This dissertation explores the use of nanocarbons both as conductive supports for redox enzyme electrochemistry and as electrocatalytic components for the nonmediated detection of biogenic analytes. More specifically, the influence of nitrogen doping of these nanocarbons (referred to herein as nitrogen-doped carbon nanotubes, or N-CNTs) on their bioelectrocatalytic performance is studied through direct enzyme adsorption and exploitation of the N-CNTs' inherent reactivity toward H₂O₂ to create H₂O₂-based sensing strategies. Both nondoped CNTs and N-CNTs may be effectively incorporated into biogenic sensing assemblies, as demonstrated herein using a variety of electrochemical techniques. Chapter 1 gives a general overview of the scope of this research and describes previous studies conducted within our laboratories that demonstrate our CNTs' promise as biogenic electrode materials. Chapter 2 describes the chemical vapor deposition (CVD) method used to prepare both CNTs and N-CNTs and establishes their suitability for use in the detection schemes outlined in later chapters through long-term stability studies. Additionally, the redox activity of Fe nanoparticles entrapped in the CNTs as a result of this CVD growth process is examined using a host of electrochemical experiments. Importantly, the data presented in this chapter show that these Fe particles do not explain the observed electrocatalytic response of the CNTs. Chapter 3 explores the direct adsorption of horseradish peroxidase (HRP) at both nondoped and N-CNTs. Spectroscopic and electrochemical assays are used to compare the extent of HRP enzymatic activity upon immobilization at both types of CNTs. Both types of HRP/CNT composites are then utilized in a quantitative H₂O₂ sensing strategy. Chapter 4 discusses the intrinsic reactivity of N-CNTs toward H₂O₂. Koutecky-Levich plots are used to demonstrate differences in H₂O₂ consumption mechanisms between NCNTs and traditional peroxidases. By replacing HRP with N-CNTs in an amperometric glucose detection scheme, the versatility of N-CNTs as a peroxidase substitute for biogenic analyte detection is demonstrated. Chapter 5 outlines future directions for this research, including possible strategies for improving electron transfer between HRP and both types of CNTs. This chapter also presents a newly developed, mediated oxidase-substrate electrochemical detection method that can easily be modified to incorporate CNTs.

Selected nucleic acid binding species (aptamers) have been shown to undergo conformational changes in the presence of ligands, and have been adapted to function as biosensors. We were interested in whether the secondary structures of aptamers could be rationally engineered to undergo ligand dependent conformational changes. To this end, we used rational and computational design methods to generate a number of aptamer biosensors. First, we built upon previous work that showed that antisense oligonucleotides bearing reporter moieties could be used to denature aptamers. Upon addition of ligands, the conformational equilibrium is shifted towards release of the antisense oligonucleotide and a concomitant increase in fluorescence. We attempted to adapt this format to the potential detection of ricin, but were unsuccessful. In order to better evaluate rational designs, we attempted to use computational modeling methods. Again, aptamer biosensors have previously been engineered based on ligand-induced reorganization of secondary structure (as opposed to oligonucleotide displacement), a so-called 'slip-structure' model. We developed an algorithm to evaluate different lisp structures, predicted both aptamers and aptazymes that should have undergone ligand-dependent changes in conformation, and experimentally evaluated the computationally predicted sequences. A number of robust biosensors that could respond to the cytokine VegF and the small molecule flavin were discovered. The computational model was further adapted to an aptamer biosensor that underwent a larger conformational change upon ligand-binding, an antiswitch. In this model, binding of the ligand stabilizes one hairpin structure at the expense of a competing structure (as opposed to merely changing the register of the hairpin as in the previously described slip structure model). Again, we were able to computationally identify a number of antiswitches that upon synthesis were responsive to the ligand theophylline. Finally we again attempted to use rational design methods to optimize not just the degree of signal but also the kinetic performance of aptamer biosensors. To this end, we developed biosensors that signaled within seconds the presence of the coagulation protein thrombin. / text

M. Tech. Electrical Engineering / For the last 3 decades, interdisciplinary studies on the Brain Computer Interface (BCI) have grown in number. This common interest has been stirred up by recent developments in technology and opportunities seen in BCI. BCI systems provide an interface for communicating and controlling the physical environment, bypassing the normal neuromuscular pathways. They thus constitute an alternative means of control for the large population of people with limited to non-existent muscular abilities. Limitations in existing systems have prevented BCIs from being used in real life applications. New approaches are now being investigated with the aim of exporting BCI to home usage. This study investigates a BCI with realistic performances for practical home usage. It proposes a BCI to be used as a modality in a multimodal control of an exoskeleton.

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During the last decade, surface plasmon resonance (SPR) has become widely used to characterize a biological surface and to characterize binding events in the fields of chemistry and biochemistry. Research in this field has been favoured by the tremendous growth in nanofabrication methods among which soft lithographies are alternatively emerging. The purpose of this thesis work was to develop soft UV nanoimprint lithography, an emerging flexible technology allowing patterning on large area of subwavelength photonic nanostructures. The main advantages offered by soft UV nanoimprint lithography concern the simple patterning procedure and the low cost of the experimental setup (see state-of-art presented in chapter 1). Chapters 2 and 3 present the fabrication of master stamps, the study of nanoimprinting parameters coupled with the optimization of the etching process in order to get metallic nanostructures with limited pattern defects. The physical mechanisms of the transmission phenomenon exalted by surface plasmons were studied based on arrays of imprinted gold nanoholes (chapter 4). Extraordinary light transmission has been experimentally demonstrated. The geometrical effects on the position transmission peak were systematically analyzed. Proof-of-concept measurements performed in simple fluidic device indicate a response to small changes in refractive index in the surface vicinity. Finally, chapter 5 proposes a novel design for the optical sensor which is based on "nanocavities" exhibiting coupled localized plasmons. This LSPR sensor offers an improvement of one order of magnitude of the Figure of Merit compared to classical LSPR sensors. The resonance properties of these innovative nanocavities have been studied from numerical simulations and discussed based on their geometrical dependence. Since this system has demonstrated higher sensitivity for detection of biomolecules, it is thus fully adapted to study immunochemical binding interactions.

