Advanced CMOS Interfaces for Bio-Nanosensors

The improvement of devices provided by Nanotechnology has put forward new classes of sensors, called bio-nanosensors, which are very promising for the detection of biochemical molecules in a large variety of applications. Their use in lab-on-a-chip could gives rise to new opportunities in many fields, from health-care and bio-warfare to environmental and high-throughput screening for pharmaceutical industry. Bio-nanosensors have great advantages in terms of cost, performance, and parallelization. Indeed, they require very low quantities of reagents and improve the overall signal-to-noise-ratio due to increase of binding signal variations vs. area and reduction of stray capacitances. Additionally, they give rise to new challenges, such as the need to design high-performance low-noise integrated electronic interfaces. This thesis is related to the design of high-performance advanced CMOS interfaces for electrochemical bio-nanosensors. The main focus of the thesis is: 1) critical analysis of noise in sensing interfaces, 2) devising new techniques for noise reduction in discrete-time approaches, 3) developing new architectures for low-noise, low-power sensing interfaces. The manuscript reports a multi-project activity focusing on low-noise design and presents two developed integrated circuits (ICs) as examples of advanced CMOS interfaces for bio-nanosensors. The first project concerns low-noise current-sensing interface for DC and transient measurements of electrophysiological signals. The focus of this research activity is on the noise optimization of the electronic interface. A new noise reduction technique has been developed so as to realize an integrated CMOS interfaces with performance comparable with state-of-the-art instrumentations. The second project intends to realize a stand-alone, high-accuracy electrochemical impedance spectroscopy interface. The system is tailored for conductivity-temperature-depth sensors in environmental applications, as well as for bio-nanosensors. It is based on a band-pass delta-sigma technique and combines low-noise performance with low-power requirements.

Electrochemical surface modification of Single walled carbon nanotubes and graphene-based electrodes for (bio)sensing applications

Sensors are devices that have shown widespread use, from the detection of gas molecules to the tracking of chemical signals in biological cells. Single walled carbon nanotube (SWCNT) and graphene based electrodes have demonstrated to be an excellent material for the development of electrochemical biosensors as they display remarkable electronic properties and the ability to act as individual nanoelectrodes, display an excellent low-dimensional charge carrier transport, and promote surface electrocatalysis. The present work aims at the preparation and investigation of electrochemically modified SWCNT and graphene-based electrodes for applications in the field of biosensors. We initially studied SWCNT films and focused on their topography and surface composition, electrical and optical properties. Parallel to SWCNTs, graphene films were investigated. Higher resistance values were obtained in comparison with nanotubes films. The electrochemical surface modification of both electrodes was investigated following two routes (i) the electrografting of aryl diazonium salts, and (ii) the electrophylic addition of 1, 3-benzodithiolylium tetrafluoroborate (BDYT). Both the qualitative and quantitative characteristics of the modified electrode surfaces were studied such as the degree of functionalization and their surface composition. The combination of Raman, X-ray photoelectron spectroscopy, atomic force microscopy, electrochemistry and other techniques, has demonstrated that selected precursors could be covalently anchored to the nanotubes and graphene-based electrode surfaces through novel carbon-carbon formation.

Biogas and bio-hydrogen: production and uses. A review

The first part of this essay aims at investigating the already available and promising technologies for the biogas and bio-hydrogen production from anaerobic digestion of different organic substrates. One strives to show all the peculiarities of this complicate process, such as continuity, number of stages, moisture, biomass preservation and rate of feeding. The main outcome of this part is the awareness of the huge amount of reactor configurations, each of which suitable for a few types of substrate and circumstance. Among the most remarkable results, one may consider first of all the wet continuous stirred tank reactors (CSTR), right to face the high waste production rate in urbanised and industrialised areas. Then, there is the up-flow anaerobic sludge blanket reactor (UASB), aimed at the biomass preservation in case of highly heterogeneous feedstock, which can also be treated in a wise co-digestion scheme. On the other hand, smaller and scattered rural realities can be served by either wet low-rate digesters for homogeneous agricultural by-products (e.g. fixed-dome) or the cheap dry batch reactors for lignocellulose waste and energy crops (e.g. hybrid batch-UASB). The biological and technical aspects raised during the first chapters are later supported with bibliographic research on the important and multifarious large-scale applications the products of the anaerobic digestion may have. After the upgrading techniques, particular care was devoted to their importance as biofuels, highlighting a further and more flexible solution consisting in the reforming to syngas. Then, one shows the electricity generation and the associated heat conversion, stressing on the high potential of fuel cells (FC) as electricity converters. Last but not least, both the use as vehicle fuel and the injection into the gas pipes are considered as promising applications. The consideration of the still important issues of the bio-hydrogen management (e.g. storage and delivery) may lead to the conclusion that it would be far more challenging to implement than bio-methane, which can potentially “inherit” the assets of the similar fossil natural gas. Thanks to the gathered knowledge, one devotes a chapter to the energetic and financial study of a hybrid power system supplied by biogas and made of different pieces of equipment (natural gas thermocatalitic unit, molten carbonate fuel cell and combined-cycle gas turbine structure). A parallel analysis on a bio-methane-fed CCGT system is carried out in order to compare the two solutions. Both studies show that the apparent inconvenience of the hybrid system actually emphasises the importance of extending the computations to a broader reality, i.e. the upstream processes for the biofuel production and the environmental/social drawbacks due to fossil-derived emissions. Thanks to this “boundary widening”, one can realise the hidden benefits of the hybrid over the CCGT system.

