Supramolecular Organization of Metal Nanoparticles in Solution and of Phenyleneethynylenes on Surfaces

Most of the procedures reported for the synthesis of metal nanoparticles involve the use of strong reducing agents or elevated temperatures. This limits the possibility of developing metal nanoparticle based sensors for the in situ detection of analytes. One of the objectives of the present investigations is to (i) develop newer methodologies for the synthesis of metal nanoparticles in aqueous medium at ambient conditions and (ii) their use in the detection of metal cations by taking advantage of the unique coordination ability. Ideally, biocompatible molecules which possess both the reducing and stabilizing groups are desirable for such applications. Formation of stable supramolecular assembly, by bringing metal nanoparticles close to each other, results in plasmon coupling and this strategy can be effectively utilized for the development of metal nanoparticle based sensors.Another objective of the present study is to understand the supramolecular organization of molecules on surfaces. Various noncovalent interactions between the molecules and with surface play a decisive role in their organizations. An in-depth understanding of these interactions is essential for device fabrications. Recent photophysical studies have revealed that phenyleneethynylene based molecular systems are ideal for device application. The second objective of the thesis focuses on understanding the (i) organization of phenyleneethynylenes on highly oriented pyrolytic graphite (HOPG) surface with atomic level precision and (ii) weak intermolecular interactions which drive their organization.

Nitrifying Bioreactors Integrated into Shrimp and Prawn Hatchery Systems: Molecular Characterization of the Nitrifying Consortia,Reactor Kinetics, Modeling and Validation

National Centre for Aquatic Animal Health, Cochin University of Science and Technology

Molecular Approaches For Characterization And Determination Of Pathogenicity Of Vibrios With Special Reference To Vibrio Harveyi From Penaeus Monodon Larval Production Systems

The present study focuses on vibrios especially Vibrio harveyi isolated from shrimp (P. monodon) larval production systems from both east and west coasts during times of mortality. A comprehensive approach has been made to work out their systematics through numerical taxonomy and group them based on RAPD profiling and to segregate the virulent from non- virulent isolates based on the presence of virulent genes as well as their phenotypic expression. The information gathered has helped to develop a simple scheme of identification based on phenotypic characters and segregate the virulent from non virulent strains of V. harveyi.

Molecular characterization of the nitrifying bacterial consortia employed for the activation of bioreactors used in brackish and marine aquaculture systems

The addition of commercial nitrifying bacterial products has resulted in significant improvement of nitrification efficiency in recirculating aquaculture systems (RAS). We developed two nitrifying bacterial consortia (NBC) from marine and brackish water as start up cultures for immobilizing commercialized nitrifying bioreactors for RAS. In the present study, the community compositions of the NBC were analyzed by universal 16S rRNA gene and bacterial amoA gene sequencing and fluorescence in situ hybridization (FISH). This study demonstrated that both the consortia involved autotrophic nitrifiers, denitrifiers as well as heterotrophs. Abundant taxa of the brackish water heterotrophic bacterial isolates were Paenibacillus and Beijerinckia spp. whereas in the marine consortia they were Flavobacterium, Cytophaga and Gramella species. The bacterial amoA clones were clustered together with high similarity to Nitrosomonas sp. and uncultured beta Proteobacteria. FISH analysis detected ammonia oxidizers belonging to b subclass of proteobacteria and Nitrosospira sp. in both the consortia, and Nitrosococcus mobilis lineage only in the brackish water consortium and the halophilic Nitrosomonas sp. only in the marine consortium. However, nitrite oxidizers, Nitrobacter sp. and phylum Nitrospira were detected in both the consortia. The metabolites from nitrifiers might have been used by heterotrophs as carbon and energy sources making the consortia a stable biofilm.

