This thesis treats the development of an integrated optical sensor array. The sensors are slot-waveguide ring resonators, integrated with on-chip surface grating couplers and light splitters, for alignment tolerant, real-time, refractive index sensing, and label-free biosensing. The work includes: the design of components and system layouts, the development of fabrication methods, the fabrication of sensor chips, the characterization of the chips, and the development of physical system models for accurate extraction of resonance wavelengths in measured spectra. The main scientific achievements include: The evaluation of a novel type of nano-structured optical waveguide for biochemical sensing. The realization of an array of such slot-waveguide sensors, integrated with microfluidic sample handling, for multiplex assays. The first study of the thermal behavior of slot-waveguide sensors and the discovery of unique temperature compensation capabilities. From an application perspective, the use of alignment tolerant surface gratings to couple light into the optical chip enables quick replacement of cartridges in the read-out instrument. Furthermore, the fabrication sequence avoids polishing of individual chips, and thus ensures that the cost benefits of silicon batch micro-fabrication can be leveraged in mass production. The high sensitivity of the slot waveguide resonators, combined with on-chip referencing and physical modeling, yields low limits of detection. The obtained volume refractive index detection limit of 5 × 10−6 refractive index units (RIU), and the surface mass density detection limit of 0.9 pg/mm2, shows that performance comparable to that of commercial non-integrated surface plasmon resonance sensors, made from bulk optical components, canbe achieved in a compact cartridge. / Qc20100715 / SABIO

Studies on genetic variation can reveal effects on traits and disease, both in humans and in model organisms. Good technology for the analysis of DNA sequence variations is critical. Currently the development towards assays for large-scale and parallel DNA sequencing and genotyping is progressing rapidly. Single base primer extension (SBE) is a robust reaction principle based on four-colour fluorescent terminating nucleotides to interrogate all four DNA nucleotides in a single reaction. In this thesis, SBE methods were applied to the analysis and discovery of single nucleotide polymorphism (SNP) in the model organism Drosophila melanogaster and in humans. The tag-array minisequencing system in a microarray format is convenient for intermediate sized genotyping projects. The system is scalable and flexible to adapt to specialized and novel applications. In Study I of the thesis a tool was established to automate quality control of clustered genotype data. By calculating “Silhouette scores”, the SNP genotype assignment can be evaluated by a single numeric measure. Silhouette scores were then applied in Study I to compare the performance of four DNA polymerases and in Study III to evaluate freeze-dried reagents in the tag-array minisequencing system. The characteristics of the tag-array minisequencing system makes it suitable for inexpensive genome-wide gene mapping in the fruit fly. In Study II a high-resolution SNP map, and 293 genotyping assays, were established across the X, 2nd and 3rd chromosomes to distinguish commonly used Drosophila strains. A database of the SNP markers and a program for automatic allele calling and identification of map positions of mutants was also developed. The utility of the system was demonstrated by rapid mapping of 14 genes that disrupt embryonic muscle patterning. In Study III the tag-array minisequencing system was adapted to a lab-on-a-chip format for diagnostic testing for mutations in the TP53 gene. Freeze-drying was evaluated for storing reagents, including thermo-sensitive enzymes, on the microchip to reduce the complexity of the integrated test. Correct genotyping results were obtained using freeze-dried reagents in each reaction step of the genotyping protocol, both in test tubes and in single polymer test chambers. The results showed the potential of the approach to be implemented in fully integrated systems. The four-colour chemistry of SBE has been developed further to allow massively parallel sequencing (MPS) of short DNA fragments as in the Genome Analyzer system (Solexa/Illumina). In Study IV MPS was used to compare Nimblegen arrays and the SureSelect solution-based system for targeted enrichment of 56 continuous human candidate-gene regions totalling 3.1 Mb in size. Both methods detected known SNPs and discovered novel SNPs in the target regions, demonstrating the feasibility for complexity reduction of sequencing libraries by hybridization methods.

