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Hydrological characteristics and flood plain vegetation of human impacted wetlands: A case study from Okhla Bird Sanctuary, National Capital Region, India
Upma Manral,Angshuman Raha,Ridhima Solanki,Syed Ainul Hussain
Asian Journal of Conservation Biology , 2012,
Abstract: Yamuna River has been subjected to severe anthropogenic pressures such as water abstraction, discharge of wastewater, development activities on river floodplains, deforestation in the river basin resulting in reduced flow, loss of habitat, deterioration of water quality and loss of biological diversity. We studied hydrological characteristics such as river flow, water depth and quality and floodplain vegetation characteristics of Okhla Bird Sanctuary (OBS), a human modified floodplain wetland formed due to the construction of Okhla barrage across the Yamuna River in National Capital Region (NCR), on the Delhi-Uttar Pradesh border. The flow data for Yamuna was collected from Delhi Jal board and irrigation department of Uttar Pradesh. Study indicates reduced flow in the river downstream Wazirabad with no release of water in the summers of 2006 and 2010. For bathymetry, GARMIN 160 C Fish Finder was used after dividing study area into 50 m x 50 m grids. About 65% area had depth less than 2 m indicating more of shallower areas. Results for water quality analysis show a dissolved oxygen level at 1.6 ± 0.84 mgl-1, Biological and Chemical Oxygen demand at 16.72 ± 4.28 mgl-1 and 39.8 ± 7.71 mgl-1 respectively, indicating a high organic load in the river. The Sanctuary is facing serious threats from the rapid proliferation of Typha angustifolia and Eichhornia crassipes which were dominant species in shallow water and open water habitats, respectively. Thus, the remaining Yamuna river flood plain in the NCR, Delhi should be declared as ecologically sensitive area and appropriate measures should be taken to maintain its integrity.
Structural Characterization of the D-Tyr-tRNATyr Deacylase from Bacillus lichenformis, an Organism of Great Industrial Importance  [PDF]
Angshuman Bagchi
Computational Molecular Bioscience (CMB) , 2011, DOI: 10.4236/cmb.2011.11001
Abstract: A new class of enzyme was established that hydrolyze the ester bond between D-Tyr bound onto its cognate t-RNA. The enzyme is called D-Tyr-tRNA deacylase. The three dimensional structure of the D-Tyr-tRNA deacylase from industrially important microorganism Bacillus lichenformis DSM13 was predicted by comparative modeling approach. Since the protein acts as a dimer a dimeric model of the enzyme was constructed. The interactions responsible for dimerization were also predicted. With the help of docking and molecular dynamics simulations the favourable binding mode of the enzyme was predicted. The probable biochemical mechanism of the hydrolysis process was elucidated. This study provides a rational framework to interpret the molecular mechanistic details of the removal of toxic D-Tyr-tRNA from the cells of industrially important microorganism Bacillus lichenformis DSM13 using the enzyme D-Tyr-tRNA deacylase.
A Brief Overview of a Few Popular and Important Protein Databases  [PDF]
Angshuman Bagchi
Computational Molecular Bioscience (CMB) , 2012, DOI: 10.4236/cmb.2012.24012
Abstract: Database is a repository of information. In today’s world there are different types of databases available. In this present review the focus is on a few popular and most widely used biological databases that store protein sequence and structure information. The databases that are of utmost importance to do basic biological research work are PDB, SCOP, CATH and UniProt/SwissProt and GenBank. These databases have different utilities & they play important roles in different fields of biology and bioinformatics. PDB provides the structural information of proteins, protein-complexes and proteins complexed with other macromolecules. SCOP & CATH store various annotations of protein sequences and structures. UniProt is a central repository of protein sequences & functions created by joining the information contained in SwissProt, TrEMBL.
