Higher accuracy protein Multiple Sequence Alignment by Stochastic Algorithm

Multiple Sequence Alignment gives insight into evolutionary, structural and functional relationships among the proteins. Here, a novel Protein Alignment by Stochastic Algorithm (PASA) is developed. Evolutionary operators of a genetic algorithm, namely, mutation and selection are utilized in combining the output of two most important sequence alignment programs and then developing an optimized new algorithm. Efficiency of protein alignments is evaluated in terms of Total Column score which is equal to the number of correctly aligned columns between a test alignment and the reference alignment divided by the total number of columns in the reference alignment. The PASA optimizer achieves, on an average, significant better alignment over the well known individual bioinformatics tools. This PASA is statistically the most accurate protein alignment method today. It can have potential applications in drug discovery processes in the biotechnology industry

An effective Nuclear Model: from Nuclear Matter to Finite Nuclei

The momentum and density dependence of mean fields in symmetric and asymmetric nuclear matter are analysed using the simple density dependent finite range effective interaction containing a single Gaussian term alongwith the zero-range terms. Within the formalism developed, it is possible to reproduce the various diverging predictions on the momentum and density dependence of isovector part of the mean field in asymmetric matter. The finite nucleus calculation is formulated for the simple Gaussian interaction in the framework of quasilocal density functional theory. The prediction of energies and charge radii of the interaction for the spherical nuclei compares well with the results of other effective theories.Comment: 10 pages, 3 figures, 2 tables, To appear in the Proceedings of the 11th International Conference on Nucleus-Nucleus Collisions (NN2012), May 27-June 1, 2012, San Antonio, Texas, US

A CATEGORICAL CONSTRUCTION OF MINIMAL MODEL

Deleanu, Frei and Hilton have developed the notion of generalized Adams completion in a categorical context; they have also suggested the dual notion, namely, Adams cocompletion of anobject in a category. The concept of rational homotopy theory was first characterized by Quillen. In fact in rational homotopy theory Sullivan introduced the concept of minimal model. In this note under a reasonable assumption, the minimal model of a 1-connected differential graded algebra can be expressed as the Adams cocompletion of the differential graded algebra with respect to a chosen set in the category of 1-connected differential graded algebras (in short d.g.a.’s) over the field of rationales and d.g.a.-homomorphism

Spatial variability of daily rainfall over Orissa, India, during the southwest summer monsoon season

Southwest summer monsoon rainfall over Orissa, a state of eastern India, shows characteristic spatial and temporal variability, due to the interaction of basic westerly flow with orography and the synoptic-scale monsoon disturbances developing over the northern Bay of Bengal and moving west-northwestwards along the monsoon trough. The aim of this study is to find out the main features of the spatial variability of daily monsoon rainfall over Orissa and associated synoptic systems. Empirical orthogonal function (EOF) analysis is a good tool to filter out the main components from any noise, and this was applied to daily monsoon rainfall (June-September) data of 31 uniformly distributed stations over a period of 20 years (1980-1999). The association of synoptic systems with significant EOFs has been confirmed by analysing daily synoptic systems over Orissa and its neighbourhood during the same period. The first three EOFs in S-mode may be attributed to good monsoon rainfall in association with low-pressure systems/cyclonic circulation (LPSC), like lows, depressions, cyclonic storms and cyclonic circulation extending up to the mid-tropospheric level over the northwest (NW) Bay/NW and the adjoining northeast (NE) Bay, over Gangetic West Bengal (GWB) and over Orissa/NW and the adjoining west central (WC) Bay. The fourth and fifth EOFs may be attributed to a weak monsoon condition being associated only with a monsoon trough without any embedded system and LPSC over the NE and the adjoining NW Bay respectively. Based on rotation of significant EOFs in T-mode, which gives better regionalization, Orissa consists of five homogeneous regions of daily monsoon rainfall: (i) eastern Orissa, (ii) western Orissa, (iii) northwest Orissa, (iv) north Orissa and (v) northeast Orissa. Eastern Orissa gets higher rainfall than the other regions, due to LPSC over NW Bay/NW and the adjoining NE Bay, western Orissa rainfall is due to LPSC over Orissa/NW and the adjoining WC Bay; likewise, northwest Orissa rainfall is due to LPSC over GWB, north Orissa rainfall is due to LPSC over the NE and the adjoining NW Bay, and northeast Orissa rainfall is due only to a monsoon trough without any significant embedded system over Orissa and adjoining land/sea areas