Schlieren visualization of shock wave phenomena over a missile-shaped body at hypersonic Mach numbers

The flow over a missile-shaped configuration is investigated by means of Schlieren visualization in short-duration facility producing free stream Mach numbers of 5.75 and 8. This visualization technique is demonstrated with a 41 degrees full apex angle blunt cone missile-shaped body mounted with and without cavity. Experiments are carried out with air as the test gas to visualize the flow field. The experimental results show a strong intensity variation in the deflection of light in a flow field, due to the flow compressibility. Shock stand-off distance measured with the Schlieren method is in good agreement with theory and computational fluid dynamic study for both the configurations. Magnitude of the shock oscillation for a cavity model may be greater than the case of a model without cavity. The picture of visualization shows that there is an outgoing and incoming flow closer to the cavity. Cavity flow oscillation was found to subside to steady flow with a decrease in the free stream Mach number.

Genome analysis: A new approach for visualization of sequence organization in genomes

In this article we describe and demonstrate the versatility of a computer program, GENOME MAPPING, that uses interactive graphics and runs on an IRIS workstation. The program helps to visualize as well as analyse global and local patterns of genomic DNA sequences. It was developed keeping in mind the requirements of the human genome sequencing programme, which requires rapid analysis of the data. Using GENOME MAPPING one can discern signature patterns of different kinds of sequences and analyse such patterns for repetitive as well as rare sequence strings. Further, one can visualize the extent of global homology between different genomic sequences. An application of our method to the published yeast mitochondrial genome data shows similar sequence organizations in the entire sequence and in smaller subsequences.

Integrating CDS/ISIS Databases with Greenstone Digital Library Software (GSDL)

CDS/ISIS is an advanced non-numerical information storage and retrieval software developed by UNESCO since 1985 to satisfy the need expressed by many institutions, especially in developing countries, to be able to streamline their information processing activities by using modern (and relatively inexpensive) technologies [1]. CDS/ISIS is available for MS-DOS, Windows and Unix operating system platforms. The formatting language of CDS/ISIS is one of its several strengths. It is not only used for formatting records for display but is also used for creating customized indexes. CDS/ISIS by itself does not facilitate in publishing its databases on the Internet nor does it facilitate in publishing on CD-ROMs. However, numbers of open source tools are now available, which enables in publishing CDS/ISIS databases on the Internet and also on CD-ROMs. In this paper, we have discussed the ways and means of integrating CDS/ISIS databases with GSDL, an open source digital library (DL) software.

Techniques for realistic visualization of fluids: A survey

Visualization of fluids has wide applications in science, engineering and entertainment. Various methodologies Of visualizing fluids have evolved which emphasize on capturing different aspects of the fluids accurately. In this survey the existing methods for realistic visualization of fluids are reviewed. The approaches are classified based on the key concept they rely on for fluid modeling. This classification allows for easy selection of the method to be adopted for visualization given an application. It also enables identification of alternative techniques for fluid modeling.

PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures

A fundamental task in bioinformatics involves a transfer of knowledge from one protein molecule onto another by way of recognizing similarities. Such similarities are obtained at different levels, that of sequence, whole fold, or important substructures. Comparison of binding sites is important to understand functional similarities among the proteins and also to understand drug cross-reactivities. Current methods in literature have their own merits and demerits, warranting exploration of newer concepts and algorithms, especially for large-scale comparisons and for obtaining accurate residue-wise mappings. Here, we report the development of a new algorithm, PocketAlign, for obtaining structural superpositions of binding sites. The software is available as a web-service at http://proline.physicslisc.emetin/pocketalign/. The algorithm encodes shape descriptors in the form of geometric perspectives, supplemented by chemical group classification. The shape descriptor considers several perspectives with each residue as the focus and captures relative distribution of residues around it in a given site. Residue-wise pairings are computed by comparing the set of perspectives of the first site with that of the second, followed by a greedy approach that incrementally combines residue pairings into a mapping. The mappings in different frames are then evaluated by different metrics encoding the extent of alignment of individual geometric perspectives. Different initial seed alignments are computed, each subsequently extended by detecting consequential atomic alignments in a three-dimensional grid, and the best 500 stored in a database. Alignments are then ranked, and the top scoring alignments reported, which are then streamed into Pymol for visualization and analyses. The method is validated for accuracy and sensitivity and benchmarked against existing methods. An advantage of PocketAlign, as compared to some of the existing tools available for binding site comparison in literature, is that it explores different schemes for identifying an alignment thus has a better potential to capture similarities in ligand recognition abilities. PocketAlign, by finding a detailed alignment of a pair of sites, provides insights as to why two sites are similar and which set of residues and atoms contribute to the similarity.

