Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning

Many processes in biology and drug discovery involve various 3D interactions between different molecules, such as protein and protein, protein and small molecule, etc. Designing a generalist model to learn universal molecular interactions is valuable yet challenging, given that different molecules are usually represented in different granularity. In this paper, we first propose to universally represent a 3D molecule as a geometric graph of sets, in contrast to conventional single-level representations. Upon the proposed unified representation, we then propose a Generalist Equivariant Transformer (GET) to effectively capture both sparse block-level and dense atom-level interactions. To be specific, GET consists of a bilevel attention module, a feed-forward module and a layer normalization module, where, notably, each module is E(3) equivariant to meet the symmetry of 3D world. Extensive experiments on the prediction of protein-protein affinity, ligand binding affinity, and ligand efficacy prediction verify the effectiveness of our proposed method against existing methods, and reveal its potential to learn transferable knowledge across different domains and different tasks.Comment: preprin

A Near-to-Far Learning Framework for Terrain Characterization Using an Aerial/Ground-Vehicle Team

In this thesis, a novel framework for adaptive terrain characterization of untraversed far terrain in a natural outdoor setting is presented. The system learns the association between visual appearance of different terrain and the proprioceptive characteristics of that terrain in a self-supervised framework. The proprioceptive characteristics of the terrain are acquired by inertial sensors recording measurements of one second traversals that are mapped into the frequency domain and later through a clustering technique classified into discrete proprioceptive classes. Later, these labels are used as training inputs to the adaptive visual classifier. The visual classifier uses images captured by an aerial vehicle scouting ahead of the ground vehicle and extracts local and global descriptors from image patches. An incremental SVM is utilized on the set of images and training sets as they are grabbed sequentially. The framework proposed in this thesis has been experimentally validated in an outdoor environment. We compare the results of the adaptive approach with the offline a priori classification approach and yield an average 12% increase in accuracy results on outdoor settings. The adaptive classifier gradually learns the association between characteristics and visual features of new terrain interactions and modifies the decision boundaries

Automatic Change-based Diagnosis of Structures Using Spatiotemporal Data and As- Designed Model

abstract: Civil infrastructures undergo frequent spatial changes such as deviations between as-designed model and as-is condition, rigid body motions of the structure, and deformations of individual elements of the structure, etc. These spatial changes can occur during the design phase, the construction phase, or during the service life of a structure. Inability to accurately detect and analyze the impact of such changes may miss opportunities for early detections of pending structural integrity and stability issues. Commercial Building Information Modeling (BIM) tools could hardly track differences between as-designed and as-built conditions as they mainly focus on design changes and rely on project managers to manually update and analyze the impact of field changes on the project performance. Structural engineers collect detailed onsite data of a civil infrastructure to perform manual updates of the model for structural analysis, but such approach tends to become tedious and complicated while handling large civil infrastructures. Previous studies started collecting detailed geometric data generated by 3D laser scanners for defect detection and geometric change analysis of structures. However, previous studies have not yet systematically examined methods for exploring the correlation between the detected geometric changes and their relation to the behaviors of the structural system. Manually checking every possible loading combination leading to the observed geometric change is tedious and sometimes error-prone. The work presented in this dissertation develops a spatial change analysis framework that utilizes spatiotemporal data collected using 3D laser scanning technology and the as-designed models of the structures to automatically detect, classify, and correlate the spatial changes of a structure. The change detection part of the developed framework is computationally efficient and can automatically detect spatial changes between as-designed model and as-built data or between two sets of as-built data collected using 3D laser scanning technology. Then a spatial change classification algorithm automatically classifies the detected spatial changes as global (rigid body motion) and local deformations (tension, compression). Finally, a change correlation technique utilizes a qualitative shape-based reasoning approach for identifying correlated deformations of structure elements connected at joints that contradicts the joint equilibrium. Those contradicting deformations can help to eliminate improbable loading combinations therefore guiding the loading path analysis of the structure.Dissertation/ThesisDoctoral Dissertation Civil and Environmental Engineering 201