Micro-fabrication of bio-MEMS based force sensor to measure the force response of living cells

Understanding how a living cell behaves has become a very important topic in today’s research field. Hence, different sensors and testing devices have been designed to test the mechanical properties of these living cells. This thesis presents a method of micro-fabricating a bio-MEMS based force sensor which is used to measure the force response of living cells. Initially, the basic concepts of MEMS have been discussed and the different micro-fabrication techniques used to manufacture various MEMS devices have been described. There have been many MEMS based devices manufactured and employed for testing many nano-materials and bio-materials. Each of the MEMS based devices described in this thesis use a novel concept of testing the specimens. The different specimens tested are nano-tubes, nano-wires, thin film membranes and biological living cells. Hence, these different devices used for material testing and cell mechanics have been explained. The micro-fabrication techniques used to fabricate this force sensor has been described and the experiments preformed to successfully characterize each step in the fabrication have been explained. The fabrication of this force sensor is based on the facilities available at Michigan Technological University. There are some interesting and uncommon concepts in MEMS which have been observed during this fabrication. These concepts in MEMS which have been observed are shown in multiple SEM images.

CHARACTERIZATION OF ASPHALT MATERIALS CONTAINING BIO OIL FROM MICHIGAN WOOD

The objective of this research is to develop sustainable wood-blend bioasphalt and characterize the atomic, molecular and bulk-scale behavior necessary to produce advanced asphalt paving mixtures. Bioasphalt was manufactured from Aspen, Basswood, Red Maple, Balsam, Maple, Pine, Beech and Magnolia wood via a 25 KWt fast-pyrolysis plant at 500 °C and refined into two distinct end forms - non-treated (5.54% moisture) and treated bioasphalt (1% moisture). Michigan petroleum-based asphalt, Performance Grade (PG) 58-28 was modified with 2, 5 and 10% of the bioasphalt by weight of base asphalt and characterized with the gas chromatography-mass spectroscopy (GC-MS), Fourier Transform Infra-red (FTIR) spectroscopy and the automated flocculation titrimetry techniques. The GC-MS method was used to characterize the Carbon-Hydrogen-Nitrogen (CHN) elemental ratio whiles the FTIR and the AFT were used to characterize the oxidative aging performance and the solubility parameters, respectively. For rheological characterization, the rotational viscosity, dynamic shear modulus and flexural bending methods are used in evaluating the low, intermediate and high temperature performance of the bio-modified asphalt materials. 54 5E3 (maximum of 3 million expected equivalent standard axle traffic loads) asphalt paving mixes were then prepared and characterized to investigate their laboratory permanent deformation, dynamic mix stiffness, moisture susceptibility, workability and constructability performance. From the research investigations, it was concluded that: 1) levo, 2, 6 dimethoxyphenol, 2 methoxy 4 vinylphenol, 2 methyl 1-2 cyclopentandione and 4-allyl-2, 6 dimetoxyphenol are the dominant chemical functional groups; 2) bioasphalt increases the viscosity and dynamic shear modulus of traditional asphalt binders; 3) Bio-modified petroleum asphalt can provide low-temperature cracking resistance benefits at -18 °C but is susceptible to cracking at -24 °C; 3) Carbonyl and sulphoxide oxidation in petroleum-based asphalt increases with increasing bioasphalt modifiers; 4) bioasphalt causes the asphaltene fractions in petroleum-based asphalt to precipitate out of the solvent maltene fractions; 5) there is no definite improvement or decline in the dynamic mix behavior of bio-modified mixes at low temperatures; 6) bio-modified asphalt mixes exhibit better rutting performance than traditional asphalt mixes; 7) bio-modified asphalt mixes have lower susceptibility to moisture damage; 8) more field compaction energy is needed to compact bio-modified mixes.

