(A) Optimization of solid body phase synthesis of RNA using the Cpep chemistry. (B) Synthesis of BODIPY labeled oligonucleotides

(A) Solid phase synthesis of oligonucleotides are well documented and are extensively studied as the demands continue to rise with the development of antisense, anti-gene, RNA interference, and aptamers. Although synthesis of RNA sequences faces many challenges, most notably the choice of the 2' -hydroxy protecting group, modified 2' -O-Cpep protected ribonucleotides were synthesized as alternitive building blocks. Altering phosphitylation procedures to incorporate 3' -N,N-diethyl phosphoramidites enhanced the overall reactivity, thus, increased the coupling efficiency without loss of integrety. Furthermore, technical optimizations of solid phase synthesis cycles were carried out to allow for successful synthesis of a homo UIO sequences with a stepwise coupling efficiency reaching 99% and a final yield of 91 %. (B) Over the past few decades, dipyrrometheneboron difluoride (BODIPY) has gained recognition as one of the most versatile fluorophores. Currently, BODIPY labeling of oligonucleotides are carried out post-synthetically and to date, there lacks a method that allows for direct incorporation of BODIPY into oligonucleotides during solid phase synthesis. Therefore, synthesis of BODIPY derived phosphoramidites will provide an alternative method in obtaining fluorescently labelled oligonucleotides. A method for the synthesis and incorporation of the BODIPY analogues into oligonucleotides by phosphoramidite chemistry-based solid phase DNA synthesis is reported here. Using this approach, BODIPY-labeled TlO homopolymer and ISIS 5132 were successfully synthesized.

Anatomo-functional magnetic resonance imaging of the spinal cord and its application to the characterization of spinal lesions in cats

Les lésions de la moelle épinière ont un impact significatif sur la qualité de la vie car elles peuvent induire des déficits moteurs (paralysie) et sensoriels. Ces déficits évoluent dans le temps à mesure que le système nerveux central se réorganise, en impliquant des mécanismes physiologiques et neurochimiques encore mal connus. L'ampleur de ces déficits ainsi que le processus de réhabilitation dépendent fortement des voies anatomiques qui ont été altérées dans la moelle épinière. Il est donc crucial de pouvoir attester l'intégrité de la matière blanche après une lésion spinale et évaluer quantitativement l'état fonctionnel des neurones spinaux. Un grand intérêt de l'imagerie par résonance magnétique (IRM) est qu'elle permet d'imager de façon non invasive les propriétés fonctionnelles et anatomiques du système nerveux central. Le premier objectif de ce projet de thèse a été de développer l'IRM de diffusion afin d'évaluer l'intégrité des axones de la matière blanche après une lésion médullaire. Le deuxième objectif a été d'évaluer dans quelle mesure l'IRM fonctionnelle permet de mesurer l'activité des neurones de la moelle épinière. Bien que largement appliquées au cerveau, l'IRM de diffusion et l'IRM fonctionnelle de la moelle épinière sont plus problématiques. Les difficultés associées à l'IRM de la moelle épinière relèvent de sa fine géométrie (environ 1 cm de diamètre chez l'humain), de la présence de mouvements d'origine physiologique (cardiaques et respiratoires) et de la présence d'artefacts de susceptibilité magnétique induits par les inhomogénéités de champ, notamment au niveau des disques intervertébraux et des poumons. L'objectif principal de cette thèse a donc été de développer des méthodes permettant de contourner ces difficultés. Ce développement a notamment reposé sur l'optimisation des paramètres d'acquisition d'images anatomiques, d'images pondérées en diffusion et de données fonctionnelles chez le chat et chez l'humain sur un IRM à 3 Tesla. En outre, diverses stratégies ont été étudiées afin de corriger les distorsions d'images induites par les artefacts de susceptibilité magnétique, et une étude a été menée sur la sensibilité et la spécificité de l'IRM fonctionnelle de la moelle épinière. Les résultats de ces études démontrent la faisabilité d'acquérir des images pondérées en diffusion de haute qualité, et d'évaluer l'intégrité de voies spinales spécifiques après lésion complète et partielle. De plus, l'activité des neurones spinaux a pu être détectée par IRM fonctionnelle chez des chats anesthésiés. Bien qu'encourageants, ces résultats mettent en lumière la nécessité de développer davantage ces nouvelles techniques. L'existence d'un outil de neuroimagerie fiable et robuste, capable de confirmer les paramètres cliniques, permettrait d'améliorer le diagnostic et le pronostic chez les patients atteints de lésions médullaires. Un des enjeux majeurs serait de suivre et de valider l'effet de diverses stratégies thérapeutiques. De telles outils représentent un espoir immense pour nombre de personnes souffrant de traumatismes et de maladies neurodégénératives telles que les lésions de la moelle épinière, les tumeurs spinales, la sclérose en plaques et la sclérose latérale amyotrophique.

