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Search Results: 1 - 10 of 849 matches for " Sibi Narayanan "
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Enhancing Lab Source Anomalous Scattering Using Cr Kα Radiation for Its Potential Application in Determining Macromolecular Structures  [PDF]
Sibi Narayanan, Devadasan Velmurugan
Crystal Structure Theory and Applications (CSTA) , 2012, DOI: 10.4236/csta.2012.13016
Abstract: Obtaining phase information for the solution of macromolecular structures is a bottleneck in X-ray crystallography. Anomalous dispersion was recognized as a powerful tool for phasing macromolecular structures. It was used mainly to supplement the isomorphous replacement or to locate the anomalous scatterer itself. The first step in solving macromolecular structures by SAD (single-wavelength anomalous diffraction) is the location of the anomalous scatterers. The SAD method for experimental phasing has evolved substantially in the recent years. A phasing tool, 5-amino-2,4,6- triiodoisophthalic acid (I3C—magic triangle), was incorporated into three proteins, lysozyme, glucose isomerase and thermolysin using quick-soaking and co-crystallization method in order to understand the binding of metal ion with proteins. The high quality of the diffraction data, the use of chromium anode X-ray radiation and the required amount of anomalous signal enabled way for successful structure determination and automated model building. An analysis and/or comparison of the sulfur and iodine anomalous signals at the Cr Kα wavelength are discussed.
Ce-SAD Phasing of Glucose Isomerase and Thermolysin Using Cu Radiation  [PDF]
Sibi Narayanan, Devadasan Velmurugan
Crystal Structure Theory and Applications (CSTA) , 2013, DOI: 10.4236/csta.2013.23013
Abstract:

Current structural genomics projects aim to solve a large number of selected protein structures as fast as possible. High degree of automation and standardization is required at every step of the whole process to speed up protein structure determination. Phase problem is a bottleneck in macromolecular structure determination and also in model building which is a time-consuming task. The simplest approach to phasing macromolecular crystal structures is the use of a SAD signal. SAD data can be collected using the in-house copper (1.54 A) wavelength source. Data collected using copper wavelength with the incorporation of anomalously scattering heavy metal atoms may serve as a powerful tool for structural biologists to solve novel protein structures as well where synchrotron beam line is not available. A short soak of protein crystals in heavy metal solution or by incorporating heavy atoms into the protein drop while crystallizing the protein (co-crystallization) leads to incorporation of these heavy metal ions into the ordered solvent shell around the protein surface. The present work aims to determine whether cerium ion can be successfully incorporated into the protein crystal through quick-soaking method while maintaining the isomorphism. The study also aims in understanding whether this metal ion can be used for phasing purpose. The intensity data are collected and analyzed for anomalous signal, substructure solution and the binding sites.

Lab Source Anomalous Scattering Using Cr Kα Radiation  [PDF]
Sibi Narayanan, Devadasan Velmurugan
Crystal Structure Theory and Applications (CSTA) , 2013, DOI: 10.4236/csta.2013.22008
Abstract: High-throughput crystallography requires a method by which the structures of proteins can be determined quickly and easily. Experimental phasing is an essential technique in determining the three-dimensional protein structures using single-crystal X-ray diffraction. In macromolecular crystallography, the phases are derived either by Molecular Replacement (MR) method using the atomic coordinates of a structurally similar protein or by locating the positions of heavy atoms that are intrinsic to the protein or that have been added (MIR, MIRAS, SIR, SIRAS, MAD and SAD). Availability of in-house lab data collection sources (Cu and Cr radiation), cryo-crystallography and improved software for heavy atom location and density modification have increased the ability to solve protein structures using SAD. SAD phasing using intrinsic anomalous scatterers like sulfur, chlorine, calcium, manganese and zinc, which are already present in the protein becomes increasingly attractive owing to the advanced phasing methods. An analysis of successful SAD phasing on three proteins, lysozyme, glucose isomerase and thermolysin based on the signal of weak anomalous scatterers such as sulfur atom and chloride ion have been carried out. This analysis also proves that even the anomalous signal provided or present naturally in a macromolecule is good enough to solve crystal structures successfully using lab source chromium-generated X-ray radiation.