Matematinis ir skaitinis biojutiklių modeliavimas yra svarbus uždavinys, kuriant naujus ir tobulinant esamus biojutiklius. Disertacijos tyrimo objektas – matematiniai bei skaitiniai modeliai, aprašantys naujoviškų lipazės aktyvumo nustatymo biojutiklių bei teorinio biojutiklio, padengto valdoma membrana, veikimą. Tyrimo tikslai – nustatyti, kokie matematiniai ir skaitiniai modeliai geriausiai tinka lipazės aktyvumo nustatymo biojutikliams aprašyti, taip pat nustatyti, kokiais parametrais pasižymėtų biojutiklis, turintis valdomą membraną, kokiomis sąlygomis išryškėtų jo privalumai ir trūkumai. Nustatyta, kad lipazės aktyvumo matavimo biojutiklio modeliavimui klasikinį modelį reikia papildyti netiesiniu nariu. Biojutiklis su valdoma membrana pasiteisintų, jei fiziškai neištraukiant jutiklio iš darbinės aplinkos, reikėtų perjunginėti jo darbo režimą iš difuzinio į kinetinį ir atvirkščiai. / Biosensor mathematical and computer modeling is an important task for the development of new biosensors and for the improvement of the existing ones. Objects of this study are mathematical and numerical models which describe operation of novel lipase activity assessment biosensors and theoretical biosensor with controllable permeability membrane. Specific aims of this thesis are to identify what mathematical and numerical models are best suited for modeling specific lipase activity assessment biosensors and to identify what parameters of operation are specific for biosensor with controllable membrane. Also to identify the conditions which would reveal the positive and negative features of controllable membrane. It was discovered that in the case of lipase activity assessment biosensor the classic mathematical model should be extended with a non-linear term (in respect to substrate). Also, it was discovered that biosensor with controllable membrane would be useful in cases when biosensor cannot be physically removed from the operating environment, but still needs to be reconfigured for operation in the kinetic or diffusion mode.

Biosensor mathematical and computer modeling is an important task for the development of new biosensors and for the improvement of the existing ones. Objects of this study are mathematical and numerical models which describe operation of novel lipase activity assessment biosensors and theoretical biosensor with controllable permeability membrane. Specific aims of this thesis are to identify what mathematical and numerical models are best suited for modeling specific lipase activity assessment biosensors and to identify what parameters of operation are specific for biosensor with controllable membrane. Also to identify the conditions which would reveal the positive and negative features of controllable membrane. It was discovered that in the case of lipase activity assessment biosensor the classic mathematical model should be extended with a non-linear term (in respect to substrate). Also, it was discovered that biosensor with controllable membrane would be useful in cases when biosensor cannot be physically removed from the operating environment, but still needs to be reconfigured for operation in the kinetic or diffusion mode. / Matematinis ir skaitinis biojutiklių modeliavimas yra svarbus uždavinys, kuriant naujus ir tobulinant esamus biojutiklius. Disertacijos tyrimo objektas – matematiniai bei skaitiniai modeliai, aprašantys naujoviškų lipazės aktyvumo nustatymo biojutiklių bei teorinio biojutiklio, padengto valdoma membrana, veikimą. Tyrimo tikslai – nustatyti, kokie matematiniai ir skaitiniai modeliai geriausiai tinka lipazės aktyvumo nustatymo biojutikliams aprašyti, taip pat nustatyti, kokiais parametrais pasižymėtų biojutiklis, turintis valdomą membraną, kokiomis sąlygomis išryškėtų jo privalumai ir trūkumai. Nustatyta, kad lipazės aktyvumo matavimo biojutiklio modeliavimui klasikinį modelį reikia papildyti netiesiniu nariu. Biojutiklis su valdoma membrana pasiteisintų, jei fiziškai neištraukiant jutiklio iš darbinės aplinkos, reikėtų perjunginėti jo darbo režimą iš difuzinio į kinetinį ir atvirkščiai.

Mediated microbial sensors utilizing two different yeast isolates (SPT1 and SPT2) were developed for the estimation of biochemical oxygen demand (BOD). Measurements of glucose/glutamic acid (GGA) standard solution with potassium ferricyanide mediation resulted in linear ranges extending from the detection limits (i.e. 2 and 5 ppm BOD) to 100 and 200 ppm BOD for the SPT1- and SPT2-based sensors, respectively. The standard error of the mean (SEW for 10 ppm. BOD measurements was 10.1% (SPT1) and 3.9% (SPT2). Response reproducibility had 10.6% error between three identically prepared SPT1 sensors. Response times for concentrations of 20 ppm BOD were within 10 minutes. For pulp mill effluent, the detection limits were 2 (SPT1) and 1 (SPT2) ppm BOD, with SEMs of 3.6% and 14.3% for the SPT1 and SPT2 sensors, respectively. Based on the results obtained in this study, it is concluded that SPT2 is the more suitable biocatalyst for pulp mill wastewater analysis. / While 18S rRNA gene sequence analyses, including BLAST homology searches, have suggested that isolate SPT1 is a close relative of Candida sojae (99.8% homology), no close matches have been found for isolate SPT2. The closest match for SPT2 was to Candida krusei (76.0% homology). Evidence from biochemical tests, fatty acid analysis, and 18S rRNA gene sequence analyses, indicates that isolate SPT2 is a novel yeast species.