Studies on Diatoms along the South West Coast of India in Relation to the Hydrological Parameters

The main objective of the study was primarily to determine the effect of hydrographical parameters especially nutrients which were supplied externally to the seawater while culturing the diatom Chaetoceros calcitrans, under laboratory conditions, and to determine its optimum concentration for ideal growth of the culture, in such a condition of increased rate of pollution due to the industrialization and effluents. Also an attempt was made to study the possible correlation of diatom abundance in the South west Coast of India with the landings of the pelagic fishery resources, especially sardine, mackerel and anchovy, since these fishes are largely diatom feeders. Positive correlation was found between the diatoms and pelagic fish landings of Thalassery and Vizhinjam area while at Cochin there was less significant correlation between the two variables

Optimization of carbon and nitrogen sources and growth factors for the production of an aquaculture probiotic (Pseudomonas MCCB 103) using response surface methodology

Aim: To develop a new medium for enhanced production of biomass of an aquaculture probiotic Pseudomonas MCCB 103 and its antagonistic phenazine compound, pyocyanin. Methods and Results: Carbon and nitrogen sources and growth factors, such as amino acids and vitamins, were screened initially in a mineral medium for the biomass and antagonistic compound of Pseudomonas MCCB 103. The selected ingredients were further optimized using a full-factorial central composite design of the response surface methodology. The medium optimized as per the model for biomass contained mannitol (20 g l)1), glycerol (20 g l)1), sodium chloride (5 g l)1), urea (3Æ3 g l)1) and mineral salts solution (20 ml l)1), and the one optimized for the antagonistic compound contained mannitol (2 g l)1), glycerol (20 g l)1), sodium chloride (5Æ1 g l)1), urea (3Æ6 g l)1) and mineral salts solution (20 ml l)1). Subsequently, the model was validated experimentally with a biomass increase by 19% and fivefold increase of the antagonistic compound. Conclusion: Significant increase in the biomass and antagonistic compound production could be obtained in the new media. Significance and Impact of the Study: Media formulation and optimization are the primary steps involved in bioprocess technology, an attempt not made so far in the production of aquaculture probiotics.

Optimization of Preparation Techniques and Dielectric Study of Polyanilines in the Microwave & High Frequency Field

The thesis deals with the preparation and dielectric characterization of Poly aniline and its analogues in ISM band frequency of 2-4 GHz that includes part of the microwave region (300 MHz to 300 GHz) of the electromagnetic spectrum and an initial dielectric study in the high frequency [O.05MHz-13 MHz]. PolyaniIine has been synthesized by an in situ doping reaction under different temperature and in the presence of inorganic dopants such as HCl H2S04, HN03, HCl04 and organic dopants such as camphorsulphonic acid [CSA], toluenesulphonic acid {TSA) and naphthalenesulphonic acid [NSA]. The variation in dielectric properties with change in reaction temperature, dopants and frequency has been studied. The effect of codopants and microemulsions on the dielectric properties has also been studied in the ISM band. The ISM band of frequencies (2-4 GHz) is of great utility in Industrial, Scientific and Medical (ISM) applications. Microwave heating is a very efficient method of heating dielectric materials and is extensively used in industrial as well as household heating applications.