Bacteria are the oldest, structurally simplest, and most abundant forms of life on earth. Its detection has always been a serious question since the emerging of modern science and technology. There has been a phenomenal growth in the field of real-time bacteria detection in recent years with emerging applications in a wide range of disciplines, including medical analysis, food, environment and many more. Two important analytical functions involved in bacteria detection are cell lysis and polymerase chain reaction (PCR). Cell lysis is required to break cells open to release DNA for use in PCR. PCR is required to reproduce millions of copies of the target genes to reach detection limit from a low DNA concentration. Conventionally, cell lysis and PCR are performed separately using specialized equipments. Those bulky machines consume much more than needed chemical reagents and are very time consuming. An efficient, cost-effective and portable solution involving Nanotechnology and Lab-on-a-Chip (LOC) technology was proposed. The idea was to utilize the excellent antibacterial property of surface-functionalized nanoparticles to perform cell lysis and then to perform PCR on the same LOC system without having to remove them from the solution for rapid detection of bacteria. Nanoparticles possess outstanding properties that are not seen in their bulk form due to their extremely small size. They were introduced to provide two novel methods for LOC cell lysis to overcome problems of current LOC cell lysis methods such as low efficiency, high cost and complicated fabrication process. The first method involved using poly(quaternary ammonium) functionalized gold and titanium dioxide nanoparticles which were demonstrated to be able to lyse E. coli completely in 10 minutes. The idea originated from the excellent antibacterial property of quaternary ammonium salts that people have been using for a long time. The second method involved using titanium dioxide nanoparticles and a miniaturized UV LED array. Titanium dioxide bears photocatalytic effect which generates highly reactive radicals to compromise cell membranes upon absorbing UV light in an aqueous environment. A considerable reduction of live E. coli was observed in 60 minutes. The thesis then evaluates the effect of nanoparticles on PCR to understand the roles nanoparticles play in PCR. It was found that gold and titanium dioxide nanoparticles induce PCR inhibition. How size of gold nanoparticles affected PCR was studied as well. Effective methods were discovered to suppress PCR inhibition caused by gold and titanium dioxide nanoparticles. The pioneering work paves a way for the integration of nanoparticle cell lysis and LOC PCR for rapid detection of bacteria. In the end, an integrated system involving nanoparticle cell lysis and microchip PCR was demonstrated. The prototyped system consisted of a physical microchip for both cell lysis and PCR, a temperature control system and necessary interface connections between the physical device and the temperature control system. The research explored solutions to improve PCR specificity in a microchip environment with gold nanoparticles in PCR. The system was capable of providing the same performance while reducing PCR cycling time by up to 50%. It was inexpensive and easy to be constructed without any complicated clean room fabrication processes. It can find enormous applications in water, food, environment and many more.

Determination of bio-material by using enzyme, fluorophore or metal-nanoparticles as markers is very important. Generally, gold-nanoparticles have been used frequently as marker for increasing the sensitivity in bio-chemical assay. In this research, gold-nanoparticles were used as marker for immunoassay, DNA sequence assay, and protein analysis. However, the size of gold-nanoparticles affects directly the results of electrochemical detection. For improving the sensitivity of electrochemical method, enlargement of gold-nanoparticles was used in this study. By electroless deposition, Au will be deposited on the surface of gold-nanoparticles. The electrochemical response will thus be increased substantially. In immunoassay and DNA sequence assay, traditional 96-wells microtiter plate was used for immobilizing antibody or oligonucleotide, and the gold-nanoparticles were marked subsequently base on the immunoreaction or protein reaction of streptavidin and biotin. After gold-nanoparticles were enlarged, they were dissolved and transferred to an electrochemical cell for square wave stripping voltammetry¡]SWSV¡^analysis. Under optimal experimental condition, dynamic range of 1 ~ 500 pg/mL and 0.52 ~ 1300 aM were found respectively for RIgG and Target DNA analysis, and a good linear relationship¡]R2 = 0.9975 and 0.9982¡^. The relative standard deviation¡]R.S.D.¡^ of blank were 2.8 % and 2.4 %¡]n = 11¡^for immunoassay and DNA assay, respectively. And the variance was 2.4 %¡]n = 9¡^and 2.4 %¡]n = 12¡^for immunoassay and DNA assay, respectively. The detection limit¡]based on S/N = 3¡^of RIgG and DNA were 0.25 pg/mL and 0.52 aM, respectively. They are very competitive compared with similar results reported in the literature. Additional, a gold nanoelectrode ensemble¡]GNEE¡^coupled microchip system was developed for bio-electrochemical analysis. Due to the difference in mobility of urea and urease were mixed and allowed the enzymatic reaction to proceed in microchannel. The enzymatic product NH4+ was determined by the coupled GNEE at the outlet of the channel. Another experiment of streptavidin conjugated gold-nanoparticles¡]streptavidin-Au¡^, reductant and gold-ion¡]Au3+¡^solution was be applied here, too. The product, NH4+ or Au3+ was passed through downstream of microchannel and detected by GNEE of electrochemical system. Satisfactory linear relationship¡]R2 = 0.9778 and 0.9657¡^were found from 0.1 mM to 50 mM for NH4+ and urea in the range of 0.02 mM to 5.0 mM, respectively. The other satisfactory linear relationship¡]R2 = 0.9842 and 0.9507¡^ were found between 3.75 mg/mL and 3.75 g/mL for Au3+ and streptavidin-Au in the range of 0.2 ng/mL to 100 ng/mL, respectively. Variances of 2.5 %¡]n = 6¡^was found for analysis of with the microchip system.