Transputer Implementation for the Shell Model and Sd Shell Calculations

This thesis consists of two parts. The first part discusses a new Shell model implementation based on communicating sequential processes. The second part contains different shell model calculations, which have been done using an earlier implementation. Sequential processing computers appear to be fast reaching their upper limits of efficiency. Presently they can perform one machine operation in every clock cycle and the silicon technology also seems to have reached its physical limits of miniaturization. Hence new software/hardware approaches should be investigated in order to meet growing computational requirements. Parallel processing has been demonstrated to be one alternative to achieve this objective. But the major problem with this approach is that many algorithms used for the solution of physical problems are not suitable for distribution over a number of processors. In part one of this work we have identified this concurrency in the shell model calculations and implemented it on the Meiko Computing Surface. Firstly we have explained the motivation for this project and then give a detailed comparison of different hardware/software that has been available to us and reasons for our preferred choice. Similarly, we also outline the advantages/disadvantages of the available parallel/sequential languages before choosing parallel C to be our language of implementation. We describe our new serial implementation DASS, the Dynamic And Structured Shell model, which forms basis for the parallel version. We have developed a new algorithm for the phase calculation of Slater Determinants, which is, superior to the previously used occupancy representation method. Both our serial and parallel implementations have adopted this representation. The PARALLEL GLASNAST, as we call it, PARALLEL GLASgow Nuclear Algorithmic Technique, is our complete implementation of the inherent parallelism in Shell model calculation and has been described in detail. It is actually based on splitting the whole calculation into three tasks, which can be distributed on the number of processors required by the chosen topology, and executed concurrently. We also give a detailed discussion of the communication/ synchronization protocols which preserve the available concurrency. We have achieved a complete overlap of the the main tasks, one responsible for arithmetically intensive operations and the other doing searching among, possibly, millions of states. It demonstrates that the implementation of these tasks has got enough built in flexibility that they could be run on any number of processors. Execution times for one and three transputers have been obtained for 28Si, which are fairly good. We have also undertaken a detailed analysis of how the amount of communication (traffic) between processors changes with the increase in the number of states. Part two describes shell model calculations for mass 21 nuclei. Previous many calculations have not taken into account the Coulomb's interaction, which is responsible for differences between mirror nuclei. They also do not use the valuable information on nucleon occupancies. We have made extensive calculations for the six isobars in mass 21 using CWC, PW and USD interactions. The results obtained in this case include, energy, spin, isospin and electromagnetic transition rates. These result are discussed and conclusions drawn. We concentrate on the comparison of the properties in of each mirror pairs. This comparison is supplemented by tables, energy level diagrams and occupancy diagrams. As we consider mirror pair individually, the mixing of states, which is caused by the short range nuclear force and the Coulomb force, becomes more evident. The other important thing we have noticed is, that some pairs of states swap their places, between a mirror pair, on the occupancy diagram, suggesting that their wave functions might have been swapped. We have undertaken a detailed study to discover any swapping states. The tests applied to confirm this include comparison of energy, electromagnetic properties and the occupancy information obtained with different interactions. We find that only the 91, 92 states in Al have swapped over. We also report some real energy gaps which exist on the basis of our calculations for Al