Studies on the fracture behaviour of polymer blends with special reference to PP/HDPE and PS/HIPS blends

Investigations on the fracture behaviour of polymer blends is the topic of this thesis. The blends selected are PP/HDPE and PS/HIPS. PP/HDPE blend is chosen due to its commercial importance and PS/HIPS blend is selected to study the transition from brittle fracture to ductile fracture.PP/HDPE blends were prepared at different compositions by melt blending at 180°C and fracture failure process was investigated by conducting notch sensitivity test and tensile test at different strain rates. The effects of two types of modifiers (particulate and elastomer) on the fracture behaviour and notch sensitivity of PP/HDPE blends were studied. The modifiers used are calcium carbonate, a hard particulate filler commonly used in plastics and Ethylene Propylene Diene Monomer (EPDM). They were added in 2%, 4% and 6% by weight of the blends.The study shows that the mechanical properties of PP/HDPE blends can be optimized by selecting proper blend compositions. The selected modifiers are found to alter and improve the fracture behaviour and notch sensitivity of the blends. Particulate fillers like calcium carbonate can be used for making the mechanical behaviour more stable at the various blend compositions. The resistance to notch sensitivity of the blends is found to be marginally lower in the presence of calcium carbonate. The elastomeric modifier EPDM produces a better stability of the mechanical behaviour. A low concentration of EPDM is sufficient to effect such a change. EPDM significantly improves the resistance to notch sensitivity of the blends. The study shows that judicious selection of modifiers can improve the fracture behaviour and notch sensitivity of PP/HDPE blends and help these materials to be used for critical applications.For investigating the transition in fracture behaviour and failure modes, PS/HIPS blends were selected. The blends were prepared by melt mixing followed by injection moulding to prepare the specimens for conducting tensile, impact and flexure tests. These tests were used to simulate the various conditions which promote failure.The tensile behaviour of unnotched and notched PS/HIPS blend samples were evaluated at slow speeds. Tensile strengths and moduli were found to increase at the higher testing speed for all the blend combinations whereas maximum strain at break was found to decrease. For a particular speed of testing, the tensile strength and modulus show only a very slight decrease as HIPS content is increased up to about 40%. However, there is a drastic decrease on increasing the HIPS content thereafter.The maximum strain at break shows only a very slight change up to about 40% HIPS content and thereafter shows a remarkable increase. The notched specimens also follow a comparable trend even though the notch sensitivity is seen high for PS rich blends containing up to 40% HIPS. The notch sensitivity marginally decreases with increase in HIPS content. At the same time, it is found to increase with the increase in strain rate. It is observed that blends containing more than 40% HIPS fail in ductile mode.The impact characteristics of PSIHIPS blends studied were impact strength, the energy absorbed by the test specimen and impact toughness. Remarkable increase in impact strength is observed as HIPS content in the blend exceeds 40%. The energy absorbed by the test specimens and the impact toughness also show a comparable trend.Flexural testing which helps to characterize the load bearing capacity was conducted on PS/HIPS blend samples at the two different testing speeds of 5mmlmin and 10 mm/min. The flexural strength increases with increase in testing speed for all the blend compositions. At both the speeds, remarkable reduction in flexural strength is observed as HIPS content in the blend exceeds 40%. The flexural strain and flexural energy absorbed by the specimens are found to increase with increase in HIPS content. At both the testing speeds, brittle fracture is observed for PS rich blends whereas HIPS rich blends show ductile mode of failure.Photoelastic investigations were conducted on PS/HIPS blend samples to analyze their failure modes. A plane polariscope with a broad source of light was utilized for the study. The coloured isochromatic fringes formed indicate the presence of residual stress concentration in the blend samples. The coverage made by the fringes on the test specimens varies with the blend composition and it shows a reducing trend with the increase in HIPS content. This indicates that the presence of residual stress is a contributing factor leading to brittle fracture in PS rich blends and this tendency gradually falls with increase in HIPS content and leads to their ductile mode of failure.