This thesis presents analysis, design, implementation, and testing of electrostatically actuated MEMS microvalves. The microvalves are specifically designed for lab-on-a-chip applications to achieve leakage ratios below 0.1 at pressure levels in the order of 101 kPa. For this purpose, two different microvalves are presented in the study. In the proposed designs, electrostatic actuation scheme is utilized to operate the microvalves in normally open and normally closed modes. Characterization of normally open microvalves show that, microvalves with radii ranging between 250

<p>Flow-based microfluidic biochips constitute an emerging technology for the automation of biochemical procedures. Recent advances in fabrication techniques have enabled the development of these devices. Increasing integration levels provide biochips with tremendous potential; a large number of bioassays, i.e., protocols for biochemistry, can be processed independently, simultaneously, and automatically on a coin-sized microfluidic platform. However, the increases in integration level introduce new challenges in the design optimization and the testing of these devices, which impede their further adoption and deployment.</p><p>This thesis is focused on enhancing the automated design and use of flow-based microfluidic biochips and on developing a set of solutions to facilitate the full exploitation of design complexities that are possible with current fabrication techniques. Four key research challenges are addressed in the thesis; these include design automation, wash optimization, testing, and defect diagnosis.</p><p>Despite the increase in the number of on-chip valves, designers are still using full-custom methodologies involving many manual steps to implement these chips. Since these chips can easily have thousands of valves, manual design procedure can be time-consuming and error-prone, and it can result in inefficient designs. This thesis presents the first problem formulation for automated control-layer design in flow-based microfluidic biochips and describes a systematic approach for solving this problem. Our goal is to find an efficient routing solution for control-layer design with a minimum number of control pins.</p><p>The problem of contamination removal in flow-based microfluidic biochips must also be addressed. Applications in biochemistry require high precision to avoid erroneous assay outcomes, and they are vulnerable to contamination between two fluidic flows with different biochemistries. This thesis proposes the first approach for automated wash optimization for contamination removal in flow-based microfluidic biochips. The proposed approach ensures effective cleaning and targets the generation of wash pathways to clean all contaminated microchannels with minimum execution time under physical constraints.</p><p>Another practical problem addressed in this thesis is the lack of test techniques for screening defective biochips before they are used for biochemical analysis. This thesis presents an efficient approach for automated testing of flow-based microfluidic biochips. The test technique is based on a behavioral abstraction of physical defects in microchannels and valves. The flow paths and flow control in the microfluidic device are modeled as a logic circuit composed of Boolean gates, which allows test generation to be carried out using standard automatic test-pattern generation tools. Based on the analysis of untestable faults in the logic-circuit model, we present a design-for-testability technique that can achieve 100\% fault coverage.</p><p>Finally, this thesis presents a technique for the automated diagnosis of leakage and blockage defects. The proposed method targets the identification of defect types and their locations based on test outcomes. It reduces the number of possible defect sites significantly while identifying their exact locations.</p><p>In summary, this thesis has led to a set of optimization and testing methods for flow-based microfluidic biochips. The results of this research are expected to not only shorten the product development cycle, but also accelerate the adoption and further development of this emerging technology by facilitating the full exploitation of design complexities that are possible with current fabrication techniques.</p> / Dissertation

Term of remote-lab is certain types of laboratories which practical experiments are directedfrom a separate area by remote controller devices. This study is part of developing andupgrading advanced vibration remote laboratory. In the new remote lab, users have theability to measure the dynamic characteristics of the test object similar to the current existingremote lab. But in addition to current existing remote lab, they are capable to modifydynamic properties of the test object remotely by attaching vibration test instruments; such asa block of mass, spring-mass or non-linear spring. Doing several accurate experimental testsremotely on the test object are the toughest issues we faced as designers. In creating anddeveloping of this remote-lab, number of different approaches was adopted for producingwell-defined tests. Also, instead of implementing routine devices and techniques for regularvibration laboratories, the new prototypes were designed by finite elements method (FEM)and LABVIEW. For instance, the desirable test object, the attachment mechanism, usefulapplications, and proper software for managing via internet were prepared.