Aspects of the biology of Brassica/Alternaria host/pathogen systems

The main purpose of this study was to further an understanding of host-pathogen interactions and th e role of phytotoxins in the host relationships of Altemaria brassicae(Berk.) Sacc. and Alternariabrassicicola(Schw.) Wilts., using microscopical, biochemical, and statistical approaches. A further aim was to assess the taxonomic positions of A.brassicae and A.brassicicola within the Altemaria along with their attributes and behaviour patterns in relation to other members of the anamorph-genus.OOn the leaf surfaces of host plants A.brassicae and A.brassicicola showed broadly similar patterns of development but with some features which distinguished them. T he larger spores of A.brassicae typically produced two to three germ -tubes whereas A.brassicicola gave rise to only one. A.brassicae generally produced m ore extensive extra-matrical growth with hyphal branching and appressoria in intercalary as well as terminal positions; hyphae of A.brassicicola produced very few branches and usually terminated in appressoria. For both fungi appressoria were formed most frequently near to or over anticlinal walls of epidermal cells. Smaller numbers of appressoria were formed over periclinal walls and, in the case of A.brassicae, over stomata. The extra-matrical development of both species was m ore or less similar on contrasting host leaf surfaces, although A.brassicae showed somewhat reduced germ -tube numbers and stomatal penetrations on leaves with a pronounced waxy bloom. M arked differences in behaviour on different hosts or between hosts and non-hosts were evident only after penetration. In the case of A.brassicae unsuccessful penetrations were associated with only localised deposition of callose in the cell wall of the challenged cell, while with A.brassicicolaun successful penetration events were associated with cell wall responses which occurred in whole single cells.In comparing A.brassicae and A. brassicicola with other Altemaria species varying in their host range and degree of parasitism, all exhibited essentially similar patterns of extra-matrical behaviour on leaves, culminating in the formation of appressoria. Distinctive host relationships were evident only in the post-penetration phase.From successful penetrations A.brassicae produced a short sub-cuticular phase whereas A.brassicicola appeared to penetrate to intracellular position in the epidermis. Subsequent colonisation involved intercellular hyphal growth and extensive callose formation in host cell walls in response to both species.Biochemical studies on different Altemaria species indicated that each produced a diverse range of metabolites which may exhibit fungitoxic and phytotoxic activity. In the present study cytotoxicity of the extracts was low. T he studies failed to identify host-specific phytotoxicity, as only crude extracts were used, but the critical role of a host specific toxin, or resistance suppressor, is postulated in the initial establishment of infection.In considering genetical variation within A.brassicae and A.brassicicola, there is little evidence of marked physiological specialisation in either species. However, in testing a small number of isolates against a dicarboximide fungicide, A.brassicae showed slight and A.brassicicola showed marked intraspecific variation in fungicide insensitivity. In testing for sensitivity to fungicides the isolates of A.brassicae used w ere found to exhibit distinctive colony growth characteristics.Multivariate statistical techniques were applied to morphological, biochemical, and pathogenic characters to examine phylogenic relationships between selected species of Altemaria.Studies of the taxonomic relationships of the Altemariaspecies are constrained by the absence of teleomorphs, but certain genera within the Pleosporaceae are suggested to accommodate this group of toxigenic, leaf spotting, facultative parasites / saprophytes

The influence of street culture on brand identity in graphic design

Problem Statement: This thesis explores the influence of street culture on brand identity in graphic design. Aspects of street culture include skateboarding, hip-hop, rap, punk, and street art. Street art is traditionally thought of as illegal or rebellious mark-making of public property or property that does not belong to the person making marks on it. Street art can also be defined as a means of crafting personal expression through the enhancement or augmentation of a natural or man-made environment. In this study, brand identity is defined as the controllable and fundamental elements of a company, product, or service brand, such as the core essence, positioning, brand name, tag line, messaging, and experience (Perry, 5). The premise of this investigation will be to examine how corporate identities have been influenced by street culture, more specifically street art, as part of the larger realm of pop culture that has originated from the New York City hip-hop scene in the late 1970s. Street art has relevant applications in the design of corporate branding, especially in the fashion and music industries since the solutions can be influenced from the ephemeral and vernacular everyday actions and objects that can be found in urban settings. This study specifically focuses on the styles, mediums, and processes that are local and specific to street art that have transitioned into more public, formalized, and mass-produced graphic design solutions for corporate identity and associated branding strategies. By comparing, contrasting, and studying how actual examples from street culture influence brand identities and strategies, it is hoped that new methods and processes will be discovered that could help graphic designers learn how to reappropriate street culture in terms of generating aesthetic solutions, conceptual directions, and voice or tone in brand solutions. Selected Key Questions: 1 In what ways has the overall street art idiom influenced some graphic designers and/or their clients? 2 How has street art inspired and influenced designers to explore new methods and processes when creating or using imagery and typography in graphic design solutions? 3 What are the different ways in which type and image have evolved as trends, or perhaps clichés, in brand identities for the music and fashion industries? 4 How has street art been a general influence on branding in the music and fashion industries? 5 How has street culture influenced visual communication intended for different age groups? 6 Are there varying motifs, elements, and themes that have emerged from street art and influenced brand identities and/or branding strategies? 7 How have different levels of abstraction and complexity of imagery or typography been used in brand identity systems? Have these abstractions been influenced by street art? 8 How have brand identities and/or branding strategies been interpreted with respect to the hip-hop subculture? Project Relevance and Importance: This study recognizes that street art is an art form, created by artists, and as such is worthy of respect and acknowledgement. This study explores design strategies and issues related to reappropriating street art in corporate identities and related branding strategies with an aim to present new methods and processes that designers can apply toward more meaningful, long-lasting identity solutions that do not misrepresent urban culture. Project Definition: Associated Areas of Study: Graphic Design, Marketing, Sociology/Urban Studies, Advertising, Branding, Cultural Anthropology Potential Application: A potential application for this thesis could involve the creation of a brand identity and/or associated brand strategy that misappropriates street art and needs to be thoughtfully amended, and one that studies a brand that does not use street art as an influence but could have in order to create a new successful solution. By comparing both approaches and how the actual solutions can be improved, it will demonstrate that the street art idiom within a larger pop-cultural perspective can offer new design strategies that could inspire graphic designers to present more appropriate and respectful design solutions. A second potential application of this study would be to define the syntax of vernacular signs and symbols that have emerged from generation-specific icons from street art for appropriate, noncommercial design solutions in a less expected and under-investigated area of industry. The design solutions, therefore, would represent an alternative way to communicate visual information to a specific audience without disrespecting the hip-hop subculture. The designs would also be placed in areas where the viewing experience to a passerby would appear to be a spontaneous or unexpected experience of message-making. Project Goals: The goals for this study are to discover how street art is currently reappropriated in brand identity and associated branding solutions and what strategies designers could explore to find influence from street art to communicate to a wide range of age groups within a specific and appropriate area of industry. Another important aspect of this study is to discover how street artists who are part of the hip-hop subculture use their talent and knowledge within the subculture to reappropriate the art from within their own branding solutions in graphic design. Based on how street artists\u27 interpret their actions and behaviors through graffiti writing or tagging, designers who do not directly belong to the hip-hop subculture could benefit from this study to better understand how they could use the influence from the art form in branding solutions to positively contribute to the design field in a noncommercial way that is respectful, meaningful, informational, and the mode of communication operates similarly to the way the art form did when it was first conceived to communicate messages. Another goal of this thesis is to prove how street art is misappropriated in many design solutions for different industry areas to promote commercial sales in such a way that misrepresents and disrespects the hip-hop subculture. It is important for street art to be represented in a way that goes beyond meeting the bottom line so that the influence of street art in brand identity can be used for a more functional purpose in which the medium and mode of communication is used in a way that is highly informational, educational, and serves a purpose other than to sell an idea or product. A final goal is to implement the theoretical research into a real-world application