Structural analyses of the interactions of SoxY and SoxZ from thermo-neutrophilic Hydrogenobacter thermophilus  [PDF]
Angshuman Bagchi, Tapash Chandra Ghosh
Journal of Biophysical Chemistry (JBPC) , 2011, DOI: 10.4236/jbpc.2011.24047
Abstract: Microbial redox reactions of inorganic sulfur compounds are one of the important reactions responsible for the recycling of this element to maintain the environmental sulfur balance. These reactions are carried out by phylogenetically diverse set of microorganisms. The sulfur oxidizing gene cluster (sox) of thermo-neutrophilic bacterium Hydrogenobacter thermophilus consists of soxYZAXB. The bacterium shows optimal thiosulfate oxidation activity at 60°C. There are practically no reports regarding the structural biology of the sulfur oxidation proc- ess in this organism. In the present context, we employed homology modeling to construct the three dimensional structures of SoxY and SoxZ from Hydrogenobacter thermophilus. With the help of docking simulations we have identified the amino acid residues of these proteins in- volved in the interactions. The thermodynamics of the protein-protein interactions have also been analyzed. The probable biochemical mechanism of the binding of thiosulfate has been elucidated. Our study provides a rational framework to understand the molecular mechanism of the sulfur oxidation biochemistry.
ALGINATE BASED NANOPARTICULATE DRUG DELIVERY FOR ANTI HIV DRUG LOPINAVIR
B Angshuman
Journal of Global Pharma Technology , 2010, DOI: 10.1234/jgpt.v2i3.162
Abstract: Sustained release lopinavir-loaded nanoparticles (LP-NP) in alginate, biodegradable hydro based polymer, were prepared by in situ nanoemulsion-polymer crosslinking approach. Four different drug-encapsulating solvents, viz., dichloromethane, n hexane, 1,2 dichloroethane, and isopropyl alcohol were used for preparation of lopinavir loaded calcium alginate nanoparticles. Lopinavir loading was confirmed quantitatively in high performance liquid chromatography (HPLC) studies. Prepared NP’s structure and surface morphology were investigated using scanning electron microscope (SEM) and size distributions were visualized in Transmission Electron Microscope (TEM). Hydrodynamic diameter of nanoparticles was 127nm, with Gaussian distribution. Sustained diffusive drug release was observed in vitro, depending on drug polymer ratio; alginate nanoparticles are able to deliver 30 to 80% of the loaded drug by the end of 24 hour. The nanoparticles prepared with 1:6 drug polymer ratio show better release pattern and control the drug release over a period of 24 hour. The release followed Higuchi kinetics rather than first order kinetics, indicating diffusion controlled drug release. The nanoparticulation technique developed can be a good choice for the development of different sustained protease inhibitor drug carriers.
Relative weak injectivity of operator system pairs
Angshuman Bhattacharya
Mathematics , 2013,
Abstract: The concept of a relatively weakly injective pair of operator systems is introduced and studied in this paper, motivated by relative weak injectivity in the C*-algebra category. E. Kirchberg \cite{Kr} proved that the C*-algebra $C^*(\mathbb{f}_\infty)$ of the free group $\mathbb{f}_\infty$ on countably many generators characterizes relative weak injectivity for pairs of C*-algebras by means of the maximal tensor product. One of the main results of this paper shows that $C^*(\mathbb{f}_\infty)$ also characterises relative weak injectivity in the operator system category. A key tool is the theory of operator system tensor products \cite{KP1,KP2}.