Τα συστήματα μοριακής διαγνωστικής έχουν έρθει στο προσκήνιο τα τελευταία χρόνια δίνοντας τη δυνατότητα για αυτοματοποιημένες, αξιόπιστες, γρήγορες και χαμηλού κόστους βιολογικές αναλύσεις. Τέτοια συστήματα χαρακτηρίζονται από σύνθετη λειτουργικότητα, η οποία συνδυάζει πληθώρα ενεργοποιητών και αισθητήρων που συνεργάζονται για την εκτέλεση βιολογικών πρωτοκόλλων. Με βάση τα πρωτόκολλα αυτά και με τη χρήση μικροροϊκών συστημάτων, τα βιολογικά δείγματα και αντιδραστήρια υποβάλλονται σε διάφορα στάδια επεξεργασίας. Κατόπιν της επεξεργασίας τους, τα δείγματα υπό μελέτη καταλήγουν πάνω στην επιφάνεια αισθητήρων, οι οποίοι είναι ειδικά ευαισθητοποιημένοι ώστε να ανιχνεύουν συγκεκριμένες βιολογικές αλληλεπιδράσεις ενδιαφέροντος και να αποκρίνονται μεταβάλλοντας αναλόγως ένα φυσικό μέγεθος, μετρήσιμο από ηλεκτρονικά κυκλώματα. Τα ηλεκτρονικά κυκλώματα ανάγνωσης των αισθητήρων αποτελούν ένα από τα κυριότερα τμήματα ενός συστήματος μοριακής διαγνωστικής, καθώς βάσει της απόκρισης αυτών προκύπτουν τα διαγνωστικά αποτελέσματα. Κατά συνέπεια, αναγνωρίζεται ο σημαντικός ρόλος που κατέχουν στη συνολική αναλυτική διαδικασία. Είναι απαραίτητο οι μετρήσεις που εκτελούν να χαρακτηρίζονται από μεγάλη ακρίβεια με υψηλή διακριτική ικανότητα για κάθε αισθητήριο στοιχείο. Ταυτόχρονα όμως, πρέπει να εξασφαλίζεται και η αξιοπιστία της μέτρησης σε επίπεδο βιολογικής διεργασίας. Σε αυτό το στόχο συντελεί η χρήση συστοιχιών αισθητήρων, με τις οποίες η ίδια μέτρηση μπορεί να εκτελεστεί παράλληλα σε πολλά στοιχεία και συνοδεύεται από μετρήσεις θετικού και αρνητικού ελέγχου. Πάνω στη συστοιχία μπορούν να εκτελεστούν και συμπληρωματικές μετρήσεις περισσότερων δειγμάτων, ώστε τα αποτελέσματα που εξάγονται να δίνουν μια πιο ολοκληρωμένη αναλυτική εικόνα. Υπό αυτό το πρίσμα, οι μεγάλου μεγέθους συστοιχίες αισθητήρων μπορούν να προσφέρουν βέλτιστα αποτελέσματα. Η παρούσα διδακτορική διατριβή επικεντρώνεται στα κυκλώματα ανάγνωσης συστοιχιών χωρητικών και ηλεκτροχημικών αισθητήρων, δύο ευρέως χρησιμοποιούμενων τεχνολογιών αισθητήρων. Η αρχή λειτουργίας των χωρητικών αισθητήρων βασίζεται στο γεγονός ότι οι αλληλεπιδράσεις βιομορίων που μελετούνται ασκούν δυνάμεις και παραμορφώνουν την ευέλικτη μεμβράνη πυριτίου που αποτελεί τον έναν οπλισμό ενός μεταβλητού πυκνωτή. Συνέπεια αυτής της παραμόρφωσης είναι η ανάλογη μεταβολή της χωρητικότητας που παρουσιάζει η μεμβράνη με το υπόστρωμα πυριτίου, μεταβολή που μετράται από το κύκλωμα. Στην περίπτωση των ηλεκτροχημικών αισθητήρων, η αντίστοιχη αλληλεπίδραση βιομορίων, με τη βοήθεια βιομορίων σήμανσης, προκαλεί τη μεταβολή της αγωγιμότητας μεταξύ των ηλεκτροδίων τους. Υπό ελεγχόμενες συνθήκες πόλωσης τάσης, το αναπτυσσόμενο ρεύμα που μετράται αντιστοιχεί στην εξέλιξη του βιολογικού φαινομένου. Ιδιαίτερη έμφαση δίνεται στις δυνατότητες κλιμάκωσης της εκάστοτε αρχιτεκτονικής ώστε να είναι επεκτάσιμη στην ανάγνωση πολύ μεγάλων συστοιχιών αισθητήρων με βέλτιστο τρόπο, διατηρώντας μικρές διαστάσεις για τα κυκλώματα ανάγνωσης. Συγχρόνως, εξασφαλίζεται με διάφορες στρατηγικές η ορθή λήψη μετρήσεων από κάθε στοιχείο, χωρίς την επίδραση από τα υπόλοιπα μέλη της συστοιχίας. Για την ανάγνωση συστοιχιών χωρητικών αισθητήρων σχεδιάστηκε και υλοποιήθηκε ολοκληρωμένο κύκλωμα σε τεχνολογία 0.35 μm, που στον πυρήνα της μέτρησης διαθέτει έναν ταλαντωτή χαλάρωσης με βρόχο υστέρησης ρεύματος. Υποστηρίζεται από προγραμματιζόμενες πηγές ρεύματος διέγερσης ώστε να καλύπτεται ένα ευρύ φάσμα χωρητικοτήτων για τους αισθητήρες. Το σύστημα πολύπλεξης που αναπτύχθηκε για τη διασύνδεση