Hippocampal Spatial Representation: Integrating Environmental and Self-motion Signals

Electrophysiological recording in freely-moving rodents has established that place cells fire when the animal occupies a specific location and grid cells fire when at several locations, arranged on a regular triangular grid. Experiments and theories suggest that place cells and grid cells 1) receive inputs reflecting both environmental and self-motion information, and 2) are functionally connected to each other. Yet it remains elusive how the environmental and self-motion inputs dictate either place cell or grid cell firing. In a series of experiments, I address this question by manipulating the inputs independently while simultaneously recording place and grid cells activity. Firstly, I introduce our visual 2-d virtual reality system, in which mice run on an air-supported Styrofoam ball with their head held but allowed to rotate in the horizontal plane. The virtual arena is projected on surrounding screens and on the floor at a viewpoint that shifts with the rotation of the ball. With sufficient training, mice can navigate freely in the virtual environment and successfully retrieve rewards from an unmarked location. Electrophysiological data confirms that place, grid, and head-direction cells show characteristic spatial tuning in VR. In a second experiment, the gain factor that maps mice’s running speed to the visual translation of the virtual environment is manipulated. Results show that place cell firings are more driven by vision while grid cells incorporate self-motion inputs better. The last experiment had mice navigate in darkness. Without visual input co-recorded place cells and grid cells both suffer disruption in spatial tuning, albeit tuning is better preserved near to environmental boundaries. These results demonstrated that environmental and self-motion signals contribute to place and grid cells’ spatial representation of different significance, and constrain models with presumptions about how the place cells and grid cells integrate inputs and interact with each other

Electrochemically controlled patterning for biosensor arrays.