Analysis and Optimization of Machining Process Using Evolutionary Algorithms

To ensure quality of machined products at minimum machining costs and maximum machining effectiveness, it is very important to select optimum parameters when metal cutting machine tools are employed. Traditionally, the experience of the operator plays a major role in the selection of optimum metal cutting conditions. However, attaining optimum values each time by even a skilled operator is difficult. The non-linear nature of the machining process has compelled engineers to search for more effective methods to attain optimization. The design objective preceding most engineering design activities is simply to minimize the cost of production or to maximize the production efficiency. The main aim of research work reported here is to build robust optimization algorithms by exploiting ideas that nature has to offer from its backyard and using it to solve real world optimization problems in manufacturing processes.In this thesis, after conducting an exhaustive literature review, several optimization techniques used in various manufacturing processes have been identified. The selection of optimal cutting parameters, like depth of cut, feed and speed is a very important issue for every machining process. Experiments have been designed using Taguchi technique and dry turning of SS420 has been performed on Kirlosker turn master 35 lathe. Analysis using S/N and ANOVA were performed to find the optimum level and percentage of contribution of each parameter. By using S/N analysis the optimum machining parameters from the experimentation is obtained.Optimization algorithms begin with one or more design solutions supplied by the user and then iteratively check new design solutions, relative search spaces in order to achieve the true optimum solution. A mathematical model has been developed using response surface analysis for surface roughness and the model was validated using published results from literature.Methodologies in optimization such as Simulated annealing (SA), Particle Swarm Optimization (PSO), Conventional Genetic Algorithm (CGA) and Improved Genetic Algorithm (IGA) are applied to optimize machining parameters while dry turning of SS420 material. All the above algorithms were tested for their efficiency, robustness and accuracy and observe how they often outperform conventional optimization method applied to difficult real world problems. The SA, PSO, CGA and IGA codes were developed using MATLAB. For each evolutionary algorithmic method, optimum cutting conditions are provided to achieve better surface finish.The computational results using SA clearly demonstrated that the proposed solution procedure is quite capable in solving such complicated problems effectively and efficiently. Particle Swarm Optimization (PSO) is a relatively recent heuristic search method whose mechanics are inspired by the swarming or collaborative behavior of biological populations. From the results it has been observed that PSO provides better results and also more computationally efficient.Based on the results obtained using CGA and IGA for the optimization of machining process, the proposed IGA provides better results than the conventional GA. The improved genetic algorithm incorporating a stochastic crossover technique and an artificial initial population scheme is developed to provide a faster search mechanism. Finally, a comparison among these algorithms were made for the specific example of dry turning of SS 420 material and arriving at optimum machining parameters of feed, cutting speed, depth of cut and tool nose radius for minimum surface roughness as the criterion. To summarize, the research work fills in conspicuous gaps between research prototypes and industry requirements, by simulating evolutionary procedures seen in nature that optimize its own systems.

Studies on the universal parameters and onset of chaos in dissipative systems

It has become clear over the last few years that many deterministic dynamical systems described by simple but nonlinear equations with only a few variables can behave in an irregular or random fashion. This phenomenon, commonly called deterministic chaos, is essentially due to the fact that we cannot deal with infinitely precise numbers. In these systems trajectories emerging from nearby initial conditions diverge exponentially as time evolves)and therefore)any small error in the initial measurement spreads with time considerably, leading to unpredictable and chaotic behaviour The thesis work is mainly centered on the asymptotic behaviour of nonlinear and nonintegrable dissipative dynamical systems. It is found that completely deterministic nonlinear differential equations describing such systems can exhibit random or chaotic behaviour. Theoretical studies on this chaotic behaviour can enhance our understanding of various phenomena such as turbulence, nonlinear electronic circuits, erratic behaviour of heart and brain, fundamental molecular reactions involving DNA, meteorological phenomena, fluctuations in the cost of materials and so on. Chaos is studied mainly under two different approaches - the nature of the onset of chaos and the statistical description of the chaotic state.

