Doctor of Philosophy

dissertationSince the late 1950s, scientists have been working toward realizing implantable devices that would directly monitor or even control the human body's internal activities. Sophisticated microsystems are used to improve our understanding of internal biological processes in animals and humans. The diversity of biomedical research dictates that microsystems must be developed and customized specifically for each new application. For advanced long-term experiments, a custom designed system-on-chip (SoC) is usually necessary to meet desired specifications. Custom SoCs, however, are often prohibitively expensive, preventing many new ideas from being explored. In this work, we have identified a set of sensors that are frequently used in biomedical research and developed a single-chip integrated microsystem that offers the most commonly used sensor interfaces, high computational power, and which requires minimum external components to operate. Included peripherals can also drive chemical reactions by setting the appropriate voltages or currents across electrodes. The SoC is highly modular and well suited for prototyping in and ex vivo experimental devices. The system runs from a primary or secondary battery that can be recharged via two inductively coupled coils. The SoC includes a 16-bit microprocessor with 32 kB of on chip SRAM. The digital core consumes 350 μW at 10 MHz and is capable of running at frequencies up to 200 MHz. The integrated microsystem has been fabricated in a 65 nm CMOS technology and the silicon has been fully tested. Integrated peripherals include two sigma-delta analog-to-digital converters, two 10-bit digital-to-analog converters, and a sleep mode timer. The system also includes a wireless ultra-wideband (UWB) transmitter. The fullydigital transmitter implementation occupies 68 x 68 μm2 of silicon area, consumes 0.72 μW static power, and achieves an energy efficiency of 19 pJ/pulse at 200 MHz pulse repetition frequency. An investigation of the suitability of the UWB technology for neural recording systems is also presented. Experimental data capturing the UWB signal transmission through an animal head are presented and a statistical model for large-scale signal fading is developed

Wireless Telemetry System for Implantable Sensors

Advanced testing of medical treatments involves experimentation on small laboratory animals, such as genetically modified mice. These subjects are used to help researchers develop medication and cures for humans. To understand the effects of the treatments, innovative telemetry systems are developed, that enable remote real-time cardiac monitoring. The latest research in the field of cardiac monitoring has revealed two major limitations with wireless implantable systems: a) the current size of implantable electronics limits the physical size of the system to larger subjects; and b) the systems only interface with one sensor type (e.g., pressure sensor only). This research focuses on the design of a wireless telemetry system architecture, intended to retrieve blood pressure and volume data. A physical prototype is created that is 2.475 cm3 and weights 4.01 g. This thesis will enable a path towards miniaturization, leading to the incorporation of a wireless system into small laboratory animals

Workshop on "Robotic assembly of 3D MEMS".

Proceedings of a workshop proposed in IEEE IROS'2007.The increase of MEMS' functionalities often requires the integration of various technologies used for mechanical, optical and electronic subsystems in order to achieve a unique system. These different technologies have usually process incompatibilities and the whole microsystem can not be obtained monolithically and then requires microassembly steps. Microassembly of MEMS based on micrometric components is one of the most promising approaches to achieve high-performance MEMS. Moreover, microassembly also permits to develop suitable MEMS packaging as well as 3D components although microfabrication technologies are usually able to create 2D and "2.5D" components. The study of microassembly methods is consequently a high stake for MEMS technologies growth. Two approaches are currently developped for microassembly: self-assembly and robotic microassembly. In the first one, the assembly is highly parallel but the efficiency and the flexibility still stay low. The robotic approach has the potential to reach precise and reliable assembly with high flexibility. The proposed workshop focuses on this second approach and will take a bearing of the corresponding microrobotic issues. Beyond the microfabrication technologies, performing MEMS microassembly requires, micromanipulation strategies, microworld dynamics and attachment technologies. The design and the fabrication of the microrobot end-effectors as well as the assembled micro-parts require the use of microfabrication technologies. Moreover new micromanipulation strategies are necessary to handle and position micro-parts with sufficiently high accuracy during assembly. The dynamic behaviour of micrometric objects has also to be studied and controlled. Finally, after positioning the micro-part, attachment technologies are necessary