Existe una demanda creciente de dispositivos de análisis multianalito, con aplicaciones potenciales en los campos de la biomedicina y biotecnología, así como en el ámbito industrial y ambiental. Para el desarrollo de estos dispositivos resulta esencial un buen control espacial durante la etapa de inmovilización de las biomoléculas de interés; cada una de ellas debe ser depositada de forma precisa sobre la superficie del sensor (por ejemplo, un transductor amperométrico), evitando solapamientos que puedan comprometer la especificidad del sistema. El objetivo de esta tesis es desarrollar diferentes métodos de patterning para la inmovilización selectiva de biomoléculas. El primer método consiste en la electrodeposición selectiva de nanopartículas de oro biofuncionalizadas para el desarrollo de biochips. Se trata de un método de patterning controlado electroquímicamente, en el que las nanopartículas de oro se modifican en primer lugar recubriéndolas con diversos enzimas y a continuación se electrodepositan selectivamente sobre la superficie de un electrodo. Como parte de esta metodología, se prepararon nanopartículas de oro biofuncionalizadas utilizando tres estrategias diferentes: a través del enlace dativo oro-tiol, por adsorción directa o mediante interacción electrostática siguiendo la técnica layer-by-layer (capa por capa). Para la funcionalización de las nanopartículas de oro se emplearon distintas biomoléculas, como los enzimas peroxidasa de rábano (HRP), glucosa oxidasa (GOX) y albúmina de suero bovino (BSA), y finalmente oligonucleótidos modificados con moléculas fluorescentes y grupos tiol. Las nanopartículas biofuncionalizadas fueron caracterizadas mediante técnicas de espectroscopía UV-visible, microscopía electrónica de transmisión (TEM) y medida del potencial zeta. Mediante espectroscopía UV-visible se observó un pico de resonancia de plasmón característico de las nanopartículas modificadas, relacionado con la estabilidad de la preparación. La medida del potencial zeta permitió la caracterización de las nanopartículas de oro modificadas capa por capa con polímero redox y enzimas. También se estudiaron los cambios en el potencial zeta de nanopartículas modificadas con BSA a distintos valores de pH. Tras la preparación de las partículas biofuncionalizadas, se llevaron a cabo estudios fundamentales de electrodeposición de nanopartículas de oro modificadas con BSA y un polímero redox, con el fin de analizar el efecto de varios parámetros: potencial aplicado, tiempo de deposición, distancia entre los electrodos, superficie del electrodo auxiliar y pH del medio. Para estudiar el comportamiento electrocatalítico de las nanopartículas modificadas una vez electrodepositadas, se llevaron a cabo experimentos utilizando coloides de oro modificados con HRP y GOX. A continuación se empleó esta metodología para el desarrollo de biochips, utilizando dos configuraciones diferentes. En la primera, se electrodepositaron nanopartículas de oro funcionalizadas con GOX y HRP y modificadas con un polímero redox sobre la superficie de un chip de electrodos interdigitados (IDE), consiguiendo eliminar por completo las repuestas no específicas. En la segunda configuración, las partículas se modificaron con una capa adicional de polímero redox, comprobando de nuevo la ausencia total de respuestas no específicas después de la electrodeposición. Esta método de patterning es genérico y puede utilizarse para la producción de diversos biochips. El segundo método de patterning también está basado en el control electroquímico, y consiste en la modificación de los electrodos con monocapas autoensambladas electroactivas cuya funcionalidad es modulable en función del potencial aplicado. En esta metodología, la monocapa electroactiva contiene grupos acetal que pueden ser desprotegidos selectivamente mediante la aplicación de un potencial en zonas específicas de la superficie del electrodo. De esta manera quedan expuestos en la superficie grupos aldehído activos, que pueden ser fácilmente conjugados con aminas primarias presentes en las biomoléculas de interés. Los enzimas GOX y HRP se usaron como proteínas modelo para comprobar la versatilidad de esta técnica. Su aplicabilidad para la fabricación de biochips se demostró con medidas amperométricas y medidas en tiempo real mediante resonancia de plasmón de superficie combinado con electroquímica (eSPR). La tercera metodología es también un sistema de patterning controlado electroquímicamente, pero en este caso se utiliza la inmovilización del 4,4-bipiridil como base para la creación de biochips. Se sintetizaron moléculas de 4,4-bipiridil funcionalizadas con grupos carboxílicos, que fueron caracterizadas electroquímicamente y a continuación conjugadas con las biomoléculas de interés para la creación de biochips. La selectividad de estos sistemas se demostró colorimétricamente, obteniéndose niveles mínimos de respuesta inespecífica. Por último, el cuarto de los métodos de patterning desarrollados está basado en la técnica de fotolitografía. Los enzimas glucosa oxidasa y sarcosina oxidasa se depositaron selectivamente junto con un polímero redox sobre la superficie de electrodos interdigitados utilizando un proceso de lift off, consiguiendo eliminar por completo las señales cruzadas o cross-talk. Como parte de esta metodología se optimizaron varios procedimientos de inmovilización de las biomoléculas, con el fin de seleccionar la estrategia más adecuada. También se llevaron a cabo ensayos con diferentes reactivos para eliminar la adsorción inespecífica. Finalmente, el sistema optimizado fue aplicado sobre IDEs fabricados mediante fotolitografía. Los sensores de glucosa y sarcosina respondieron de forma selectiva a sus respectivos sustratos, con ausencia total de cross-talk. La presente tesis está estructurada en 7 capítulos. En el Capítulo I se exponen las bases del desarrollo de biochips, métodos de patterning con control electroquímico, otros métodos de patterning selectivo y las técnicas de fotolitografía, así como un resumen de la tesis. El Capítulo 2 y 3 describe la síntesis de coloides de oro, la modificación con biomoléculas, los estudios de estabilidad y los estudios fundamentales de electrodeposición de las nanopartículas de oro modificadas sobre la superficie de los electrodos. En el Capítulo 4 se muestra la aplicación de la electrodeposición de nanopartículas de oro biofuncionalizadas para la creación de biochips. El Capítulo 5 describe la inmovilización selectiva de biomoléculas mediante la desprotección electroquímica de monocapas