Preparation and characterisation of certain II-VI, I-III-VI2 semiconductor thin films and transparent conducting oxides

There is an increasing demand for renewable energies due to the limited availability of fossil and nuclear fuels and due to growing environmental problems. Photovoltaic (PV) energy conversion has the potential to contribute significantly to the electrical energy generation in the future. Currently, the cost for photovoltaic systems is one of the main obstacles preventing production and application on a large scale. The photovoltaic research is now focused on the development of materials that will allow mass production without compromising on the conversion efficiencies. Among important selection criteria of PV material and in particular for thin films, are a suitable band gap, high absorption coefficient and reproducible deposition processes capable of large-volume and low cost production. The chalcopyrite semiconductor thin films such as Copper indium selenide and Copper indium sulphide are the materials that are being intensively investigated for lowering the cost of solar cells. Conversion efficiencies of 19 % have been reported for laboratory scale solar cell based on CuInSe2 and its alloys. The main objective of this thesis work is to optimise the growth conditions of materials suitable for the fabrication of solar cell, employing cost effective techniques. A typical heterojunction thin film solar cell consists of an absorber layer, buffer layer and transparent conducting contacts. The most appropriate techniques have been used for depositing these different layers, viz; chemical bath deposition for the window layer, flash evaporation and two-stage process for the absorber layer, and RF magnetron sputtering for the transparent conducting layer. Low cost experimental setups were fabricated for selenisation and sulphurisation experiments, and the magnetron gun for the RF sputtering was indigenously fabricated. The films thus grown were characterised using different tools. A powder X-ray diffractometer was used to analyse the crystalline nature of the films. The energy dispersive X-ray analysis (EDX) and scanning electron microscopy i (SEM) were used for evaluating the composition and morphology of the films. Optical properties were investigated using the UV-Vis-NIR spectrophotometer by recording the transmission/absorption spectra. The electrical properties were studied using the two probe and four probe electrical measurements. Nature of conductivity of the films was determined by thermoprobe and thermopower measurements. The deposition conditions and the process parameters were optimised based on these characterisations.

Selective N-monomethylation of aniline using Zn1-x CoxFe2O4( x=0, 0.2, 0.5, 0.8 and 1.0)type systems

A series of ferrites having the general formula Zn1-xCoxFe2O4 (x=0, 0.2, 0.5, 0.8 and 1.0)were prepared by soft chemical route. The materials were characterized by adopting various physico-chemical methods. The reaction of aniline with methanol was studied in a fixed-bed reactor system as a potential source for the production of various methyl anilines. It was observed that systems possessing low ‘ x’ values are highly selective and active for N-monoalkylation of aniline leading to N-methylaniline. Reaction parameters were properly varied to optimize the reaction conditions for obtaining N-methylaniline selectively and in better yield. Among the systems Zn0.8Co0.2Fe2O4 is remarkable due to its very high activity and excellent stability. Under the optimized conditions N-methylaniline selectivity exceeded 98%. Even at a methanol to aniline molar ratio of 2, the yield of N-methylaniline was nearly 50%, whereas its yield exceeded 71% at the molar ratio of 5. ZnFe2O4, though executed better conversion than Zn0.8Co0.2Fe2O4 in the initial period of the run, deactivates quickly as the reaction proceeds. The Lewis acidity of the catalysts is mainly responsible for the good performance. Cation distribution in the spinel lattice influences their acido-basic properties and, hence, these factors have been considered as helpful parameters to evaluate the activity of the systems.

Novel adhesive systems based on neoprene-phenolic blends

The aim of the investigation is to develop new high performance adhesive systems based on neoprene-phenolic blends. Initially the effect of addition of all possible ingredients like fillers, adhesion promoters, curing agents and their optimum compositions to neoprene solution is investigated. The phenolic resin used is a copolymer of phenol-cardanolformaldehyde prepared in the laboratory. The optimum ratio between phenol and cardanol that gives the maximum bond strength in metal-metal, rubber-rubber and rubber-metal specimens has been identified. Further the ratio between total phenols and formaldehyde is also optimised. The above adhesive system is further modified by the addition of epoxidized phenolic novolacs. For this purpose, phenolic novolac resins are prepared in different stoichiometric ratios and are subsequently epoxidized. The effectiveness of the adhesive for bonding different metal and rubber substrates is another part of the study. To study the ageing behaviour, different bonded specimens are exposed to high temperature, hot water and salt water and adhesive properties have been evaluated. The synthesized resins have been characterized by FTIR , HNMR spectroscopy. The molecular weights of the resins have been obtained by GPC. Thermogravimetric analysis and differential scanning calorimetry are used to study the thermal properties. The fractured surface analysis is studied by scanning electron microscopy. The study has brought to light the influence of phenol/ formaldehyde stoichiometric ratio, addition of cardanol (a renewable resource), adhesion promoters and suitability of the adhesive for different substrates and the age resistance of adhesive joints among other things.

