Searching for rotating galaxy clusters in SDSS and 2dFGRS

We present a result of searching for galaxy clusters that show an indication of global rotation using a spectroscopic sample of galaxies in SDSS and 2dFGRS. We have determined the member galaxies of 899 Abell clusters covered in SDSS and 2dFGRS using the redshift and the positional data of galaxies, and have estimated the ratio of the cluster rotation amplitude to the cluster velocity dispersion and the velocity gradient across the cluster. We have found 12 tentative rotating clusters that have large ratios of rotation amplitude to dispersion and large velocity gradients. We have determined the morphological parameters for 12 tentative rotating clusters using the positional information of the member galaxies: the ellipticity of the dispersion ellipse is in the range of 0.08$-$0.57, and the position angle of major or minor axis does not appear to be related to the position angle of rotation axis. We have investigated the substructures in the sample of tentative rotating clusters, finding from the Dressler-Shectman plots that the majority (9 out of 12) of clusters show an evidence of substructure due to the spatially correlated velocities of galaxies. We have selected six probable rotating clusters (A0954, A1139, A1399, A2162, A2169, and A2366) that show a single number density peak around the cluster center with a spatial segregation of the high and low velocity galaxies. We have found no strong evidences of a recent merging for the probable rotating clusters: the probable rotating clusters do not deviate significantly from the relation of the X-ray luminosity and the velocity dispersion or the virial mass of the clusters, and two probable rotating clusters (A0954 and A1399) have small values of the peculiar velocities and the clustercentric distances of the brightest cluster galaxies.Comment: 33 pages, 9 figures. To appear in Ap

Chemoinformatics Research at the University of Sheffield: A History and Citation Analysis

This paper reviews the work of the Chemoinformatics Research Group in the Department of Information Studies at the University of Sheffield, focusing particularly on the work carried out in the period 1985-2002. Four major research areas are discussed, these involving the development of methods for: substructure searching in databases of three-dimensional structures, including both rigid and flexible molecules; the representation and searching of the Markush structures that occur in chemical patents; similarity searching in databases of both two-dimensional and three-dimensional structures; and compound selection and the design of combinatorial libraries. An analysis of citations to 321 publications from the Group shows that it attracted a total of 3725 residual citations during the period 1980-2002. These citations appeared in 411 different journals, and involved 910 different citing organizations from 54 different countries, thus demonstrating the widespread impact of the Group's work

New Optical Insights into the Mass Discrepancy of Galaxy Clusters: The Cases of A1689 and A2218

We analyze the internal structures of clusters A1689 and A2218 by applying a recent development of the method of wavelet analysis, which uses the complete information obtained from optical data, i.e. galaxy positions and redshifts. We find that both clusters show the presence of structures superimposed along the line of sight with different mean redshifts and smaller velocity dispersions than that of the system as a whole, suggesting that the clusters could be cases of the on-going merging of clumps. In the case of A2218 we find an acceptable agreement between our estimate of optical virial mass and X-ray and gravitational lensing masses. On the contrary, in the case of A1689 we find that our mass estimates are smaller than X-ray and gravitational lensing ones at both small and large radii. In any case, at variance with earlier claims, there is no evidence that X-ray mass estimates are underestimated.Comment: 8 pages, 2 eps figures, Use LaTeX2e, accepted by Astrophysical Journal, in press November 1997, Vol.49

Clustering files of chemical structures using the Szekely-Rizzo generalization of Ward's method

Ward's method is extensively used for clustering chemical structures represented by 2D fingerprints. This paper compares Ward clusterings of 14 datasets (containing between 278 and 4332 molecules) with those obtained using the Szekely–Rizzo clustering method, a generalization of Ward's method. The clusters resulting from these two methods were evaluated by the extent to which the various classifications were able to group active molecules together, using a novel criterion of clustering effectiveness. Analysis of a total of 1400 classifications (Ward and Székely–Rizzo clustering methods, 14 different datasets, 5 different fingerprints and 10 different distance coefficients) demonstrated the general superiority of the Székely–Rizzo method. The distance coefficient first described by Soergel performed extremely well in these experiments, and this was also the case when it was used in simulated virtual screening experiments

Multicolor Photometry Study of the Galaxy Cluster A2589: Dynamics, Luminosity Function and Star Formation History