autoensambladas electroactivas. En el Capítulo 6 se muestra la síntesis, caracterización e inmovilización selectiva de derivados de 4,4- bipiridil funcionalizados con HRP. El Capítulo 7 describe el patterning selectivo en la escala micrométrica de dos oxidasas sobre un chip de electrodos interdigitados mediante fotolitografía. Finalmente, el Capítulo 8 resume las conclusiones y el trabajo futuro.There is an increasing demand of multianalyte sensing devices having potential applications in biomedical, biotechnological, industrial and environmental fields. A good spatial control during biomolecule deposition step is strictly necessary; each biomolecule has to be precisely deposited on the surface of the relevant sensor (eg., an amperometric transducer), avoiding mixing that can compromise the biosensor specificity. The aim of this thesis is to develop different patterning methods for the selective immobilization of biomolecules. The first method is selective electrodeposition of biofunctionalized Au nanoparticles for biosensor arrays. This is an electrochemically controlled patterning method where the Au nanoparticles modified by the enzymes initially and later the enzyme modified Au nanoparticles were electrodeposited selectively on the electrode surface. As a part of this methodology, initially biofunctionalized Au nanoparticles were prepared using three different approcahes. One is Au-thiol dative bonding, the second is direct adsorption and finally electrostatic layerby- layer approach. Different biomolecules like horse radish peroxidase(HRP), glucose oxidase (GOX), bovine serum albumin(BSA), and finally fluorescence labelled oilgonucleotide thiols were used to attch to the Au nanoparticles. Biofunctionalized Au nanoparticles were characterized by different techniques like zeta sizer, UV-Vis spectroscopy, transmission electron microscopy (TEM). UV-Vis spectroscopy showed the successfull modification of Au nanoparticles with a characterstic surface plasmon peak related to the stability. By using zeta sizer, layer-by-layer modification of the Au nanoparticles with redox polymer and enzymes were characterized successfully. Changes of the Au nanoparticles modified with BSA was characterised at different pH s by using the zeta sizer. After the preparation of biofunctionalized particles, some fundamental studies were done with electrodeposition of Au nanoparticles modified with medically important BSA, redox polymer to see how different parameters like potential, time of deposition, interelectrode distance, counter electrode sized, pH, effect the electrodeposition. As a part of these fundamental studies Au colloids modified with HRP and GOX were deposited for studying the electrocalaytic behaviour of the enzymes on the Au nanoparticles after electrodeposition. Later this methodology was applied for creating biosensor arrays by using two different approaches. In the first approach, GOX and HRP functionalized redox polymer modified Au nanoparticles were electrodeposited successfully on an interdigitated electrode (IDE) array with complete absence of non-specific response. In the second approach the particles were modified with an extra redox polymer layer and proved that there is complete absence of nonspecific response after electrodeposition. Moreover, this patterning methodology is generic and can be used for production of different biochips. The second method is another electrochemically controlled patterning method where the electrodes were immobilized with self assembled monolayers with electroactive functionalities which can be tunable with potentials. In this methodology, electroactive self-assembled monolayer contains an active ligand aldehyde which can be readily conjugated to the primary amine group of the biomolecule is protected in the form of acetal. Later when a active potential was applied to the underlying electrode surface, the acetal functionality is deprotected to reveal the aldehyde functionality which was further conjugated to the biomolecule. Two enzymes GOX, HRP were used as model proteins to prove the versatility of this technique. Amperometric as well as real time measurements proved the selective applicability of this technique for creation of biosensor arrays. The third methodology is also an electrochemically controlled patterning methodology where the special advantage of the electrochemically-controlled immobilization of the 4,4-bipyridyl was taken as base for the creation of biosensor arrays. In this methodology, carboxylic acid functionalised 4,4, bipyridyl molecules were synthesized and characterized by electrochemistry. Later the biomolecules were conjugated to these special molecules for the creation of sensor arrays. Proof of selectivity was shown using colourimetrically with minimal non-specific response. Finally in the fourth method which is based on the photolithography technique, two different oxidases GOX & SOX were patterned along with redox polymer selectively on an IDE array using the lift off process with complete absence of cross-talk. As a part of this methodology, different immobilization methods were optimized initially for checking the best optimisation strategy. Later different reagents were tried to optimise the best reagent that prevents the non-specific adsorption. Later this optimised system was applied on the pholithographically created IDE array. Sarcosine and glucose sensors responded selectively to their substrates with complete absence of cross talk. This thesis is structured in 7 chapters. Chapter 1 establishes to basics of the biosensor arrays, electrochemically controlled patterning methods, other selectively patterned methods, photolithography and summary of this thesis. Chapter 2 describes about the gold colloid synthesis, modification with the biomolecules, stability studies. Chapter 3 decribes fundamental studies of the electrodeposition of the functionalised Au nanoparticles on the electrode surface. Chapter 4 describes the application of the electrodeposition of the protein functionalised Au nanoparticles for the creation of biosensor arrays. Chapter 5 describes the selective immobilization of biomolecules through electrochemical deprotection of electroactive self-assembled monolayers. Chapter 6 describes the synthesis, characterization and selective immobilization of HRP functionalized 4,4-bipyridyl derivatives. Chapter 7 describes the selective microscale protein patterning of two oxidases on an IDE array through photolithography. Finally chapter 8 summarizes the conclusions and the future work