Molecular genetic characterization of endemic red -tailed barb,Gonoproktoptems curmuca (Hamilton - Buchanan, 1807)

The family Cyprinidae is the largest of freshwater fishes and, with the possible exception of Gobiidae, the largest family of vertebrates.Various members of this family are important as food fish, as aquarium fish, and in biological research. In this study, a fish species from this family exclusively found in the west flowing rivers originating from the Western Ghat region — Gonoproktopterus curmuca — was taken for population genetic analysis.There was an urgent need for restoration ecology by the development of apt management strategies to exploit resources judiciously. One of the strategies thus developed for the scientific management of these resources was to identify the natural units of the fishery resources under exploitation (Altukov, 1981). These natural units of a species can otherwise be called as stocks. A stock can be defined as a panmictic population of related individuals within a single species that is genetically distinct from other such populations.It is believed that a species may undergo micro evolutionary process and differentiate into genetically distinct sub-populations or stocks in course of time, if reproductively and geographically isolated.In recent times, there has been a wide spread degradation of natural aquatic environment due to anthropogenic activities and this has resulted in the decline and even extinction of some fish species. In such situations, evaluation of the genetic diversity of fish resources assumes important to conservation.The species selected for the study, was short-listed as one of the candidates for stock-specific, propagation assisted rehabilitation and management programme in rivers where it is naturally distributed. In connection with this, captive breeding and milt cryopreservation techniques of the species have been developed by the National Bureau of Fish Genetic Resources, Lucknow. However, for a scientific stock-specific rehabilitation programme, information on the stock structure and basic genetic profile of the species are essential and that is not available in case of G. curmuca. So the present work was taken up to identify molecular genetic markers like allozymes, microsatellites and RAPDs and, to use these markers to discriminate the distinct populations of the species, if any, in areas of its natural distribution. The genetic markers were found to be powerful tools to analyze the population genetic structure of the red-tailed barb and demonstrated clear cut genetic differentiation between pairs of populations examined. Geographic isolation by land distance is likely to be the factor that contributed to the restricted gene flow between the river systems. So the present study emphasizes the need for stock-wise, propagation assisted-rehabilitation of the natural populations of red-tailed barb, Gonoprokfopterus curmuca.

Biochemical and molecular characterization of pathogenic vibrios from hatcheries and aquaculture farms