Integrated modular microfluidic system for forensic Alu DNA typing

Driven by the numerous applications of genome-related research, fully integrated microfluidic systems have been developed that have advanced the capabilities of molecular and, in particular, genetic analyses. A brief overview on integrated microfluidic systems for DNA analysis is given in Chapter 1 followed by a report on micro-capillary electrophoresis (µCE) of Alu elements with laser-induced fluorescence (LIF) detection, in which the monomorphic Alu insertions on the X and Y chromosomes were utilized to detect male DNA in large female DNA background (Y: X = 1:19) without cell sorting prior to the determination. The polymorphic Alu loci with known restricted geographical distribution were used for ethnicity determination. A valveless integrated microsystem that consists of three modules is discussed as well: (1) A solid-phase extraction (SPE) module microfabricated on polycarbonate, for DNA extraction from whole cell lysates (extraction bed capacity ~209 ±35.6 ng/cm² of total DNA). (2) A continuous-flow polymerase chain reaction (CFPCR) module fabricated in polycarbonate (Tg ~150 ºC) in which selected gene fragments were amplified using biotin and fluorescently-labeled primers accomplished by continuously shuttling small packets of PCR reagents and template through isothermal zones. (3) µCE module fabricated in poly(methylmethacrylate), which utilized a bioaffinity selection and purification bed (2.9-µL) to preconcentrate and purify the PCR products generated from the CFPCR module prior to µCE. Biotin-labeled CFPCR products were hydrostatically pumped through the streptavidin-modified bed where they were extracted onto the surface of the poly(methylmethacrylate) micropillars (50-µm width; 100-µm height; total surface area of ~117 mm²). This SPE process demonstrated high selectivity for biotinylated amplicons and utilized the strong streptavidin/biotin interaction (Kd =10-15M) to generate high recoveries. The SPE selected CFPCR products were thermally denatured and single stranded DNA released for size-based separations and LIF detection. The multiplexed SPE-CFPCR-µCE yielded detectable fluorescence signal (S/N≥3; LOD ~75 cells) for Alu DNA amplicons for gender and ethnicity determinations with a separation efficiency of ~1.5 x105 plates/m. Compared to traditional cross-T injection procedures typically used for µCE, the affinity preconcentration and injection procedure generated signal enhancements of 17-40 fold, critical for CFPCR thermal cyclers due to Taylor dispersion associated with their operation

Analysis of methods for physical and biological characterization and validation of microphysiological systems (MPSs)

