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.

Design and Development of Compact Chipless RFID Tags with High Data Encoding Capacity

The main objective of this thesis is to develop a compact chipless RFID tag with high data encoding capacity. The design and development of chipless RFID tag based on multiresonator and multiscatterer methods are presented first. An RFID tag using using SIR capable of 79bits is proposed. The thesis also deals with some of the properties of SIR like harmonic separation, independent control on resonant modes and the capability to change the electrical length. A chipless RFID reader working in a frequency band of 2.36GHz to 2.54GHz has been designed to show the feasibility of the RFID system. For a practical system, a new approach based on UWB Impulse Radar (UWB IR) technology is employed and the decoding methods from noisy backscattered signal are successfully demonstrated. The thesis also proposes a simple calibration procedure, which is able to decode the backscattered signal up to a distance of 80cm with 1mW output power.

Design and Synthesis of Donor-Acceptor Low Band Gap Copolymers for Photoconductive and Non-linear Optical Applications

The main focus of the present study was to develop ideal low band gap D-A copolymers for photoconducting and non-linear optical applications. This chapter summarizes the overall research work done. Designed copolymers were synthesized via direct arylation or Suzuki coupling reactions. Copolymers were characterized by theoretical and experimental methods. The suitability of these copolymers in photoconducting and optical limiting devices has been investigated.The results suggest that the copolymers investigated in the present study have a good non-linear optical response and are comparable to or even better than the D-A copolymers reported in the literature and hence could be chosen as ideal candidates with potential applications for non-linear optics. The results also show that the structures of the polymers have great impact on NLO properties. Copolymers studied here exhibits good optical limiting property at 532 nm wavelength due to two-photon absorption (TPA) process. The results revealed that the two copolymers, (P(EDOT-BTSe) and P(PH-TZ)) exhibited strong two-photon absorption and superior optical power limiting properties, which are much better than that of others.

Design and Development of Fiber Grating Based Chemical and Bio-Sensors

International School of Photonics

Design and Development of Spectral Signature Based Chipless RFID Tags

The main objective of this thesis is to design and develop spectral signature based chipless RFID tags Multiresonators are essential component of spectral signature based chipless tags. To enhance the data coding capacity in spectral signature based tags require large number of resonances in a limited bandwidth. The frequency of the resonators have to be close to each other. To achieve this condition, the quality factor of each resonance needs to be high. The thesis discusses about various types of multiresonators, their practical implementation and how they can be used in design. Encoding of data into spectral domain is another challenge in chipless tag design. Here, the technique used is the presence or absence encoding technique. The presence of a resonance is used to encode Logic 1 and absence of a speci c resonance is used to encode Logic 0. Di erent types of multiresonators such as open stub multiresonators, coupled bunch hairpin resonators and shorted slot ground ring resonator are proposed in this thesis.

Theoretical Design and Synthesis of Donor-Acceptor Conjugated Polymers for Photovoltaic and NLO Applications

Polymers with conjugated π-electron backbone display unusual electronic properties such as low energy optical transition, low ionization potentials, and high electron affinities. The properties that make these materials attractive include a wide range of electrical conductivity, mechanical flexibility and thermal stability. Some of the potential applications of these conjugated polymers are in sensors, solar cells, field effect transistors, field emission and electrochromic displays, supercapacitors and energy storage. With recent advances in the stability of conjugated polymer materials, and improved control of properties, a growing number of applications are currently being explored. Some of the important applications of conducting polymers include: they are used in electrostatic materials, conducting adhesives, shielding against electromagnetic interference (EMI), artificial nerves, aircraft structures, diodes, and transistors.

Micro-electromechanical structural design and optimization of vertical cavity photonic devices with wide continuous tuning

Diese Arbeit umfaßt das elektromechanische Design und die Designoptimierung von weit durchstimmbaren optischen multimembranbasierten Bauelementen, mit vertikal orientierten Kavitäten, basierend auf der Finiten Element Methode (FEM). Ein multimembran InP/Luft Fabry-Pérot optischer Filter wird dargestellt und umfassend analysiert. In dieser Arbeit wird ein systematisches strukturelles Designverfahren dargestellt. Genaue analytische elektromechanischer Modelle für die Bauelemente sind abgeleitet worden. Diese können unschätzbare Werkzeuge sein, um am Anfang der Designphase schnell einen klaren Einblick zur Verfügung zu stellen. Mittels des FEM Programms ist der durch die nicht-lineare Verspannung hervorgerufene versteifende Effekt nachgeforscht und sein Effekt auf die Verlängerung der mechanischen Durchstimmungsstrecke der Bauelemente demonstriert worden. Interessant war auch die Beobachtung, dass die normierte Relation zwischen Ablenkung und Spannung ein unveränderliches Profil hat. Die Deformation der Membranflächen der in dieser Arbeit dargestellten Bauelementformen erwies sich als ein unerwünschter, jedoch manchmal unvermeidbarer Effekt. Es zeigt sich aber, dass die Wahl der Größe der strukturellen Dimensionen den Grad der Membrandeformation im Falle der Aktuation beeinflusst. Diese Arbeit stellt ein elektromechanisches in FEMLAB implementierte quasi-3D Modell, das allgemein für die Modellierung dünner Strukturen angewendet werden kann, dar; und zwar indem man diese als 2D-Objekte betrachtet und die dritte Dimension als eine konstante Größe (z.B. die Schichtdicke) oder eine Größe, welche eine mathematische Funktion ist, annimmt. Diese Annahme verringert drastisch die Berechnungszeit sowie den erforderlichen Arbeitsspeicherbedarf. Weiter ist es für die Nachforschung des Effekts der Skalierung der durchstimmbaren Bauelemente verwendet worden. Eine neuartige Skalierungstechnik wurde abgeleitet und verwendet. Die Ergebnisse belegen, dass das daraus resultierende, skalierte Bauelement fast genau die gleiche mechanische Durchstimmung wie das unskalierte zeigt. Die Einbeziehung des Einflusses von axialen Verspannungen und Gradientenverspannungen in die Berechnungen erforderte die Änderung der Standardimplementierung des 3D Mechanikberechnungsmodus, der mit der benutzten FEM Software geliefert wurde. Die Ergebnisse dieser Studie zeigen einen großen Einfluss der Verspannung auf die Durchstimmungseigenschaften der untersuchten Bauelemente. Ferner stimmten die Ergebnisse der theoretischen Modellrechnung mit den experimentellen Resultaten sehr gut überein.