κάθε μέλους από τις συστοιχίες αισθητήρων πάνω στον πυρήνα ανάγνωσης μπορεί να διαχειριστεί πεπλεγμένες συστοιχίες, όπου τα στοιχεία είναι οργανωμένα με κοινές γραμμές και στήλες ηλεκτρικών επαφών στους οπλισμούς τους. Με αυτόν τον τρόπο είναι δυνατή η δημιουργία μεγάλων συστοιχιών με μικρό πλήθος ακροδεκτών διασύνδεσης. Η πρόκληση της ανάγνωσης τέτοιου είδους συστοιχιών έγκειται στις αλληλεπιδράσεις μεταξύ των στοιχείων, λόγω ανεπιθύμητων μονοπατιών στο ρεύμα φόρτισης του ταλαντωτή. Μία πρώτη αντιμετώπιση αυτού του προβλήματος διαφωνίας γίνεται με τη χρήση διακοπτών δύο καταστάσεων στις μονάδες πολύπλεξης, ώστε να ελέγχεται ο τρόπος με τον οποίο διεγείρεται το μετρούμενο καθώς και τα υπόλοιπα στοιχεία κατά τη μέτρηση. Με διαδοχικές μετρήσεις υπό διαφορετικές συνδεσμολογίες στους πολυπλέκτες και με κατάλληλη μαθηματική επεξεργασία, μπορούν να εξαχθούν ακριβείς μετρήσεις για την κατάσταση κάθε αισθητήρα της συστοιχίας. Η στατικότητα του συστήματος κατά τη διάρκεια των διαδοχικών μετρήσεων που είναι προϋπόθεση για το σωστό υπολογισμό των αποτελεσμάτων, βασίζεται στην ιδιαίτερα αργή εξέλιξη των βιολογικών φαινομένων στην επιφάνεια των αισθητήρων. Στα πλαίσια της διατριβής έγινε και ένας επανασχεδιασμός του κυκλώματος ανάγνωσης συστοιχιών, σε επίπεδο σχηματικού και φυσικού σχεδιασμού, του οποίου η λειτουργία επιβεβαιώθηκε με post-layout εξομοιώσεις. Σε αυτή την ανάπτυξη έγινε προσθήκη επιπλέον υπομονάδων και η βελτίωση των υπαρχουσών. Από τα κύρια χαρακτηριστικά αυτού του σχεδιασμού είναι μια μονάδα απομονωτή, που προσφέρει έναν δεύτερο τρόπο αντιμετώπισης του προβλήματος διαφωνίας μεταξύ των στοιχείων, αποτρέποντας το ρεύμα φόρτισης του ταλαντωτή να οδηγηθεί προς μη επιθυμητά στοιχεία. Επιπλέον, οι μονάδες ταλάντωσης που χρησιμοποιεί το επανασχεδιασμένο κύκλωμα είναι δύο, για ταυτόχρονη ανάγνωση αισθητήρων και ταχύτερη σάρωση μεγάλων συστοιχιών, με το εύρος του προγραμματιζόμενου ρεύματος να είναι μεγαλύτερο, καλύπτοντας μεγαλύτερο φάσμα αισθητήρων. Τέλος, αυτή η έκδοση του κυκλώματος έχει πιο αυτόνομο χαρακτήρα, με την ενσωμάτωση ενός υποσυστήματος σειριακής επικοινωνίας και ελέγχου. Για τη δεύτερη τεχνολογία αισθητήρων που καλύπτει η παρούσα διατριβή, των ηλεκτροχημικών αισθητήρων, σχεδιάστηκαν και υλοποιήθηκαν κυκλώματα ανάγνωσης συστοιχιών με χρήση διακριτών στοιχείων, καθώς επίσης και κυκλώματα με το βασικό πυρήνα μέτρησης να υλοποιείται σε ολοκληρωμένη μορφή με τεχνολογία 90 nm. Για τους σχεδιασμούς αυτούς έχει αναπτυχθεί η τεχνική της υβριδικής πολύπλεξης, βάσει της οποίας τα μέλη της συστοιχίας ομαδοποιούνται καταλλήλως, ώστε να επιτευχθούν οι απαιτούμενες επιδόσεις σε ρυθμούς δειγματοληψίας από το κύκλωμα ανάγνωσης, ενώ παράλληλα το μέγεθος του κυκλώματος παραμένει μικρό. Η υβριδική πολύπλεξη συνδυάζει διαδοχική ανάγνωση με παράλληλη ανάγνωση στοιχείων, κάνοντας χρήση πολυπλεκτών και κατάλληλου αριθμού υποσυστημάτων μέτρησης που επαναχρησιμοποιούνται για πολλά αισθητήρια στοιχεία. Η ιδιαιτερότητα που έχουν αυτού του τύπου οι μετρήσεις έγκειται στην απαίτηση για διαρκή πόλωση όλων των στοιχείων χωρίς διακοπή της ροής του ρεύματος μέσω αυτών, που καλύπτεται μέσω ειδικά διαμορφωμένων πολυπλεκτών δύο καταστάσεων οι οποίοι εξασφαλίζουν τις σωστές συνθήκες λειτουργίας. Επιπρόσθετες βελτιώσεις που παρέχει η υλοποίηση του κυκλώματος ανάγνωσης σε μορφή ολοκληρωμένου είναι η δυνατότητα εναλλαγής μεταξύ δύο τύπων κυκλωμάτων μέτρησης, με χρήση ενισχυτή διαντίστασης και ολοκληρωτή. Οι δύο τρόποι μέτρησης χρησιμοποιούνται συμπληρωματικά, ώστε να καλυφθεί μεγάλη