Microphysiological systems (MPSs), also known as 'Organ-On-a-Chip' (OCC), have revolutionized the way of understanding biology. These systems, which include three-dimensional co-culture and microfluidic technology, aim to mimic human physiology with in-vitro culture systems. Their purpose is to increase the knowledge of biological processes, as well as to provide an effective diagnostic tool for the analysis of different drugs. Standardization of MPSs implies the robustness and reproducibility of these devices and is desirable for their industrialization, production and regularization. However, due to the early stage of academic and commercial development of this technology, no standardization procedure exists in the literature to date. Therefore, experts recommend focusing on the characterization or qualification of these devices. This characterization and qualification of microphysiological systems involves testing the different elements that make up the device to ensure that their configuration mimics the physiology of the human structures represented, behaving and providing values as similar as possible to those of the tissues in vivo. It is in this context that this thesis attempts to develop a characterization protocol applicable to any 'Organ-On-a-Chip' system based on the tests carried out and compiled in the literature of devices in the experimental or commercialization phase. Specifically, a characterization and qualification procedure is presented in which the membrane permeability is monitored in real time depending on device elements such as the presence or not of cell culture, the application or not of microfluids, among others. The choice of the assays to be performed, from among those described in the protocol, will depend on the elements of the OCC to be characterized.Els sistemes microfisiològics (MPSs), també coneguts com a "Organ-On-a-Chip" (OCC), han revolucionat la manera d'entendre la biologia. Aquests sistemes, que inclouen el co-cultiu tridimensional i la tecnologia microfluídica, pretenen imitar la fisiologia humana amb els sistemes de cultiu in-vitro. El seu objectiu és augmentar el coneixement dels processos biològics, així com proporcionar una eina de diagnòstic eficaç per a l'anàlisi de diferents fàrmacs. L'estandardització de MPSs implica la robustesa i reproductibilitat d'aquests dispositius i és desitjable per a la seva industrialització, producció i regularització. No obstant això, a causa de la primera etapa del desenvolupament acadèmic i comercial d'aquesta tecnologia, no existeix cap procediment d'estandardització en la literatura fins a data d’avui. Per tant, els experts recomanen centrar-se en la caracterització o qualificació d'aquests dispositius. Aquesta caracterització i qualificació de sistemes microfisiològics implica provar els diferents elements que componen el dispositiu per assegurar que la seva configuració imiti la fisiologia de les estructures humanes representades, comportant-se i proporcionant valors el més similars possible als dels teixits in-vivo. És en aquest context que aquesta tesi intenta desenvolupar un protocol de caracterització aplicable a qualsevol sistema "Organ-On-a-Chip" basat en les proves realitzades i compilades en la literatura de dispositius en la fase experimental o de comercialització. Concretament, es presenta un procediment de caracterització i qualificació en el qual la permeabilitat de la membrana es controla en temps real depenent dels elements del dispositiu com la presència o no del cultiu cel·lular, l'aplicació o no de microfluids, entre d'altres. L'elecció dels assaigs a realitzar, d'entre els descrits en el protocol, dependrà dels elements de l'OCC que el caracteritzin.Los sistemas microfisiológicos (MPSs), también conocidos como "Organ-On-a-Chip" (OCC), han revolucionado la forma de entender la biología. Estos sistemas, que incluyen el co-cultivo tridimensional y la tecnología microfluídica, pretenden imitar la fisiología humana con sistemas de cultivo in vitro. Su finalidad es aumentar el conocimiento de los procesos biológicos, así como proporcionar una herramienta de diagnóstico eficaz para el análisis de diferentes fármacos. La estandarización de los MPSs implica la robustez y reproducibilidad de estos dispositivos y es deseable para su industrialización, producción y regularización. Sin embargo, debido a la temprana etapa de desarrollo académico y comercial de esta tecnología, hasta la fecha no existe en la literatura ningún procedimiento de estandarización. Por ello, los expertos recomiendan centrarse en la caracterización o cualificación de estos dispositivos. Esta caracterización y cualificación de los sistemas microfisiológicos implica probar los diferentes elementos que componen el dispositivo para asegurar que su configuración imita la fisiología de las estructuras humanas representadas, comportándose y proporcionando valores lo más similares posibles a los de los tejidos in vivo. Es en este contexto en el que esta tesis trata de desarrollar un protocolo de caracterización aplicable a cualquier sistema 'Organ-On-a-Chip' basado en las pruebas realizadas y recopiladas en la literatura de dispositivos en fase experimental o de comercialización. En concreto, se presenta un procedimiento de caracterización y cualificación en el que se monitoriza en tiempo real la permeabilidad de la membrana en función de elementos del dispositivo como la presencia o no de cultivo celular, la aplicación o no de microfluidos, entre otros. La elección de los ensayos a realizar, de entre los descritos en el protocolo, dependerá de los elementos del OCC a caracterizar.Outgoin