Realizing a flexible constraint length Viterbi decoder for software radio on a de Bruijn interconnection network

Building flexible constraint length Viterbi decoders requires us to be able to realize de Bruijn networks of various sizes on the physically provided interconnection network. This paper considers the case when the physical network is itself a de Bruijn network and presents a scalable technique for realizing any n-node de Bruijn network on an N-node de Bruijn network, where n < N. The technique ensures that the length of the longest path realized on the network is minimized and that each physical connection is utilized to send only one data item, both of which are desirable in order to reduce the hardware complexity of the network and to obtain the best possible performance.

Java Memory Model aware Software validation

The Java Memory Model (JMM) provides a semantics of Java multithreading for any implementation platform. The JMM is defined in a declarative fashion with an allowed program execution being defined in terms of existence of "commit sequences" (roughly, the order in which actions in the execution are committed). In this work, we develop OpMM, an operational under-approximation of the JMM. The immediate motivation of this work lies in integrating a formal specification of the JMM with software model checkers. We show how our operational memory model description can be integrated into a Java Path Finder (JPF) style model checker for Java programs.

Method of Design Through Structuring of Meanings

This research shows a new approach and development of a design methodology, based on the perspective of meanings. In this study the design process is explored as a development of the structure of meanings. The processes of search and evaluation of meanings form the foundations of developing this structure. In order to facilitate the use and operation of the meanings, the WordNet lexical database and an existing visualization of WordNet — Visuwords — is used for the process of meaning search. The basic tool used for evaluation process is the WordNet::Similarity software, measuring the relatedness of meanings in the database. In this way it is measuring the degree of interconnections between different meanings. This kind of search and evaluation techniques are later on incorporated into our methodology of the structure of meanings to support the design process. The measures of relatedness of meanings are developed as convergence criteria for application in the processes of evaluation. Further on, the methodology for the structure of meanings developed here is used to construct meanings in a verification of product design. The steps of the design methodology, including the search and evaluation processes involved in developing the structure of the meanings, are elucidated. The choices, made by the designer in terms of meanings are supported by consequent searches and evaluations of meanings to be implemented in the designed product. In conclusion, the paper presents directions for developing and further extensions of the proposed design methodology.

Register Allocation and Optimal Spill code Scheduling in Software Pipelined Loops using 0-1 Integer Linear Programming Formulation

In achieving higher instruction level parallelism, software pipelining increases the register pressure in the loop. The usefulness of the generated schedule may be restricted to cases where the register pressure is less than the available number of registers. Spill instructions need to be introduced otherwise. But scheduling these spill instructions in the compact schedule is a difficult task. Several heuristics have been proposed to schedule spill code. These heuristics may generate more spill code than necessary, and scheduling them may necessitate increasing the initiation interval. We model the problem of register allocation with spill code generation and scheduling in software pipelined loops as a 0-1 integer linear program. The formulation minimizes the increase in initiation interval (II) by optimally placing spill code and simultaneously minimizes the amount of spill code produced. To the best of our knowledge, this is the first integrated formulation for register allocation, optimal spill code generation and scheduling for software pipelined loops. The proposed formulation performs better than the existing heuristics by preventing an increase in II in 11.11% of the loops and generating 18.48% less spill code on average among the loops extracted from Perfect Club and SPEC benchmarks with a moderate increase in compilation time.