Convex hulls in concept induction

Classification learning is dominated by systems which induce large numbers of small axis-orthogonal decision surfaces. This strongly biases such systems towards particular hypothesis types but there is reason believe that many domains have underlying concepts which do not involve axis orthogonal surfaces. Further, the multiplicity of small decision regions mitigates against any holistic appreciation of the theories produced by these systems, notwithstanding the fact that many of the small regions are individually comprehensible. This thesis investigates modeling concepts as large geometric structures in n-dimensional space. Convex hulls are a superset of the set of axis orthogonal hyperrectangles into which axis orthogonal systems partition the instance space. In consequence, there is reason to believe that convex hulls might provide a more flexible and general learning bias than axis orthogonal regions. The formation of convex hulls around a group of points of the same class is shown to be a usable generalisation and is more general than generalisations produced by axis-orthogonal based classifiers, without constructive induction, like decision trees, decision lists and rules. The use of a small number of large hulls as a concept representation is shown to provide classification performance which can be better than that of classifiers which use a large number of small fragmentary regions for each concept. A convex hull based classifier, CH1, has been implemented and tested. CH1 can handle categorical and continuous data. Algorithms for two basic generalisation operations on hulls, inflation and facet deletion, are presented. The two operations are shown to improve the accuracy of the classifier and provide moderate classification accuracy over a representative selection of typical, largely or wholly continuous valued machine learning tasks. The classifier exhibits superior performance to well-known axis-orthogonal-based classifiers when presented with domains where the underlying decision surfaces are not axis parallel. The strengths and weaknesses of the system are identified. One particular advantage is the ability of the system to model domains with approximately the same number of structures as there are underlying concepts. This leads to the possibility of extraction of higher level mathematical descriptions of the induced concepts, using the techniques of computational geometry, which is not possible from a multiplicity of small regions