DEVELOPMENT OF CONFOCAL IMAGING TECHNIQUES FOR PROBING INTERFACIAL DYNAMICS IN MICROSCALE, GAS-LIQUID, TWO-PHASE FLOW

Micro-scale, two-phase flow is found in a variety of devices such as Lab-on-a-chip, bio-chips, micro-heat exchangers, and fuel cells. Knowledge of the fluid behavior near the dynamic gas-liquid interface is required for developing accurate predictive models. Light is distorted near a curved gas-liquid interface preventing accurate measurement of interfacial shape and internal liquid velocities. This research focused on the development of experimental methods designed to isolate and probe dynamic liquid films and measure velocity fields near a moving gas-liquid interface. A high-speed, reflectance, swept-field confocal (RSFC) imaging system was developed for imaging near curved surfaces. Experimental studies of dynamic gas-liquid interface of micro-scale, two-phase flow were conducted in three phases. Dynamic liquid film thicknesses of segmented, two-phase flow were measured using the RSFC and compared to a classic film thickness deposition model. Flow fields near a steadily moving meniscus were measured using RSFC and particle tracking velocimetry. The RSFC provided high speed imaging near the menisci without distortion caused the gas-liquid interface. Finally, interfacial morphology for internal two-phase flow and droplet evaporation were measured using interferograms produced by the RSFC imaging technique. Each technique can be used independently or simultaneously when.

NON-CHROMATOGRAPHIC PURIFICATION OF SYNTHETIC BIO-OLIGOMERS

Synthetic oligonucleotides and peptides have found wide applications in industry and academic research labs. There are ~60 peptide drugs on the market and over 500 under development. The global annual sale of peptide drugs in 2010 was estimated to be $13 billion. There are three oligonucleotide-based drugs on market; among them, the FDA newly approved Kynamro was predicted to have a $100 million annual sale. The annual sale of oligonucleotides to academic labs was estimated to be $700 million. Both bio-oligomers are mostly synthesized on automated synthesizers using solid phase synthesis technology, in which nucleoside or amino acid monomers are added sequentially until the desired full-length sequence is reached. The additions cannot be complete, which generates truncated undesired failure sequences. For almost all applications, these impurities must be removed. The most widely used method is HPLC. However, the method is slow, expensive, labor-intensive, not amendable for automation, difficult to scale up, and unsuitable for high throughput purification. It needs large capital investment, and consumes large volumes of harmful solvents. The purification costs are estimated to be more than 50% of total production costs. Other methods for bio-oligomer purification also have drawbacks, and are less favored than HPLC for most applications. To overcome the problems of known biopolymer purification technologies, we have developed two non-chromatographic purification methods. They are (1) catching failure sequences by polymerization, and (2) catching full-length sequences by polymerization. In the first method, a polymerizable group is attached to the failure sequences of the bio-oligomers during automated synthesis; purification is achieved by simply polymerizing the failure sequences into an insoluble gel and extracting full-length sequences. In the second method, a polymerizable group is attached to the full-length sequences, which are then incorporated into a polymer; impurities are removed by washing, and pure product is cleaved from polymer. These methods do not need chromatography, and all drawbacks of HPLC no longer exist. Using them, purification is achieved by simple manipulations such as shaking and extraction. Therefore, they are suitable for large scale purification of oligonucleotide and peptide drugs, and also ideal for high throughput purification, which currently has a high demand for research projects involving total gene synthesis. The dissertation will present the details about the development of the techniques. Chapter 1 will make an introduction to oligodeoxynucleotides (ODNs), their synthesis and purification. Chapter 2 will describe the detailed studies of using the catching failure sequences by polymerization method to purify ODNs. Chapter 3 will describe the further optimization of the catching failure sequences by polymerization ODN purification technology to the level of practical use. Chapter 4 will present using the catching full-length sequence by polymerization method for ODN purification using acid-cleavable linker. Chapter 5 will make an introduction to peptides, their synthesis and purification. Chapter 6 will describe the studies using the catching full-length sequence by polymerization method for peptide purification.

Application of self-organizing techniques for the distribution of heterogeneous multi-tasks in multi-robot systems

This paper focuses on the general problem of coordinating of multi-robot systems, more specifically, it addresses the self-election of heterogeneous and specialized tasks by autonomous robots. In this regard, it has proposed experimenting with two different techniques based chiefly on selforganization and emergence biologically inspired, by applying response threshold models as well as ant colony optimization. Under this approach it can speak of multi-tasks selection instead of multi-tasks allocation, that means, as the agents or robots select the tasks instead of being assigned a task by a central controller. The key element in these algorithms is the estimation of the stimuli and the adaptive update of the thresholds. This means that each robot performs this estimate locally depending on the load or the number of pending tasks to be performed. It has evaluated the robustness of the algorithms, perturbing the number of pending loads to simulate the robot’s error in estimating the real number of pending tasks and also the dynamic generation of loads through time. The paper ends with a critical discussion of experimental results.