Approximate Reasoning in Fuzzy Resolution  [PDF]
Banibrata Mondal, Swapan Raha
International Journal of Intelligence Science (IJIS) , 2013, DOI: 10.4236/ijis.2013.32010
Abstract:

Resolution is an useful tool for mechanical theorem proving in modelling the refutation proof procedure, which is mostly used in constructing a proof of a theorem. An attempt is made to utilize approximate reasoning methodology in fuzzy resolution. Approximate reasoning is a methodology which can deduce a specific information from general knowledge and specific observation. It is dependent on the form of general knowledge and the corresponding deductive mechanism. In ordinary approximate reasoning, we derive from AB and by some mechanism. In inverse approximate reasoning, we conclude from AB and using an altogether different mechanism. An important observation is that similarity is inherent in fuzzy set theory. In approximate reasoning methodology-

A Review on Phylogenetic Analysis: A Journey through Modern Era  [PDF]
Sourav Singha Roy, Rakhi Dasgupta, Angshuman Bagchi
Computational Molecular Bioscience (CMB) , 2014, DOI: 10.4236/cmb.2014.43005
Abstract: Phylogenetic analysis may be considered to be a highly reliable and important bioinformatics tool. The importance of phylogenetic analysis lies in its simple manifestation and easy handling of data. The simple tree representation of the evolution makes the phylogenetic analysis easier to comprehend and represent as well. The varied applications of phylogenetics in different fields of biology make this analysis an absolute necessity. The different aspects of phylogenetic analysis have been described in a comprehensive manner. This review may be useful to those who would like to have a firsthand knowledge of phylogenetics.
Exploring the role of SoxA and SoxX in sulphur oxidation in Allochromatium vinosum through Protein - protein docking : An in silico approach
Angshuman Bagchi,Sujay Ray
Pure and Applied Biology , 2013, DOI: nil
Abstract: Thiosulphate (S2O32-) is a stable and environmentally abundant sulphur compound of intermediate oxidation state and fulfils an important role in the natural sulphur cycle. There are main two types of thiosulfate-oxidizing Sox enzyme system type one group 1 forms sulfur globules as intermediates Allochromatium vinosum (A.vino or A.vinosum)), group 2 which does not form sulphur globules as intermediate form for example Paracoccus pantotrophus . Sox genes in A. vinosum, are separated into three gene clusters. Cluster one comprises Alvin_2108 to Alvin_2112.The second gene cluster extends between Alvin_2165 and Alvin_2167 .The third gene cluster includes Alvin_2168 to Alvin_2182.Where SoxX, SoxA, are encoded by Alvin_2168 to Alvin_2169. In the present work, homology modeling has been used to build the three dimensional structures of SoxA, and SoxX. With the help of protein -protein docking and Protein Interaction Calculator (PIC) sever the amino acid residues of these proteins involved in the interactions have been identified. The interactions between the SoxA, and SoxX proteins are mediated mainly through hydrogen bonding, hydrophobic interaction, electrostatic interaction. Possible mechanisms of interaction between the SoxA, and SoxX have identified in spite the absence of SoxK.
Novel Design of High Polarized Inverter Using Minimum Number of Rotated Cells and Related Kink Energy Calculation in Quantum dot Cellular Automata
Angshuman Khan,Ratna Chakrabarty
International Journal of Soft Computing & Engineering , 2013,
Abstract: Quantum Dot Cellular Automata (QCA) has been emerged as a cut-in nano-technology in the field of digital logic architecture. It is the most emerging technology in nanoscience. QCA designed circuits require lesser power & it has high switching speed and high packaging density with respect to current CMOS technology. One of the basic building blocks of QCA circuits is QCA inverter. The conventional QCA inverters require more normal cells and it has less polarization. In this paper, we have designed high polarized inverters using minimum number of rotated (45 ) QCA cells. Till now, the conventional inverters which have large polarization, they require three to five normal cells. We have designed the novel inverter using three rotated cells whose polarization is more than the conventional three normal cells inverter. We increasing the polarization i.e. make the three rotated cells inverter circuit more fault- free by adding extra rotated cells at the output section. In each case, the designed rotated cells inverters have more polarization (i.e. more fault free) than conventional inverters though it has same number of cells. Our finally designed high polarized rotated cells inverter has five cells and its polarization is greater than any type of conventional inverters designed till now. Also, here we calculate the kink energy of each rotated cells inverters.
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