The role of dynamical polarization of the ligand-to-metal charge transfer excitations in the ab initio determination of effective exchange parameters

The role of the bridging ligand on the effective Heisenberg coupling parameters is analyzed in detail. This analysis strongly suggests that the ligand-to-metal charge transfer excitations are responsible for a large part of the final value of the magnetic coupling constant. This permits us to suggest a variant of the difference dedicated configuration interaction (DDCI) method, presently one of the most accurate and reliable for the evaluation of magnetic effective interactions. This method treats the bridging ligand orbitals mediating the interaction at the same level than the magnetic orbitals and preserves the high quality of the DDCI results while being much less computationally demanding. The numerical accuracy of the new approach is illustrated on various systems with one or two magnetic electrons per magnetic center. The fact that accurate results can be obtained using a rather reduced configuration interaction space opens the possibility to study more complex systems with many magnetic centers and/or many electrons per center.

EVALUATION OF THERMODYNAMIC PARAMETERS OF THE ATMOSPHERE BY A FORTRAN PROGRAM

Thermodynamic parameters of the atmosphere form part of the input to numerical forecasting models. Usually these parameters are evaluated from a thermodynamic diagram. Here, a technique is developed to evaluate these parameters quickly and accurately using a Fortran program. This technique is tested with four sets of randomly selected data and the results are in agreement with the results from the conventional method. This technique is superior to the conventional method in three respects: more accuracy, less computation time, and evaluation of additional parameters. The computation time for all the parameters on a PC AT 286 machine is II sec. This software, with appropriate modifications, can be used, for verifying various lines on a thermodynamic diagram

Variations of surface boundary layer parameters associated with Cyclone Gonu over the Arabian Sea using QuikSCAT data

This study attempted to quantify the variations of the surface marine atmospheric boundary layer (MABL) parameters associated with the tropical Cyclone Gonu formed over the Arabian Sea during 30 May–7 June 2007 (just after the monsoon onset). These characteristics were evaluated in terms of surface wind, drag coefficient, wind stress, horizontal divergence, and frictional velocity using 0.5◦ × 0.5◦ resolution Quick Scatterometer (QuikSCAT) wind products. The variation of these different surface boundary layer parameters was studied for three defined cyclone life stages: prior to the formation, during, and after the cyclone passage. Drastic variations of the MABL parameters during the passage of the cyclone were observed. The wind strength increased from 12 to 22 m s−1 in association with different stages of Gonu. Frictional velocity increased from a value of 0.1–0.6 m s−1 during the formative stage of the system to a high value of 0.3–1.4 m s−1 during the mature stage. Drag coefficient varied from 1.5 × 10−3 to 2.5 × 10−3 during the occurrence of Gonu. Wind stress values varied from 0.4 to 1.1 N m−2. Wind stress curl values varied from 10 × 10−7 to 45 × 10−7 N m−3. Generally, convergent winds prevailed with the numerical value of divergence varying from 0 to –4 × 10−5 s−1. Maximum variations of the wind parameters were found in the wall cloud region of the cyclone. The parameters returned to normally observed values in 1–3 days after the cyclone passage

Characteristic Study of the Boundary Layer Parameters over the Arabian Sea and the Bay of Bengal Using the QuikSCAT Dataset