δυναμική περιοχή λειτουργίας και γρήγορη απόκριση, αλλά και υψηλή ανάλυση, ανάλογα με τις απαιτήσεις κατά τη διάρκεια της πειραματικής διαδικασίας. Για το χαρακτηρισμό των κυκλωμάτων ανάγνωσης που αναπτύχθηκαν και για τις δύο τεχνολογίες αισθητήρων, έγιναν μετρήσεις με πρότυπα φορτία, καθώς και με συστοιχίες, για να εξαχθούν συμπεράσματα για την απόκρισή τους. Κατόπιν των ελέγχων καλής λειτουργίας των κυκλωμάτων και των μεθόδων που ακολουθούνται, πραγματοποιήθηκαν και επιτυχείς μετρήσεις βιολογικής σημασίας, που επιβεβαιώθηκαν από συστήματα αναφοράς. / Molecular diagnostics systems have come to the forefront in recent years allowing for automated, reliable, rapid and inexpensive bioassays. Such systems are characterized by complex functionality, which combines variety of actuators and sensors that cooperate to perform biological protocols. Based on these protocols and using microfluidic systems, biological samples and reagents are subjected to various processing steps. Following this treatment, the samples under study are placed on the surface of sensors, which are functionalized to detect specific biological interactions of interest and respond accordingly by changing a physical quantity, measurable by electronic circuits. The sensor readout electronic circuits are one of the main parts of a molecular diagnostics system, as the diagnostic results are based on their response. Consequently, it is recognized that they hold an important role in the overall analytical process. It is necessary that the measurements they perform are highly accurate with high resolution for each sensor element. At the same time, the reliability of the measurement at a biological process level must be ensured. To this aim contributes the use of sensor arrays, with which the same measurement can be performed in parallel on many elements and accompanied by positive and negative control measurements. On the array, additional measurements of multiple samples can be performed, so that the output results give a more comprehensive analytical picture. In this light, large sensor arrays can provide optimal results. This thesis focuses on the readout circuitry for capacitive and electrochemical sensor arrays, two widely used sensor technologies. The operating principle of capacitive sensors is based on the fact that the interactions between the biomolecules under study exert forces and deform the flexible silicon film constituting an armature of a variable capacitor. The consequence of this deformation is a proportional change in capacitance between the film and the silicon substrate, a variation measured by the circuit. In the case of electrochemical sensors, the respective interaction of biomolecules, with the aid of labeling biomolecules, causes a change in conductivity between their electrodes. Under controlled bias voltage conditions, the resulting current that is measured corresponds to the progress of the biological phenomenon. Particular emphasis is given to the scalability potential of each architecture, so it can be optimally expanded for reading very large sensor arrays, maintaining small dimensions for the readout circuits. At the same time, through various strategies it is ensured that measurements of each element are properly acquired, without influence from other members in the array. To read out the capacitive sensor arrays an integrated circuit based on a 0.35 μm technology was designed and implemented, which at its measuring core uses a relaxation oscillator with a current