INTEGRATED MICROSYSTEM-BASED APPROACH FOR DETECTION AND TREATMENT OF BACTERIAL BIOFILMS ON URINARY CATHETERS

Biofilms are a ubiquitous mode of growth for bacteria and present a significant challenge in healthcare due to their resistant nature towards traditional antibiotic therapy. Particularly, biofilms can form on indwelling urinary catheters, leading to catheter-associated urinary tract infections, which are one of the most prevalent healthcare-acquired infections. In recent years, microsystems-based approaches have been developed to measure and study bacterial biofilms. In this dissertation, microsystems are adapted for the catheterized urinary tract environment to address biofilm infections in situ. Specifically, a proof-of-concept device comprised of gold interdigitated electrodes on a flexible polyimide substrate is fabricated and characterized in vitro. This substrate allows the device to conform seamlessly with the cylindrical surface of a catheter. Real-time impedance sensing is demonstrated, showing an average decrease in impedance of 30.3% following 24 hours of biofilm growth. The device also applies the bioelectric effect, which yields an increase in impedance of 12% and the lowest biomass relative to control treatments. Furthermore, 3D-printed molds and commercial modeling software show that the cylindrical conformation does not have an appreciable impact on performance. This device is integrated with a commercially available Foley catheter using two disparate approaches: (1) integration of the flexible proof-of-concept device using a 3D-printed catheter insert and (2) electroless plating directly onto the catheter lumen. In addition to electrode integration, miniaturized electronic systems are developed to control sensing and treatment wirelessly with a minimal form factor. A smartphone mobile application is developed in conjunction with this effort, to provide a user-friendly interface for the system. Several functions are verified with the integrated system, including biofilm sensing, wireless signal transmission, bladder drainage, and balloon inflation. To decrease the risk associated with this system for future research in vivo and in a clinical setting, sensing and treatment are evaluated under realistic conditions. The biochemical aspect of the catheterized environment is recreated using artificial urine, and the physical aspect is recreated using a silicone model of a human bladder and a programmable pump. A 13.0% decrease in impedance is associated with bacterial growth; this decreased magnitude relative to the proof-of-concept device is due to the reduced degree of growth in artificial urine. The bioelectric effect is demonstrated as well, showing a reduction in planktonic bacteria of 1.50×107 CFU/ml and adhered biomass equivalent to OD590nm = 0.072 relative to untreated samples. This work provides a framework for developing microsystem-based tools for biofilm infection management and research from proof-of-concept to integrated system, particularly for CAUTI. The results demonstrate that the cylindrical conformation does not interfere with device sensing or treatment performance and that the system maintains functionality under realistic conditions, laying the groundwork for future in vivo and clinical testing. The system will provide in situ and real-time data regarding catheter biofilm colonization in a way that is not possible with existing techniques. Finally, the system can serve to reduce reliance on antibiotics and reduce the spread of antibiotic resistance in CAUTI and other vulnerable areas

Integration technologies for implantable microsystems

Microsystems targeted for implantation require careful consideration of power, thermals, size, reliability, and biocompatibility. The presented research explored appropriate integration technologies for an implantable drug delivery system suitable for use in mice weighing less than 20 grams. Microsystems technology advancements include in situ pump diaphragm formation; integrated, low volume microfluidic coupling technologies; and incorporation of a low voltage, low-power pump actuation with a zero-power off state. Utility of the developed integration technologies have been tested through in vitro reliability and validation experiments. A four-chamber peristaltic pump was created using micromachining (e.g. thin film deposition and Si etching) and direct write techniques. A novel phase change material based actuator was designed and fabricated to deflect deformable diaphragms into and out of four pump chambers while the diaphragms isolated the pumped fluid from the working material. Polyimide capillary tubing with 140-μm OD was integrated in-plane and acted as fluidic interconnects to a drug supply and to the pharmaceutical delivery site. Parylene C conformal coating and the design for gap occlusion provided sealed, flexible tubing connections to the micropump. The per chamber actuation power of 10.1 mW at 0.083 Hz resulted in fluid flow of over 100 nL/min with an efficiency of 11 mJ/nL