An eco-friendly way to fire retardant flexible polyurethane foam: layer-by-layer assembly of fully bio-based substances

The objective of the present study is to develop fully renewable and environmentally benign techniques for improving the fire safety of flexible polyurethane foams (PUFs). A multilayered coating made from cationic chitosan (CS) and anionic alginate (AL) was deposited on PUFs through layer-by-layer assembly. This coating system exhibits a slight influence on the thermal stability of PUF, but significantly improves the char formation during combustion. Cone calorimetry reveals that 10 CS-AL bilayers (only 5.7% of the foams weight) lead to a 66% and 11% reduction in peak heat release rate and total heat release, respectively, compared with those of the uncoated control. The notable decreased fire hazards of PUF are attributed to the CS-AL coatings being beneficial to form an insulating protective layer on the surface of burning materials that inhibits the oxygen and heat permeation and slows down the flammable gases in the vapor phase, and thereby improves the flame resistance. This water-based, environmentally benign natural coating will stimulate further efforts in improving fire safety for a variety of polymer substrates.

Uncertainty in optical bio-sensors due to the spectral displacement of the interference modes of the transduction signal. Incertidumbre en bio-sensores ópticos asociada al desplazamiento espectral de los modos de interferencia de la señal de transducción

The analysis of the interference modes has an increasing application, especially in the field of optical biosensors. In this type of sensors, the displacement Δν of the interference modes of the transduction signal is observed when a particular biological agent is placed over the biosensor. In order to measure this displacement, the position of a maximum (or a minimum) of the signal must be detected before and after placing the agent over the sensor. A parameter of great importance for this kind of sensors is the period Pν of the signal, which is inversely proportional to the optical thickness h0 of the sensor in the absence of the biological agent. The increase of this period improves the sensitivity of the sensor but it worsens the detection of the maximum. In this paper, authors analyze the propagation of uncertainties in these sensors when using least squares techniques for the detection of the maxima (or minima) of the signal. Techniques described in supplement 2 of the ISO-GUM Guide are used. The result of the analysis allows a metrological educated answer to the question of which is the optimal period Pν of the signal. El análisis del comportamiento de los modos de interferencia tiene una aplicación cada vez más amplia, especialmente en el campo de los biosensores ópticos. En este tipo de sensores se observa el desplazamiento Δν de los modos de interferencia de la señal de transducción al reconocer un de-terminado agente biológico. Para medir ese desplazamiento se debe detectar la posición de un máximo o mínimo de la señal antes y después de dicho desplazamiento. En este tipo de biosensores un parámetro de gran importancia es el periodo Pν de la señal el cual es inversamente proporcional al espesor óptico h0 del sensor en ausencia de agente biológico. El aumento de dicho periodo mejora la sensibilidad del sensor pero parece dificultar la detección del mínimo o máximo. Por tanto, su efecto sobre la incertidumbre del resultado de la medida presenta dos efectos contrapuestos: la mejora de la sensibilidad frente a la dificultad creciente en la detección del mínimo ó máximo. En este trabajo, los autores analizan la propagación de incertidumbres en estos sensores utilizando herramientas de ajuste por MM.CC. para la detección de los mínimos o máximos de la señal y técnicas de propagación de incertidumbres descritas en el suplemento 2 de la Guía ISO-GUM. El resultado del análisis permite dar una respuesta, justificada desde el punto de vista metrológico, de en que condiciones es conveniente o no aumentar el periodo Pν de la señal.

Bio-climatic Design Handbook: designing public space to reach urban sustainability.

The "Bio-climatic Design Handbook: guidelines for the development of planning regulations" is a tool for urban planning and design professionals planning for the construction of public space taking into account bioclimatic and environmental standards. Based on environmental conditions assessment, urban design guidelines are given. These take into account various scales; from the territory to the microclimatic reality. From these general keys for the design of public space the handbook performs recommendations on specific case studies. The application of bioclimatic techniques in urban design promotes comfort in the public space and the respect for the existing environment, while it influences the energy consumption of buildings that conform this open space. The tool was developed in the context of BIOURB project, where Spain and Portugal cooperate writing this bilingual handbook. The case studies are located in this cross-border region.