The marine atmospheric boundary layer (MABL) plays a vital role in the transport of momentum and heat from the surface of the ocean into the atmosphere. A detailed study on the MABL characteristics was carried out using high-resolution surface-wind data as measured by the QuikSCAT (Quick scatterometer) satellite. Spatial variations in the surface wind, frictional velocity, roughness parameter and drag coe±cient for the di®erent seasons were studied. The surface wind was strong during the southwest monsoon season due to the modulation induced by the Low Level Jetstream. The drag coe±cient was larger during this season, due to the strong winds and was lower during the winter months. The spatial variations in the frictional velocity over the seas was small during the post-monsoon season (»0.2 m s¡1). The maximum spatial variation in the frictional velocity was found over the south Arabian Sea (0.3 to 0.5 m s¡1) during the southwest monsoon period, followed by the pre-monsoon over the Bay of Bengal (0.1 to 0.25 m s¡1). The mean wind-stress curl during the winter was positive over the equatorial region, with a maximum value of 1.5£10¡7 N m¡3, but on either side of the equatorial belt, a negative wind-stress curl dominated. The area average of the frictional velocity and drag coe±cient over the Arabian Sea and Bay of Bengal were also studied. The values of frictional velocity shows a variability that is similar to the intraseasonal oscillation (ISO) and this was con¯rmed via wavelet analysis. In the case of the drag coe±cient, the prominent oscillations were ISO and quasi-biweekly mode (QBM). The interrelationship between the drag coe±cient and the frictional velocity with wind speed in both the Arabian Sea and the Bay of Bengal was also studied.

Optimization of carbon and nitrogen sources and growth factors for the production of an aquaculture probiotic (Pseudomonas MCCB 103) using response surface methodology

Aim: To develop a new medium for enhanced production of biomass of an aquaculture probiotic Pseudomonas MCCB 103 and its antagonistic phenazine compound, pyocyanin. Methods and Results: Carbon and nitrogen sources and growth factors, such as amino acids and vitamins, were screened initially in a mineral medium for the biomass and antagonistic compound of Pseudomonas MCCB 103. The selected ingredients were further optimized using a full-factorial central composite design of the response surface methodology. The medium optimized as per the model for biomass contained mannitol (20 g l)1), glycerol (20 g l)1), sodium chloride (5 g l)1), urea (3Æ3 g l)1) and mineral salts solution (20 ml l)1), and the one optimized for the antagonistic compound contained mannitol (2 g l)1), glycerol (20 g l)1), sodium chloride (5Æ1 g l)1), urea (3Æ6 g l)1) and mineral salts solution (20 ml l)1). Subsequently, the model was validated experimentally with a biomass increase by 19% and fivefold increase of the antagonistic compound. Conclusion: Significant increase in the biomass and antagonistic compound production could be obtained in the new media. Significance and Impact of the Study: Media formulation and optimization are the primary steps involved in bioprocess technology, an attempt not made so far in the production of aquaculture probiotics

Optimization of medium for the production of a novel aquaculture probiotic, Micrococcus MCCB 104 using central composite design

A marine isolate of jáÅêçÅçÅÅìë MCCB 104 has been identified as an aquaculture probiotic antagonistic to sáÄêáç. In the present study different carbon and nitrogen sources and growth factors in a mineral base medium were optimized for enhanced biomass production and antagonistic activity against the target pathogen, sáÄêáç=Ü~êîÉóá, following response surface methodology (RSM). Accordingly the minimum and maximum limits of the selected variables were determined and a set of fifty experiments programmed employing central composite design (CCD) of RSM for the final optimization. The response surface plots of biomass showed similar pattern with that of antagonistic activity, which indicated a strong correlation between the biomass and antagonism. The optimum concentration of the carbon sources, nitrogen sources, and growth factors for both biomass and antagonistic activity were glucose (17.4 g/L), lactose (17 g/L), sodium chloride (16.9 g/L), ammonium chloride (3.3 g/L), and mineral salts solution (18.3 mL/L). © KSBB