Magnetic DNA detection sensor for point-of-care diagnostics

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University LondonThis thesis focuses on inductive base sensor design at MHz range frequency. The background theory, design, experiments and results for a new magnetic particles sensor is presented. A new magnetic sensor based on a planar coil was investigated for DNA pathogen detection. Change in inductance of the planar coil due to the presence of magnetic particles with varying mass was measured. The experimental set-up consisted of different sized planar coil with associated electronics for inductance measurements. The best sensor performance was accomplished using two different inductors while oscillating at frequencies 2.4MHz using 9.5μH inductor and 7.2MHz with 85μH inductor. The sensor has very large signal to noise ratio (580×103), while the average amount of frequency drift was 0.58. This sensor was tested with various types of magnetic particles. In addition, iron-oxide nanoparticles were synthesized through water in oil microemulsion method and with an average size of 25nm. The best sensitivity achieved for detection of 50μg iron-oxide particles was with the bead size of 10nm. 81Hz frequency shift was attained in regard to that amount of particles. This research shows that increasing the resonance frequency to 7.2MHz can cause the larger output signal difference (frequency shift) in the presence of magnetic particles; however, the sensor stability is the most important factor for determining the detection resolution and sensitivity. The sensitivity is better if the sensor can detect smaller amount of magnetic sample. The results of this research demonstrate that while the sample consists of smaller size particles, the sensor can detect the lower amount of sample. This is due to the heating effect of nanoparticles. On the other hand the sample distance from the sensor has a major impact on the sensitivity too; the shorter the distance, the higher the sensitivity. This technique can potentially be extended to detect several different types of bacterial pathogens and can be modified for multiplex quantitative detection. This sensing technique will be incorporated into a handheld, disposable microfluidic chip for point-of-care diagnostics for sexually transmitted diseases. Key words: Point of care diagnostics, Magnetic particle Detection, Molecular detection, Inductive sensin

Polymer Microsystems for the Enrichment of Circulating Tumor Cells and their Clinical Demonstration

Cancer research is centered on the discovery of new biomarkers that could unlock the obscurities behind the mechanisms that cause cancer or those associated with its spread (i.e., metastatic disease). Circulating tumor cells (CTCs) have emerged as attractive biomarkers for the management of many cancer-related diseases due primarily to the ease of securing them from a simple blood draw. However, their rarity (~1 CTC per mL of whole blood) makes enrichment analytically challenging. Microfluidic systems are viewed as exquisite platforms for the clinical analysis of CTCs due to their ability to be used in an automated fashion, minimizing sample loss and contamination. This has formed the basis of the reported research, which focused on the development of microfluidic systems for CTC analysis. The system reported herein consisted of a modular design and targeted the analysis of CTCs using pancreatic ductal adenocarcinoma (PDAC) as the model disease for determining the utility of the system. The system was composed of 3 functional modules; (i) a thermoplastic CTC selection module consisting of high aspect ratio (30 µm x 150 µm) channels; (ii) an impedance sensor module for label-less CTC counting; and (iii) a staining and imaging module for phenotype identification of selected CTCs. The system could exhaustively process 7.5 mL of blood in \u3c45 min with CTC recoveries \u3e90% directly from whole blood. In addition, significantly reduced assay turnaround times (8 h to 1.5 h) was demonstrated. We also show the ability to detect KRAS gene mutations from CTCs enriched by the microfluidic system. As a proof-of-concept, the ability to identify KRAS point mutations using a PCR/LDR/CE assay from as low as 10 CTCs enriched by the integrated microfluidic system was demonstrated. Finally, the clinical utility of the polymer-based microfluidic device for the analysis of circulating multiple myeloma cells (CMMCs) was demonstrated as well. Parameters such as translational velocity and recovery of CMMCs were optimized and found to be 1.1 mm/s and 71%, respectively. Also demonstrated was on-chip immunophenotyping and clonal testing of CMMCs, which has been reported to be prognostically significant. Further, a pilot study involving 26 patients was performed using the polymer microfluidic device with the aim of correlating the number of CMMCs with disease activity. An average of 347 CMMCs/mL of whole blood was recovered from blood volumes of approximately 0.5 mL