Vibrio are important during hatchery rearing. aquaculture phase and post-harvest quality of shrimps. Vibrio spp are of concern to shrimp farmers and hatchery operators because certain species can cause Vibriosis. Vibrio species are of concern to humans because certain species cause serious diseases.With the progress in aquaculture, intensive systems used for shrimp aquaculture create an artificial environment that increases bacterial growth. To maintain the productivity of such an intensive aquaculture, high inputs of fish protein have to be employed for feeding together with high levels of water exchange and the massive use of antibiotics/ probiotics / chemicals. It seems that the combination of these conditions favours the proliferation of vibrios and enhances their virulence and disease prevalence. The risk of a microbial infection is high, mainly at larval stages. The effect and severity are related to Vibrio species and dose, water, feed, shrimp quality and aquaculture management.Consumption of seafood can occasionally result in food-bome illnesses due to the proliferation of indigenous pathogens like Vibrio.Of the l2 pathogenic Vibrio species, 8 species are known to be directly food associated. Strict quality guidelines have been laid by the importing nations, for the food products that enter their markets. The microbiological quality requirement for export of frozen shrimp products is that V.cholerae, V.parahaemolyticus and V. vulnificus should be absent in 25g of the processed shrimp (Export Inspection Council of India, 1995). The mere presence of these pathogenic Vibrios is sufficient for the rejection of the exported product.The export rejections cause serious economic loss to the shrimp industry and might harm the brand image of the shrimp products from the countiy.There is a need for an independent study on the incidence of different pathogenic vibrios in shrimp aquaculture and investigate their biochemical characteristics to have a better understanding about the growth and survival of these organisms in the shrimp aquaculture niche. PCR based methods (conventional PCR, duplex PCR, multiplex-PCR and Real Time PCR) for the detection of the pathogenic Vibrios is important for rapid post-harvest quality assessment. Studies on the genetic heterogeneity among the specific pathogenic vibrio species isolated from shrimp aquaculture system provide; valuable information on the extent of genetic diversity of the pathogenic vibrios, the shrimp aquaculture system.So the present study was undertaken to study the incidence of pathogenic Vibrio spp. in Penaeus monodon shrimp hatcheries and aquaculture farms, to carry out biochemical investigations of the pathogenic Vibrio spp isolated from P. monodon hatchery and. aquaculture environments, to assess the effect of salt (NaCl) on the growth and enzymatic activities of pathogenic Vibrio spp., to study the effect of preservatives, and chemicals on the growth of pathogenic Vibrio spp. and to employ polymerase chain reaction (PCR) methods for the detection of pathogenic V ibrio spp.Samples of water (n=7) and post-larvae (n=7) were obtained from seven Penaeus monodon hatcheries and samples of water (n=5), sediment (n=5) and shrimp (n=5) were obtained from five P. monodon aquaculture farms located on the East Coast of lndia. The microbiological examination of water, sediment, post-larvae and shrimp samples was carried out employing standard methods and by using standard media.The higher bacterial loads were obtained in pond sediments which can be attributed to the accumulation of organic matter at the pond bottom which stimulated bacterial growth.Shrimp head. (4.78 x 105 +/- 3.0 x 104 cfu/g) had relatively higher bacterial load when compared to shrimp muscle 2.7 x 105 +/- 1.95 x 104 cfu/g). ln shrimp hatchery samples, the post-larvae (2.2 x 106 +/- 1.9 x 106 cfu/g) had higher bacterial load than water (5.6 x 103 +/- 3890 cfu/ml).The mean E.coli counts were higher in aquaculture pond sediment (204+/-13 cfu/g) and pond water (124+/-88 cfu/ml). Relatively lower Escherichia coli counts were obtained from shrimp samples (12+/-11 to 16+/-16.7 cfu/g). The presence of E.coli in aquaculture environment might have been from the source water. E.coli was not detected in hatchery waters and post-larvae.

Phenylethynylarene Based Donor-Acceptor Systems: Design, Synthesis and Photophysical Studies

This thesis Entitled phenylethynylarene based Donor-Acceptor systems:Desigh,Synthesis and Photophysical studies. A strategy for the design of donor-acceptor dyads, wherein decay of the charge separated (CS) state to low lying local triplet levels could possibly be prevented, is proposed. In order to examine this strategy, a linked donor-acceptor dyad BPEPPT with bis(phenylethYlly/)pyrene (BPEP) as the light absorber and acceptor and phenothiazine (PT) as donor was designed and photoinduced electron transfer in the dyad investigated. Absorption spectra of the dyad can be obtained by adding contributions due 10 the BPEP and PT moieties indicating that the constituents do not interact in the ground stale. Fluorescence of the BPEP moiety was efficiently quenched by the PT donor and this was attributed to electron lransfer from PT to BPEP. Picosecond transient absorption studies suggested formation of a charge separated state directly from the singlet excited state of BPEP. Nanosecond flash photolysis experiments gave long-ived transient absorptions assignable to PT radical cation and BPEP radical anion. These assignments were confirmed by oxygen quenching studies and secondary electron transfer experiments. Based on the available data, energy level diagram for BPEP-PT was constructed. The long lifetime of the charge separated state was attributed to the inverted region effects. The CS state did not undergo decay to low lying BPEP triplet indicating the success of our strategy

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.