hysteresis loop. It is complemented by programmable excitation current sources to cover a wide range of capacitances for the sensors. The multiplexing system that was developed to connect each member of the sensor arrays on the readout core can handle 'entangled' arrays, where the elements are arranged with common lines and columns of electrical contacts at their armatures. In this way it is possible to create large arrays with a small number of interface terminals. The challenge of reading such arrays lies in the interactions between the elements, because of side paths in the oscillator charging current. A first way to address this crosstalk problem is the use of two-state switches in the multiplexing units, in order to control the way in which the measured element is excited, as well as the other array elements, during measurement. Through successive measurements under different connection configurations on the multiplexers and appropriate mathematical processing, accurate measurements for the status of each sensor in the array can be obtained. The measured system can be considered static during successive measurements, which is a prerequisite for the correct calculation of results, due to the very slow progress of biological phenomena on the surface of the sensors. In the course of this thesis, a redesign of the array readout circuit was made, at a schematic and physical layout design level, the function of which was confirmed by post-layout simulations. In this development extra submodules were incorporated and existing ones were improved. One of the main features of this design is a buffer unit, which offers a second way of addressing the crosstalk problem between the elements, by preventing the oscillator charging current to excite undesirable elements. Furthermore, the redesigned circuit uses two oscillation units for simultaneous sensor readout and faster scanning of large arrays, with the range of their programmable current being greater, covering a larger spectrum of sensors. Finally, this version of the circuit has a more autonomous nature, by incorporating a serial communication and control subsystem. For the second sensor technology covered by this thesis, the electrochemical sensors, array readout circuits were designed and implemented using discrete components, as well as circuits with the basic measurement core being implemented in integrated form using a 90 nm technology. For these designs the technique of hybrid multiplexing was developed, whereby the members of the array are grouped appropriately to achieve the required performance in sampling rate from the readout circuit, while the size of the circuit remains small. Hybrid multiplexing combines sequential and parallel element reading, using multiplexers and the appropriate number of measurement subsystems that are reused for many sensing elements. The particularity of this type of measurements is the requirement for continuous biasing of all elements without interruptions in the current flow through them, which is addressed by specially configured two-state multiplexers that ensure the correct operating conditions. Additional enhancements offered by the implementation of the readout circuit in integrated form is the ability to switch between two types of measurement circuits, using a transimpedance amplifier and an integrator. The two modes of measurement are used in complement, to cover a wide operating dynamic range and fast response, and also high resolution, depending on the requirements during the experimental process. For the characterization of the readout circuits developed for both sensor technologies, measurements were made using standard loads, as well as arrays, to draw conclusions about their response. Following the validation of the proper operation of the circuits and methods used, successful measurements of biological significance were made, which were confirmed by reference systems.