Footwear bio-modelling: An industrial approach

There is a growing need within the footwear sector to customise the design of the last from which a specific footwear style is to be produced. This customisation is necessary for user comfort and health reasons, as the user needs to wear a suitable shoe. For this purpose, a relationship must be established between the user foot and the last with which the style will be made; up until now, no model has existed that integrates both elements. On the one hand, traditional customised footwear manufacturing techniques are based on purely artisanal procedures which make the process arduous and complex; on the other hand, geometric models proposed by different authors present the impossibility of implementing them in an industrial environment with limited resources for the acquisition of morphometric and structural data for the foot, apart from the fact that they do not prove to be sufficiently accurate given the non-similarity of the foot and last. In this paper, two interrelated geometric models are defined, the first, a bio-deformable foot model and the second, a deformable last model. The experiments completed show the goodness of the model, with it obtaining satisfactory results in terms of comfort, efficiency and precision, which make it viable for use in the sector.

(Bio)funcionalização de superfícies nanoestruturadas para eletrocatálise e desenvolvimento de biossensores eletroquímicos e óticos

Tese de doutoramento, Química (Química Física), Universidade de Lisboa, Faculdade de Ciências, 2016

The development and optimisation of a fast pyrolysis process for bio-oil production

A two-tier study is presented in this thesis. The first involves the commissioning of an extant but at the time, unproven bubbling fluidised bed fast pyrolysis unit. The unit was designed for an intended nominal throughput of 300 g/h of biomass. The unit came complete with solids separation, pyrolysis vapour quenching and oil collection systems. Modifications were carried out on various sections of the system including the reactor heating, quenching and liquid collection systems. The modifications allowed for fast pyrolysis experiments to be carried out at the appropriate temperatures. Bio-oil was generated using conventional biomass feedstocks including Willow, beechwood, Pine and Miscanthus. Results from this phase of the research showed however, that although the rig was capable of processing biomass to bio-oil, it was characterised by low mass balance closures and recurrent operational problems. The problems included blockages, poor reactor hydrodynamics and reduced organic liquid yields. The less than optimal performance of individual sections, particularly the feed and reactor systems of the rig, culminated in a poor overall performance of the system. The second phase of this research involved the redesign of two key components of the unit. An alternative feeding system was commissioned for the unit. The feed system included an off the shelf gravimetric system for accurate metering and efficient delivery of biomass. Similarly, a new bubbling fluidised bed reactor with an intended nominal throughput of 500g/h of biomass was designed and constructed. The design leveraged on experience from the initial commissioning phase with proven kinetic and hydrodynamic studies. These units were commissioned as part of the optimisation phase of the study. Also as part of this study, two varieties each, of previously unreported feedstocks namely Jatropha curcas and Moringa olifiera oil seed press cakes were characterised to determine their suitability as feedstocks for liquid fuel production via fast pyrolysis. Consequently, the feedstocks were used for the production of pyrolysis liquids. The quality of the pyrolysis liquids from the feedstocks were then investigated via a number of analytical techniques. The oils from the press cakes showed high levels of stability and reduced pH values. The improvements to the design of the fast pyrolysis unit led to higher mass balance closures and increased organic liquid yields. The maximum liquid yield obtained from the press cakes was from African Jatropha press cake at 66 wt% on a dry basis.

Analytical techniques for the study of soft contact lens spoilation

Soft contact lens wear has become a common phenomenon in recent times. The contact lens when placed in the eye rapidly undergoes change. A film of biological material builds up on and in the lens matrix. The long term wear characteristics of the lens ultimately depend on this process. With time distinct structures made up of biological material have been found to build up on the lens. A fuller understanding of this process and how it relates to the lens chemistry could lead to contact lenses that are better tolerated by the eye. The tear film is a complex biological fluid, it is this fluid that bathes the lens during wear. It is reasonable to suppose that it is material derived from this source that accumulates on the lens. To understand this phenomenon it was decided to investigate the make up and conformation of the protein species that are found on and in the lens. As inter individual variations in tear fluid composition have been found it is important to be able to study the proteins on a single lens. Many of the analytical techniques used in bio research are not suitable for this study because of the lack of sensitivity. Work with poly acrylamide electrophoresis showed the possibility of analyzing the proteins extracted from a single lens. The development of a biotin avidin electro-blot and an enzyme linked aniibody electro-blot, lead to the high sensitivity detection and identification of the proteins present. The extraction of proteins from a lens is always incomplete. A method that analyses the proteins in situ would be a great advancement. Fourier transform infra red microscopy was developed to a point where a thin section of a contact lens could yield information about the proteins present and their conformation. The three dimensional structure of the gross macroscopic structures termed white spots was investigated using confocal laser microscopy.