Design. Fabrication and Characterization of Fiber Optic Sensors for Physical and Chemical Applications

Advent of lasers together with the advancement in fiber optics technology has revolutionized the sensor technology. Advancement in the telemetric applications of optical fiber based measurements is an added bonus. The present thesis describes variety of fiber based sensors using techniques like micro bending, long period grating and evanescent waves. Sensors to measure various physical and chemical parameters are described in this thesis.

Field Equilibrium Finite Elements for Structural Analysis

Many finite elements used in structural analysis possess deficiencies like shear locking, incompressibility locking, poor stress predictions within the element domain, violent stress oscillation, poor convergence etc. An approach that can probably overcome many of these problems would be to consider elements in which the assumed displacement functions satisfy the equations of stress field equilibrium. In this method, the finite element will not only have nodal equilibrium of forces, but also have inner stress field equilibrium. The displacement interpolation functions inside each individual element are truncated polynomial solutions of differential equations. Such elements are likely to give better solutions than the existing elements.In this thesis, a new family of finite elements in which the assumed displacement function satisfies the differential equations of stress field equilibrium is proposed. A general procedure for constructing the displacement functions and use of these functions in the generation of elemental stiffness matrices has been developed. The approach to develop field equilibrium elements is quite general and various elements to analyse different types of structures can be formulated from corresponding stress field equilibrium equations. Using this procedure, a nine node quadrilateral element SFCNQ for plane stress analysis, a sixteen node solid element SFCSS for three dimensional stress analysis and a four node quadrilateral element SFCFP for plate bending problems have been formulated.For implementing these elements, computer programs based on modular concepts have been developed. Numerical investigations on the performance of these elements have been carried out through standard test problems for validation purpose. Comparisons involving theoretical closed form solutions as well as results obtained with existing finite elements have also been made. It is found that the new elements perform well in all the situations considered. Solutions in all the cases converge correctly to the exact values. In many cases, convergence is faster when compared with other existing finite elements. The behaviour of field consistent elements would definitely generate a great deal of interest amongst the users of the finite elements.

Acoustic radiation and scattering from cylindrical bodies and analysis of transducer arrays

New mathematical methods to analytically investigate linear acoustic radiation and scattering from cylindrical bodies and transducer arrays are presented. Three problems of interest involving cylinders in an infinite fluid are studied. In all the three problems, the Helmholtz equation is used to model propagation through the fluid and the beam patterns of arrays of transducers are studied. In the first problem, a method is presented to determine the omni-directional and directional far-field pressures radiated by a cylindrical transducer array in an infinite rigid cylindrical baffle. The solution to the Helmholtz equation and the displacement continuity condition at the interface between the array and the surrounding water are used to determine the pressure. The displacement of the surface of each transducer is in the direction of the normal to the array and is assumed to be uniform. Expressions are derived for the pressure radiated by a sector of the array vibrating in-phase, the entire array vibrating in-phase, and a sector of the array phase-shaded to simulate radiation from a rectangular piston. It is shown that the uniform displacement required for generating a source level of 220 dB ref. μPa @ 1m that is omni directional in the azimuthal plane is in the order of 1 micron for typical arrays. Numerical results are presented to show that there is only a small difference between the on-axis pressures radiated by phased cylindrical arrays and planar arrays. The problem is of interest because cylindrical arrays of projectors are often used to search for underwater objects. In the second problem, the errors, when using data-independent, classical, energy and split beam correlation methods, in finding the direction of arrival (DOA) of a plane acoustic wave, caused by the presence of a solid circular elastic cylindrical stiffener near a linear array of hydrophones, are investigated. Scattering from the effectively infinite cylinder is modeled using the exact axisymmetric equations of motion and the total pressures at the hydrophone locations are computed. The effect of the radius of the cylinder, a, the distance between the cylinder and the array, b, the number of hydrophones in the array, 2H, and the angle of incidence of the wave, α, on the error in finding the DOA are illustrated using numerical results. For an array that is about 30 times the wavelength and for small angles of incidence (α<10), the error in finding the DOA using the energy method is less than that using the split beam correlation method with beam steered to α; and in some cases, the error increases when b increases; and the errors in finding the DOA using the energy method and the split beam correlation method with beam steered to α vary approximately as a7 / 4 . The problem is of interest because elastic stiffeners – in nearly acoustically transparent sonar domes that are used to protect arrays of transducers – scatter waves that are incident on it and cause an error in the estimated direction of arrival of the wave. In the third problem, a high-frequency ray-acoustics method is presented and used to determine the interior pressure field when a plane wave is normally incident on a fluid cylinder embedded in another infinite fluid. The pressure field is determined by using geometrical and physical acoustics. The interior pressure is expressed as the sum of the pressures due to all rays that pass through a point. Numerical results are presented for ka = 20 to 100 where k is the acoustic wavenumber of the exterior fluid and a is the radius of the cylinder. The results are in good agreement with those obtained using field theory. The directional responses, to the plane wave, of sectors of a circular array of uniformly distributed hydrophones in the embedded cylinder are then computed. The sectors are used to simulate linear arrays with uniformly distributed normals by using delays. The directional responses are compared with the output from an array in an infinite homogenous fluid. These outputs are of interest as they are used to determine the direction of arrival of the plane wave. Numerical results are presented for a circular array with 32 hydrophones and 12 hydrophones in each sector. The problem is of interest because arrays of hydrophones are housed inside sonar domes and acoustic plane waves from distant sources are scattered by the dome filled with fresh water and cause deterioration in the performance of the array.

Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10

An alkaline protease gene (Eap) was isolated for the first time from a marine fungus, Engyodontium album. Eap consists of an open reading frame of 1,161 bp encoding a prepropeptide consisting of 387 amino acids with a calculated molecular mass of 40.923 kDa. Homology comparison of the deduced amino acid sequence of Eap with other known proteins indicated that Eap encode an extracellular protease that belongs to the subtilase family of serine protease (Family S8). A comparative homology model of the Engyodontium album protease (EAP) was developed using the crystal structure of proteinase K. The model revealed that EAP has broad substrate specificity similar to Proteinase K with preference for bulky hydrophobic residues at P1 and P4. Also, EAP is suggested to have two disulfide bonds and more than two Ca2? binding sites in its 3D structure; both of which are assumed to contribute to the thermostable nature of the protein.

Molecular characterization of a crustin-like, putative antimicrobial peptide, Fi-crustin, from the Indian white shrimp, Fenneropenaeus indicus

Fish & Shellfish Immunology 28 (2010) 216-220

Molecular characterization and phylogenetic analysis of a penaeidin-like antimicrobial peptide, Fi-penaeidin from Fenneropenaeus indicus

Antimicrobial peptides (AMPs) play a major role in innate immunity. Penaeidins are a family of AMPs that appear to be expressed in all penaeid shrimps. Penaeidins are composed of an N-terminal proline-rich domain, followed by a C-terminal domain containing six cysteine residues organized in two doublets. This study reports the first penaeidin AMP sequence, Fi-penaeidin (GenBank accession number HM243617) from the Indian white shrimp, Fenneropenaeus indicus. The full length cDNA consists of 186 base pairs encoding 61 amino acidswith an ORF of 42 amino acids and contains a putative signal peptide of 19 amino acids. Comparison of F. indicus penaeidin (Fi-penaeidin) with other known penaeidins showed that it shared maximum similarity with penaeidins of Farfantepenaeus paulensis and Farfantepenaeus subtilis (96% each). Fi-penaeidin has a predicted molecular weight (MW) of 4.478 kDa and theoretical isoelectric point (pI) of 5.3

Using Neural Network Classifier Support Vector Machine Regression for the prediction of Melting Point of Drug – like compounds

In our study we use a kernel based classification technique, Support Vector Machine Regression for predicting the Melting Point of Drug – like compounds in terms of Topological Descriptors, Topological Charge Indices, Connectivity Indices and 2D Auto Correlations. The Machine Learning model was designed, trained and tested using a dataset of 100 compounds and it was found that an SVMReg model with RBF Kernel could predict the Melting Point with a mean absolute error 15.5854 and Root Mean Squared Error 19.7576

Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10

An alkaline protease gene (Eap) was isolated for the first time from a marine fungus, Engyodontium album. Eap consists of an open reading frame of 1,161 bp encoding a prepropeptide consisting of 387 amino acids with a calculated molecular mass of 40.923 kDa. Homology comparison of the deduced amino acid sequence of Eap with other known proteins indicated that Eap encode an extracellular protease that belongs to the subtilase family of serine protease (Family S8). A comparative homology model of the Engyodontium album protease (EAP) was developed using the crystal structure of proteinase K. The model revealed that EAP has broad substrate specificity similar to Proteinase K with preference for bulky hydrophobic residues at P1 and P4. Also, EAP is suggested to have two disulfide bonds and more than two Ca2? binding sites in its 3D structure; both of which are assumed to contribute to the thermostable nature of the protein.