The Greater than Class C (GTCC) Environmental Impact Statement (EIS) evaluated the potential impacts from the construction and operation of a new facility or facilities, or use of an existing facility, employing various disposal methods (geologic repository, intermediate depth borehole, enhanced near surface trench, and above grade vault) at six federal sites and generic commercial locations. For three of the locations being considered as possible locations, consulting tribes were brought in to comment on their perceptions on how GTCC low level radioactive waste would affect Native American resources (land, water, air, plants, animals, archaeology, etc.) short and long term. The consulting tribes produced essays that were incorporated into the EIS and these essays are in turn included in this collection. This essay was produced by members of the culturally affiliated tribes to Los Alamos National Lab.

Microfluidics has seen an explosion in growth in the past few years, providing researchers with new and exciting lab-on-chip platforms with which to perform a wide variety of biological and biochemical experiments. In this work, a volume quantification tool is developed, demonstrating the ability to measure the volume of individual cells at high resolution and while enabling microfluidic sample manipulations. Care is taken to maximise measurement sensitivity, range and accuracy, though novel use of buoyancy and dynamically tunable microchannels. This first demonstration of a microfluidic tunable volume sensor meant volume sensing over a much wider range, enabling the detection of ̴ 1 µm3 E.coli that would otherwise go undetected. Software was written that enables pressure-driven flow control on the scale of individual cells, which is used to great success in (a) sorting cells based on size measurement and (b) monitoring the growth of cells. While there are a number of macroscopic techniques capable of sorting cells, microscopic lab-on-chip equivalents have only recently started to emerge. In this work, a label-free, volume sensor operating at high resolution is used in conjunction with pressure-driven flow control to actively extract particle/cell subpopulations. Next, a microfluidic growth monitoring device is demonstrated, whereby a cell is flowed back and forth through a volume sensor. The integration of sieve valves allows cell media to be quickly exchanged. The combination of dynamic trapping and rapid media exchange is an important technological contribution to the field, one that opens the door to studies focusing on cell volumetric response to drugs and environmental stimuli. This technology was designed and fabricated in-house using soft lithography techniques readily available in most biotechnology labs. The main thesis body contains four scientific articles that detail this work (Chapters 2-5), all published in peer-reviewed scientific journals. These are preceded by an introductory chapter which provides an overview to the theory underlying this work, in particular the non-intuitive physics at the microscale and the Coulter principle.