In this paper we present a multicolor photometry for A2589 ($z=0.0414$) with 15 intermediate bands in the Beijing-Arizona-Taiwan-Connecticut (BATC) system which covers an optical wavelength range from 3000 \AA\ to 10000 \AA. The spectral energy distributions (SEDs) for more than 5000 sources are achieved down to {\it V} $\sim$ 20 mag in about 1 deg$^{2}$ field. A2589 has been also covered by the Sloan Digital Sky Survey (SDSS) in photometric mode only. A cross-identification of the BATC-detected galaxies with the SDSS photometric catalog achieves 1199 galaxies brighter than $i=19.5$ mag, among which 68 member galaxies with known spectroscopic redshifts are found. After combining the SDSS five-band photometric data and the BATC SEDs, the technique of photometric redshift is applied to these galaxies for selecting faint member galaxies. The color-magnitude relation is taken as a further restriction of early-type cluster galaxies. As a result, 106 galaxies are newly selected as member galaxies. Spatial distribution of member galaxies shows a north-south elongation which agrees with the X-ray brightness profile and the orientation of central cD galaxy, NGC 7647. No substructures are detected on the basis of positions and radial velocities of cluster galaxies, indicating that A2589 is a well-relaxed system. The luminosity function of A2589 exhibits a peak at $M_{R} \sim -20$ mag and a dip at $M_{R} \sim -19$ mag. The low-density outer regions are the preferred habitat of faint galaxies. With the evolutionary population synthesis model, PEGASE, the environmental effect on the star formation properties for 68 spectroscopically confirmed member galaxies is studied. The outlier faint galaxies tend to have longer time scales of star formation, shorter mean stellar ages, and lower metallicities of interstellar medium, which can be interpreted in the context of hierarchical cosmological scenario.Comment: 2011 Accepted to A

ProteinDBS v2.0: a web server for global and local protein structure search

ProteinDBS v2.0 is a web server designed for efficient and accurate comparisons and searches of structurally similar proteins from a large-scale database. It provides two comparison methods, global-to-global and local-to-local, to facilitate the searches of protein structures or substructures. ProteinDBS v2.0 applies advanced feature extraction algorithms and scalable indexing techniques to achieve a high-running speed while preserving reasonably high precision of structural comparison. The experimental results show that our system is able to return results of global comparisons in seconds from a complete Protein Data Bank (PDB) database of 152 959 protein chains and that it takes much less time to complete local comparisons from a non-redundant database of 3276 proteins than other accurate comparison methods. ProteinDBS v2.0 supports query by PDB protein ID and by new structures uploaded by users. To our knowledge, this is the only search engine that can simultaneously support global and local comparisons. ProteinDBS v2.0 is a useful tool to investigate functional or evolutional relationships among proteins. Moreover, the common substructures identified by local comparison can be potentially used to assist the human curation process in discovering new domains or folds from the ever-growing protein structure databases. The system is hosted at http://ProteinDBS.rnet.missouri.edu

Extending the 5S Framework of Digital Libraries to support Complex Objects, Superimposed Information, and Content-Based Image Retrieval Services

Advanced services in digital libraries (DLs) have been developed and widely used to address the required capabilities of an assortment of systems as DLs expand into diverse application domains. These systems may require support for images (e.g., Content-Based Image Retrieval), Complex (information) Objects, and use of content at fine grain (e.g., Superimposed Information). Due to the lack of consensus on precise theoretical definitions for those services, implementation efforts often involve ad hoc development, leading to duplication and interoperability problems. This article presents a methodology to address those problems by extending a precisely specified minimal digital library (in the 5S framework) with formal definitions of aforementioned services. The theoretical extensions of digital library functionality presented here are reinforced with practical case studies as well as scenarios for the individual and integrative use of services to balance theory and practice. This methodology has implications that other advanced services can be continuously integrated into our current extended framework whenever they are identified. The theoretical definitions and case study we present may impact future development efforts and a wide range of digital library researchers, designers, and developers

Using Dali for Protein Structure Comparison

The exponential growth in the number of newly solved protein structures makes correlating and classifying the data an important task. Distance matrix alignment (Dali) is used routinely by crystallographers worldwide to screen the database of known structures for similarity to newly determined structures. Dali is easily accessible through the web server (http://ekhidna.biocenter.helsinki.fi/dali). Alternatively, the program may be downloaded and pairwise comparisons performed locally on Linux computers. © 2020, Springer Science+Business Media, LLC, part of Springer Nature.Peer reviewe