4′-Methyl-1H-14′,19′-dioxa-4′-azaspiro[indole-3,5′-tetracyclo[18.4.0.02,6.08,13]tetracosane]-1′(24′),8′,10′,12′,20′,22′-hexaene-2,7′(3H)-dione
Sibi Narayanan,Thothadri Srinivasan,Santhanagopalan Purushothaman,Raghavachary Raghunathan
Acta Crystallographica Section E , 2012, DOI: 10.1107/s1600536812046132
Abstract: In the title compound, C29H28N2O4, the indoline ring system is essentially planar, with a maximum deviation of 0.027 (2) ; the carbonyl O atom lies 0.102 (1) out of the least-squares plane of the indole ring. The pyrrolidine ring adopts a C-envelope conformation, with a C atom displaced by 0.643 (2) from the mean plane formed by the remaining ring atoms. The pyrrolidine ring makes a dihedral angle of 86.1 (8)° with the indoline ring system. In the crystal, N—H...O hydrogen bonds result in the formation of cyclic centrosymmetric dimers [R22(8)]. C—H...π interactions also occur, leading to a chain along the b-axis direction. There is a rather weak π–π electron interaction between the pyrrazole and benzene rings, with a centroid–centroid distance of 3.765 (1) .
4′-Methyl-14′,19′-dioxa-4′-azaspiro[acenaphthylene-1,5′-tetracyclo[18.4.0.02,6.08,13]tetracosane]-1′(24′),8′,10′,12′,20′,22′-hexaene-2,7′(1H)-dione
Sibi Narayanan,Thothadri Srinivasan,Santhanagopalan Purushothaman,Raghavachary Raghunathan
Acta Crystallographica Section E , 2012, DOI: 10.1107/s1600536812046144
Abstract: In the title compound, C33H29NO4, the acenaphthylene ring system is essentially planar (r.m.s. deviation = 0.0290 ). The pyrrolidine ring adopts a C-envelope conformation with a C atom displaced by 0.671 (2) from the mean-plane formed by the remaining ring atoms. The pyrrolidine ring is fused to acenaphthylene ring system making a dihedral angle of 88.0 (7)°. In the crystal, molecules are linked into R22(9) dimers via C—H...N and C—H...O hydrogen bonds. Two C atoms act as donors to the same O atom acceptor, resulting in the formation of R21(7) ring motifs. These two motifs combine to form hydrogen-bonded sheets running along the a- and b-axis directions.
Ethyl 8,13-dioxa-21-azapentacyclo[18.5.1.02,7.014,19.021,25]hexacosa-2(7),3,5,14,16,18-hexaene-26-carboxylate
Sibi Narayanan,Thothadri Srinivasan,Santhanagopalan Purushothaman,Raghavachary Raghunathan
Acta Crystallographica Section E , 2013, DOI: 10.1107/s1600536812049094
Abstract: In the title compound, C26H31NO4, the five-membered rings of the central pyrrolizine system adopt N-envelope conformations. The ethyl acetate group adopts an extended conformation. The dihedral angle between the benzene rings is 36.6 (1)°. In the crystal, C—H...O hydrogen bonds form a zigzag chain running along the b-axis directions. The crystal structure is futher consolidated by C—H...π interactions.
Ethyl 27-oxo-15-oxa-2,20-diazahexacyclo[18.6.1.01,8.02,6.09,14.021,26]heptacosa-9,11,13,21,23,25-hexaene-7-carboxylate
Sibi Narayanan,Thothadri Srinivasan,Santhanagopalan Purushothaman,Raghavachary Raghunathan
Acta Crystallographica Section E , 2013, DOI: 10.1107/s1600536812049082
Abstract: In the title compound, C27H30N2O4, the pyrrolidine ring adopts a twisted conformation. The indoline ring system is almost perpendicular to the mean plane of the pyrrolidine ring, making a dihedral angle of 81.7 (8)°. In the crystal, molecules are linked into centrosymmetric dimers with graph-set motif R22(16) via pairs of C—H...O hydrogen bonds. The terminal ethyl group of the ester group is disordered over two sets of sites, with a site-occupancy ratio of 0.587 (11):0.413 (11).