Studies in molecular spectroscopy

This thesis is divided into two parts. The first part deals with some studies in molecular mechanics Using spectroscopic data and has four chapters in it. Certain approximation methods for the evaluation of molecular force fields are herein developed The second part, which consists of the last two chaptcrs, deals with infrared spectral studies of ternary liquid systems and a polymer film prepared by glow discharge method.

Investigations on Nonlinear and Radiative Properties of Certain Phatonic Materials

Light in its physical and philosophical sense has captured the imagination of human mind right from the dawn of civilization. The invention of lasers in the 60’s caused a renaissance in the field of optics. This intense, monochromatic, highly directional radiation created new frontiers in science and technology. The strong oscillating electric field of laser radiation creates a. polarisation response that is nonlinear in character in the medium through which it passes and the medium acts as a new source of optical field with alternate properties. It was in this context, that the field of optoelectronics which encompasses the generation, modulation, transmission etc. of optical radiation has gained tremendous importance. Organic molecules and polymeric systems have emerged as a class of promising materials of optoelectronics because they offer the flexibility, both at the molecular and bulk levels, to optimize the nonlinearity and other suitable properties for device applications. Organic nonlinear optical media, which yield large third-order nonlinearities, have been widely studied to develop optical devices like high speed switches, optical limiters etc. Transparent polymeric materials have found one of their most promising applicationsin lasers, in which they can be used as active elements with suitable laser dyes doped in it. The solid-matrix dye lasers make possible combination of the advantages of solid state lasers with the possibility of tuning the radiation over a broad spectral range. The polymeric matrices impregnated with organic dyes have not yet widely used because of the low resistance of the polymeric matrices to laser damage, their low dye photostability, and low dye stability over longer time of operation and storage. In this thesis we investigate the nonlinear and radiative properties of certain organic materials and doped polymeric matrix and their possible role in device development

Design and study of self-assembled functional organic and hybrid systems for biological applications