Sedimentology and Geochemistry of core sediments from the Ashtamudi estuary and the adjoining coastal plain,central Kerala,India

The evolution of coast through geological time scale is dependent on the transgression-regression event subsequent to the rise or fall of sea level. This event is accounted by investigation of the vertical sediment deposition patterns and their interrelationship for paleo-enviornmental reconstruction. Different methods like sedimentological (grain size and micro-morphological) and geochemical (elemental relationship) analyses as well as radiocarbon dating are generally used to decipher the sea level changes and paleoclimatic conditions of the Quaternary sediment sequence. For the Indian coast with a coastline length of about 7500 km, studies on geological and geomorphological signatures of sea level changes during the Quaternary were reported in general by researchers during the last two decades. However, for the southwest coast of India particularily Kerala which is famous for its coastal landforms comprising of estuaries, lagoons, backwaters, coastal plains, cliffs and barrier beaches, studies pertaining to the marine transgression-regression events in the southern region are limited. The Neendakara-Kayamkulam coastal stretch in central Kerala where the coast is manifested with shore parallel Kayamkulam Lagoon on one side and shore perpendicular Ashtamudi Estuary on the other side indicating existence of an uplifted prograded coastal margin followed by barrier beaches, backwater channels, ridge and runnel topography is an ideal site for studying such events. Hence the present study has been taken up in this context to address the gap area. The location for collection of core samples representing coastal plain, estuarylagoon and offshore regions have been identified based on published literature and available sedimentary records. The objectives of the research work are:  To study the lithological variations and depositional environments of sediment cores along the coastal plain, estuary-lagoon and offshore regions between Kollam and Kayamkulam in the central Kerala coast  To study the transportation and diagenetic history of sediments in the area  To investigate the geochemical characterization of sediments and to elucidate the source-sink relationship  To understand the marine transgression-regression events and to propose a conceptual model for the region The thesis comprises of 8 chapters. The first chapter embodies the preamble for the selection and significance of this research work. The study area is introduced with details on its physiographical, geological, geomorphological, rainfall and climate information. A review of literature, compiling the research on different aspects such as physico-chemical, geomorphological, tectonics, transgression-regression events are presented in the second chapter and they are broadly classified into three viz:- International, National and Kerala. The field data collection and laboratory analyses adopted in the research work are discussed in the third chapter. For collection of sediment core samples from the coastal plains, rotary drilling method was employed whereas for the estuary-lagoon and offshore locations the gravity/piston corer method was adopted. The collected subsurficial samples were analysed for texture, surface micro-texture, elemental analysis, XRD and radiocarbon dating techniques for age determination. The fourth chapter deals with the textural analysis of the core samples collected from various predefined locations of the study area. The result reveals that the Ashtamudi Estuary is composed of silty clay to clayey type of sediments whereas offshore cores are carpeted with silty clay to relict sand. Investigation of the source of sediments deposited in the coastal plain located on either side of the estuary indicates the dominance of terrigenous to marine origin in the southern region whereas it is predominantly of marine origin towards the north. Further the hydrodynamic conditions as well as the depositional enviornment of the sediment cores are elucidated based on statistical parameters that decipher the deposition pattern at various locations viz., coastal plain (open to closed basin), Ashtamudi Estuary (partially open to restricted estuary to closed basin) and offshore (open channel). The intensity of clay minerals is also discussed. From the results of radiocarbon dating the sediment depositional environments were deciphered.The results of the microtextural study of sediment samples (quartz grains) using Scanning Electron Microscope (SEM) are presented in the fifth chapter. These results throw light on the processes of transport and diagenetic history of the detrital sediments. Based on the lithological variations, selected quartz grains of different environments were also analysed. The study indicates that the southern coastal plain sediments were transported and deposited mechanically under fluvial environment followed by diagenesis under prolonged marine incursion. But in the case of the northern coastal plain, the sediments were transported and deposited under littoral environment indicating the dominance of marine incursion through mechanical as well as chemical processes. The quartz grains of the Ashtamudi Estuary indicate fluvial origin. The surface texture features of the offshore sediments suggest that the quartz grains are of littoral origin and represent the relict beach deposits. The geochemical characterisation of sediment cores based on geochemical classification, sediment maturity, palaeo-weathering and provenance in different environments are discussed in the sixth chapter. In the seventh chapter the integration of multiproxies data along with radiocarbon dates are presented and finally evolution and depositional history based on transgression–regression events is deciphered. The eighth chapter summarizes the major findings and conclusions of the study with recommendation for future work.