Nutrient Removal Efficiencies of Chlorella vulgaris from Urban Wastewater for Reduced Eutrophication  [PDF]
Ravipratap Singh, Rohan Birru, G. Sibi
Journal of Environmental Protection (JEP) , 2017, DOI: 10.4236/jep.2017.81001
Abstract: Urban wastewater contains both organic and inorganic nutrients and discharge of untreated water increases nitrogen and phosphorous content in water bodies leading to eutrophication problem. Physical and chemical treatment of urban waste water produces large quantities of waste sludge associated with secondary pollution. Microalgae can assimilate nutrients especially nitrogen and phosphorous from wastewater for their growth and produce valuable biomass and lipid. This study was performed to determine the growth of Chlorella vulgaris in urban wastewater (UWW) and Bold’s basal medium (BBM) thereby identifying cost effective growth medium for microalga cultivation. In addition, nutrient removal abilities of C. vulgaris from various dilutions of urban waste water were explored at 10 days cultivation period. Specific growth rate, biomass and lipid content were higher in microalgae grown in urban waste water than BBM. The highest lipid productivity of 14.31 mg·L?1·day?1 was achieved in the culture grown in UWW medium which exceeded the BBM at 1.15 fold. The amount of nutrient removal tended to increase with higher dilutions of UWW. Removal rates of upto 87.9% and 98.4% were recorded for total nitrogen and total phosphorous by C. vulgaris. The results emphasized that urban waste water as a cost effective growth medium for higher biomass and lipid production accompanied with the nutrient removal efficiency of microalgae to reduce eutrophication.
The Park of Renewable Energy geoethical project
Patrizia Sibi,Mario Valletta
Annals of Geophysics , 2012, DOI: 10.4401/ag-5552
Abstract: The Park of Renewable Energy is an environmental technology park in the middle of Italy that has an innovative integrated system for the production of renewable energy. Recently, the Park launched a public invitation: to become part of a great widespread community for the production of renewable energy, and to promote energy conservation and a sustainable lifestyle. This empowerment process that turns consumers into energy producers – and also into those who convey the culture of sustainability – might, over time, give life to a community that actually lives according to the geoethical principles of biosustainability. The route for the identification and dissemination of the Park of Renewable Energy community is an interesting example of the generative process, whereby rather than doggedly pursuing a predetermined objective, such as a model to be implemented, the actors involved, “look for directions and values that are inherent in the means available” [Bateson 2000], including communication networks and methodologies of social participation. The community components focus their attention on the action and relationship effects, rather than on ways to reach a predefined goal. In this perspective, the Park of Renewable Energy experience aims to become an interesting object of observation and reflection for its green ethics. This ecological approach promises unexpected new creations: there is a chance we will at last see the birth of a sustainable form of social organization adapted to the human community.
Literature Review of Single Machine Scheduling Problem with Uniform Parallel Machines  [PDF]
Panneerselvam Senthilkumar, Sockalingam Narayanan
Intelligent Information Management (IIM) , 2010, DOI: 10.4236/iim.2010.28056
Abstract: This paper presents a survey of single machine scheduling problem with uniform parallel machines. The single machine scheduling problem with uniform parallel machines consists of n jobs, each with single operation, which are to be scheduled on m parallel machines with different speeds. These parallel machines are also called proportional machines or related machines. There are several measures of performance which are to be optimized in uniform parallel machines scheduling. Since, this scheduling problem is a combinatorial problem; usage of a heuristic is inevitable to obtain solution in polynomial time. This paper gives a classification of the literatures of this scheduling problem in three major categories, viz. offline scheduling, online scheduling and miscellaneous scheduling. In total, the available literatures are classified into 17 subgroups. Under each of the first two categories, the available literatures are discussed under different groups based on different measures of performance and non-preemptive/preemptive nature of the jobs. In the last category, the literatures are discussed under three subgroups, namely non-preemptive jobs, preemptive jobs and periodic jobs.
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