Design and Implementation of a Flexible Robot

This robot has low natural frequencies of vibration. Insights into the problems of designing joint and link flexibility are discussed. The robot has three flexible rotary actuators and two flexible, interchangeable links, and is controlled by three independent processors on a VMEbus. Results from experiments on the control of residual vibration for different types of robot motion are presented. Impulse prefiltering and slowly accelerating moves are compared and shown to be effective at reducing residual vibration.

Design and Control of a Closed-Loop Brushless Torque Actuator

This report explores the design and control issues associated with a brushless actuator capable of achieving extremely high torque accuracy. Models of several different motor - sensor configurations were studied to determine dynamic characteristics. A reaction torque sensor fixed to the motor stator was implemented to decouple the transmission dynamics from the sensor. This resulted in a compact actuator with higher bandwidth and precision than could be obtained with an inline or joint sensor. Testing demonstrated that closed-loop torque accuracy was within 0.1%, and the mechanical bandwidth approached 300 Hz.

Design and Control of an Anthropomorphic Robotic Finger with Multi-point Tactile Sensation

The goal of this research is to develop the prototype of a tactile sensing platform for anthropomorphic manipulation research. We investigate this problem through the fabrication and simple control of a planar 2-DOF robotic finger inspired by anatomic consistency, self-containment, and adaptability. The robot is equipped with a tactile sensor array based on optical transducer technology whereby localized changes in light intensity within an illuminated foam substrate correspond to the distribution and magnitude of forces applied to the sensor surface plane. The integration of tactile perception is a key component in realizing robotic systems which organically interact with the world. Such natural behavior is characterized by compliant performance that can initiate internal, and respond to external, force application in a dynamic environment. However, most of the current manipulators that support some form of haptic feedback either solely derive proprioceptive sensation or only limit tactile sensors to the mechanical fingertips. These constraints are due to the technological challenges involved in high resolution, multi-point tactile perception. In this work, however, we take the opposite approach, emphasizing the role of full-finger tactile feedback in the refinement of manual capabilities. To this end, we propose and implement a control framework for sensorimotor coordination analogous to infant-level grasping and fixturing reflexes. This thesis details the mechanisms used to achieve these sensory, actuation, and control objectives, along with the design philosophies and biological influences behind them. The results of behavioral experiments with a simple tactilely-modulated control scheme are also described. The hope is to integrate the modular finger into an %engineered analog of the human hand with a complete haptic system.

BioJADE: A Design and Simulation Tool for Synthetic Biological Systems

The next generations of both biological engineering and computer engineering demand that control be exerted at the molecular level. Creating, characterizing and controlling synthetic biological systems may provide us with the ability to build cells that are capable of a plethora of activities, from computation to synthesizing nanostructures. To develop these systems, we must have a set of tools not only for synthesizing systems, but also designing and simulating them. The BioJADE project provides a comprehensive, extensible design and simulation platform for synthetic biology. BioJADE is a graphical design tool built in Java, utilizing a database back end, and supports a range of simulations using an XML communication protocol. BioJADE currently supports a library of over 100 parts with which it can compile designs into actual DNA, and then generate synthesis instructions to build the physical parts. The BioJADE project contributes several tools to Synthetic Biology. BioJADE in itself is a powerful tool for synthetic biology designers. Additionally, we developed and now make use of a centralized BioBricks repository, which enables the sharing of BioBrick components between researchers, and vastly reduces the barriers to entry for aspiring Synthetic Biologists.

Assembly Design and Evaluation in an Augmented Reality Environment

The technologies and methodologies of assembly design and evaluation in the early design stage are highly significant to product development. This paper looks at a promising technology to mix real components (e.g. physical prototypes, assembly tools, machines, etc.) with virtual components to create an Augmented Reality (AR) interface for assembly process evaluation. The goal of this paper is to clarify the methodologies and enabling technologies of how to establish an AR assembly simulation and evaluation environment. The architecture of an AR assembly system is proposed and the important functional modules including AR environment set-up, design for assembly (DFA) analysis and AR assembly sequence planning in an AR environment are discussed in detail.

Design and Development of 3-DOF Modular Micro Parallel Kinematic Manipulator

This paper presents the research and development of a 3-legged micro Parallel Kinematic Manipulator (PKM) for positioning in micro-machining and assembly operations. The structural characteristics associated with parallel manipulators are evaluated and the PKMs with translational and rotational movements are identified. Based on these identifications, a hybrid 3-UPU (Universal Joint-Prismatic Joint-Universal Joint) parallel manipulator is designed and fabricated. The principles of the operation and modeling of this micro PKM is largely similar to a normal size Stewart Platform (SP). A modular design methodology is introduced for the construction of this micro PKM. Calibration results of this hybrid 3-UPU PKM are discussed in this paper.