more than one attribute values in distributed database systems. Indices provide fast and efficient access of data and so become a major aspect in centralized database systems. Most of the centralized database systems use B + tree or other types of index structures such as bit vector, graph structure, grid file etc. But in distributed database systems no index model is found in the literature. Therefore efficient access is a major problem in distributed databases. Our proposed index model avoids the query-flooding problem of existing system and thus optimizes network bandwidth.

Sediment mobility in the Pomeranian Bight (Baltic Sea): a case study based on sidescan-sonar images and hydrodynamic modelling

Sidescan-sonar surveys were performed on a 2×4 km area of seafloor in the southern Baltic Sea (Pomeranian Bight) in 1996 and 1998. Overlapping sub-areas of the individual surveys showing characteristic details were processed into geographically referenced mosaics. Sediment types were identified from echo characteristics and by comparison with granulometric data. The sea bottom covered by the mosaics consists predominantly of sand, with subordinate lag sediments with stones and small ripple fields consisting of coarse sand to fine gravel. A comparison of the two mosaics did not reveal any significant changes of the sea bottom over the 2-year period. Characteristic sedimentary features remained almost unchanged over this period on detailed sonar images of smaller sub-areas. Substantial transport of sandy sediments can thus be excluded in the course of the observation period. Grid files of advective velocity components and orbital velocity of wave motion of a three-dimensional hydrodynamical model for the period from September 1996 to October 1997 were used to estimate the current regime in the study area for the interval between the two sidescan surveys. Comparing critical velocities for the dominant sediment types with the results of the numerical bottom current simulations and the observations from sidescan images, it is apparent that strong current events during the modelled time interval were still too weak to resuspend and transport sand of any grain size, even though maximum current velocities of 30 cm/s at the seafloor were modelled. Only a few patches of newly accumulated (acoustically soft) material (mud, fluff and/or soft plant remnants), with a horizontal extension of about 10 m at a terrain step feature, were recognised in the 1998 mosaic. Our results imply that sand deposits in the southern Baltic Sea can remain stationary over time periods of several years, and that the transport of organic material, nutrients and associated pollutants to depositional areas in deeper water is predominantly accomplished by the movement of material finer than sand. A significant portion of this fine material is evidently transported in the bottom boundary layer under conditions of moderate hydrodynamical forcing.

고정 그리드 인덱싱에서 공간과 시간 필터링을 이용한 범위 질의 처리

최근 들어 이동 통신 분야에서 이동하는 고객을 위한 위치 기반 서비스가 중요한 서비스로 부각되고 있다. 이동객체 응용의 경우 갱신 연산이 많고, 부하가 특정 지역에 집중되는 특징이 있다. 윈도우 나 원형 형태의 범위질의는 위치 기반 서비스에서 중요한 질의 중 하나이다. 이러한 범위질의에서는 부분 포함된 셀과 완전 포함된 셀을 구분해야할 필요가 있다. 또한 올바른 한정된 객체를 골라내기 위해 시간 영역을 고려할 필요성이 있다. 본 논문에서는 갱신연산을 최소화하기 위해 고안되어진 2번째 단계에 고정 그리드 구조를 적용한 2단계 인덱스 구조를 적용한다. VP 필터링과 윈도우 셀 필터링 기법을 이용한 공간 셀 필터링 기법과 Time Zone 개념을 사용하여 시공간 개념이 결합된 필터링 기법을 제안한다. 제안된 방법의 성능 측정을 위해서 다른 필터링 조합을 가지고 다양한 윈도우 질의와 원 질의에 대해서 실험 결과를 보인다. Recently, the location-based service for moving customers is becoming one of the most important service in mobile communication area. For moving object applications, there are lots of update operations and such update loads are concentrated on some particular area unevenly. Range queries, whose range can be window or circular, are the most essential query types in LBS. We need to distinguish completely contained cells from partially contained cells in those range queries. Also, it is necessary to consider temporal dimension to filter out qualifying objects correctly. In this paper, we adopt two-level index structures with fixed grid file structures in the second level, which are designed to minimize update operations. We propose a spatial ceil filtering method using VP filtering and a combined spatio-temporal filtering method using time gone concepts. Some experimental results are shown for various window queries and circular queries with different filtering combinations to show the performance tradeoffs of the proposed methods.