The focus of self-assembly as a strategy for the synthesis has been confined largely to molecules, because of the importance of manipulating the structure of matter at the molecular scale. We have investigated the influence of temperature and pH, in addition to the concentration of the capping agent used for the formation of the nano-bio conjugates. For example, the formation of the narrower size distribution of the nanoparticles was observed with the increase in the concentration of the protein, which supports the fact that γ-globulin acts both as a controller of nucleation as well as stabiliser. As analyzed through various photophysical, biophysical and microscopic techniques such as TEM, AFM, C-AFM, SEM, DLS, OPM, CD and FTIR, we observed that the initial photoactivation of γ-globulin at pH 12 for 3 h resulted in small protein fibres of ca. Further irradiation for 24 h, led to the formation of selfassembled long fibres of the protein of ca. 5-6 nm and observation of surface plasmon resonance band at around 520 nm with the concomitant quenching of luminescence intensity at 680 nm. The observation of light triggered self-assembly of the protein and its effect on controlling the fate of the anchored nanoparticles can be compared with the naturally occurring process such as photomorphogenesis.Furthermore,our approach offers a way to understand the role played by the self-assembly of the protein in ordering and knock out of the metal nanoparticles and also in the design of nano-biohybrid materials for medicinal and optoelectronic applications. Investigation of the potential applications of NIR absorbing and water soluble squaraine dyes 1-3 for protein labeling and anti-amyloid agents forms the subject matter of the third chapter of the thesis. The study of their interactions with various proteins revealed that 1-3 showed unique interactions towards serum albumins as well as lysozyme. 69%, 71% and 49% in the absorption spectra as well as significant quenching in the fluorescence intensity of the dyes 1-3, respectively. Half-reciprocal analysis of the absorption data and isothermal titration calorimetric (ITC) analysis of the titration experiments gave a 1:1 stoichiometry for the complexes formed between the lysozyme and squaraine dyes with association constants (Kass) in the range 104-105 M-1. We have determined the changes in the free energy (ΔG) for the complex formation and the values are found to be -30.78, -32.31 and -28.58 kJmol-1, respectively for the dyes 1, 2 and 3. Furthermore, we have observed a strong induced CD (ICD) signal corresponding to the squaraine chromophore in the case of the halogenated squaraine dyes 2 and 3 at 636 and 637 nm confirming the complex formation in these cases. To understand the nature of interaction of the squaraine dyes 1-3 with lysozyme, we have investigated the interaction of dyes 1-3 with different amino acids. These results indicated that the dyes 1-3 showed significant interactions with cysteine and glutamic acid which are present in the side chains of lysozyme. In addition the temperature dependent studies have revealed that the interaction of the dye and the lysozyme are irreversible. Furthermore, we have investigated the interactions of these NIR dyes 1-3 with β- amyloid fibres derived from lysozyme to evaluate their potential as inhibitors of this biologically important protein aggregation. These β-amyloid fibrils were insoluble protein aggregates that have been associated with a range of neurodegenerative diseases, including Huntington, Alzheimer’s, Parkinson’s, and Creutzfeldt-Jakob diseases. We have synthesized amyloid fibres from lysozyme through its incubation in acidic solution below pH 4 and by allowing to form amyloid fibres at elevated temperature. To quantify the binding affinities of the squaraine dyes 1-3 with β-amyloids, we have carried out the isothermal titration calorimetric (ITC) measurements. The association constants were determined and are found to be 1.2 × 105, 3.6× 105 and 3.2 × 105 M-1 for the dyes, 1-3, respectively. To gain more insights into the amyloid inhibiting nature of the squaraine dyes under investigations, we have carried out thioflavin assay, CD, isothermal titration calorimetry and microscopic analysis. The addition of the dyes 1-3 (5μM) led to the complete quenching in the apparent thioflavin fluorescence, thereby indicating the destabilization of β-amyloid fibres in the presence of the squaraine dyes. Further, the inhibition of the amyloid fibres by the squaraine dyes 1-3, has been evidenced though the DLS, TEM AFM and SAED, wherein we observed the complete destabilization of the amyloid fibre and transformation of the fibre into spherical particles of ca. These results demonstrate the fact that the squaraine dyes 1-3 can act as protein labeling agents as well as the inhibitors of the protein amyloidogenesis. The last chapter of the thesis describes the synthesis and investigation of selfassembly as well as bio-imaging aspects of a few novel tetraphenylethene conjugates 4-6.Expectedly, these conjugates showed significant solvatochromism and exhibited a hypsochromic shift (negative solvatochromism) as the solvent polarity increased, and these observations were justified though theoretical studies employing the B3LYP/6-31g method. We have investigated the self-assembly properties of these D-A conjugates though variation in the percentage of water in acetonitrile solution due to the formation of nanoaggregates. Further the contour map of the observed fluorescence intensity as a function of the fluorescence excitation and emission wavelength confirmed the formation of J-type aggregates in these cases. To have a better understanding of the type of self-assemblies formed from the TPE conjugates 4-6, we have carried out the morphological analysis through various microscopic techniques such as DLS, SEM and TEM. 70%, we observed rod shape architectures having ~ 780 nm in diameter and ~ 12 μM in length as evidenced through TEM and SEM analysis. We have made similar observations with the dodecyl conjugate 5 at ca. 70% and 50% water/acetonitrile mixtures, the aggregates formed from 4 and 5 were found to be highly crystalline and such structures were transformed to amorphous nature as the water fraction was increased to 99%. To evaluate the potential of the conjugate as bio-imaging agents, we have carried out their in vitro cytotoxicity and cellular uptake studies though MTT assay, flow cytometric and confocal laser scanning microscopic techniques. Thus nanoparticle of these conjugates which exhibited efficient emission, large stoke shift, good stability, biocompatibility and excellent cellular imaging properties can have potential applications for tracking cells as well as in cell-based therapies. In summary we have synthesized novel functional organic chromophores and have studied systematic investigation of self-assembly of these synthetic and biological building blocks under a variety of conditions. The investigation of interaction of water soluble NIR squaraine dyes with lysozyme indicates that these dyes can act as the protein labeling agents and the efficiency of inhibition of β-amyloid indicate, thereby their potential as anti-amyloid agents.