Biosensors and CMOS Interface Circuits

abstract: Analysing and measuring of biological or biochemical processes are of utmost importance for medical, biological and biotechnological applications. Point of care diagnostic system, composing of biosensors, have promising applications for providing cheap, accurate and portable diagnosis. Owing to these expanding medical applications and advances made by semiconductor industry biosensors have seen a tremendous growth in the past few decades. Also emergence of microfluidics and non-invasive biosensing applications are other marker propellers. Analyzing biological signals using transducers is difficult due to the challenges in interfacing an electronic system to the biological environment. Detection limit, detection time, dynamic range, specificity to the analyte, sensitivity and reliability of these devices are some of the challenges in developing and integrating these devices. Significant amount of research in the field of biosensors has been focused on improving the design, fabrication process and their integration with microfluidics to address these challenges. This work presents new techniques, design and systems to improve the interface between the electronic system and the biological environment. This dissertation uses CMOS circuit design to improve the reliability of these devices. Also this work addresses the challenges in designing the electronic system used for processing the output of the transducer, which converts biological signal into electronic signal.Dissertation/ThesisM.S. Electrical Engineering 201

Interfacing cells with organic transistors: a review of in vitro and in vivo applications

Recently, organic bioelectronics has attracted considerable interest in the scientific community. The impressive growth that it has undergone in the last 10 years has allowed the rise of the completely new field of cellular organic bioelectronics, which has now the chance to compete with consolidated approaches based on devices such as micro-electrode arrays and ISFET-based transducers both inin vitroandin vivoexperimental practice. This review focuses on cellular interfaces based on organic active devices and has the intent of highlighting the recent advances and the most innovative approaches to the ongoing and everlasting challenge of interfacing living matter to the “external world” in order to unveil the hidden mechanisms governing its behavior. Device-wise, three different organic structures will be considered in this work, namely the organic electrochemical transistor (OECT), the solution-gated organic transistor (SGOFET - which is presented here in two possible different versions according to the employed active material, namely: the electrolyte-gated organic transistor - EGOFET, and the solution gated graphene transistor - gSGFET), and the organic charge modulated field effect transistor (OCMFET). Application-wise, this work will mainly focus on cellular-based biosensors employed inin vitroandin vivocellular interfaces, with the aim of offering the reader a comprehensive retrospective of the recent past, an overview of the latest innovations, and a glance at the future prospects of this challenging, yet exciting and still mostly unexplored scientific field

Integrated CMOS Capacitance Sensor And Microactuator Control Circuits For On-Chip Cell Monitoring

"Cell Clinics," CMOS/MEMS hybrid microsystems for on-chip investigation of biological cells, are currently being engineered for a broad spectrum of applications including olfactory sensing, pathogen detection, cytotoxicity screening and biocompatibility characterization. In support of this effort, this research makes two primary contributions towards designing the cell-based lab-on-a-chip systems. Firstly it develops CMOS capacitance sensors for characterizing cell-related properties including cell-surface attachment, cell health and growth. Assessing these properties is crucial to all kinds of cell applications. The CMOS sensors measure substrate coupling capacitances of anchorage-dependent cells cultured on-chip in a standard in vitro environment. The biophysical phenomenon underlying the capacitive behavior of cells is the counterionic polarization around the insulating cell bodies when exposed to weak, low frequency electric fields. The measured capacitance depends on a variety of factors related to the cell, its growth environment and the supporting substrate. These include membrane integrity, morphology, adhesion strength and substrate proximity. The demonstrated integrated cell sensing technique is non-invasive, easy-to-use and offers the unique advantage of automated real time cell monitoring without the need for disruptive external forces or biochemical labeling. On top of the silicon-based cell sensing platform, the cell clinics microsystem comprises MEMS structures forming an array of lidded microvials for confining single cells or small cell groups within controllable microenvironments in close proximity to the sensor sites. The opening and closing of the microvial lids are controlled by actuator hinges employing an electroactive polymer material that can electrochemically actuate. In macro-scale setups such electrochemical actuation reactions are controlled by an electronic instrument called potentiostat. In order to enable system miniaturization and enhance portability of cell clinics, this research makes its second contribution by implementing and demonstrating a CMOS potentiostat module for in situ control of the MEMS actuators

CMOS IMAGE SENSORS FOR LAB-ON-A-CHIP MICROSYSTEM DESIGN

The work described herein serves as a foundation for the development of CMOS imaging in lab-on-a-chip microsystems. Lab-on-a-chip (LOC) systems attempt to emulate the functionality of a cell biology lab by incorporating multiple sensing modalidites into a single microscale system. LOC are applicable to drug development, implantable sensors, cell-based bio-chemical detectors and radiation detectors. The common theme across these systems is achieving performance under severe resource constraints including noise, bandwidth, power and size. The contributions of this work are in the areas of two core lab-on-a-chip imaging functions: object detection and optical measurements

Integrated Electronics for Molecular Biosensing

This thesis, Integrated electronics for molecular biosensing, focuses on different approaches to sense the presence and activity of a specific analyte by using integrated electronic platforms. The aim of the first platform is to detect the enzyme telomerase. Telomerase causes the elongation of telomeres, which are part of the chromosomes, and determines the lifespan of cells. Telomerase expression is a marker of malignity in tumoral cells and its evaluation can be exploited for early diagnosis of many types of cancer cells. To detect the telomerase enzyme, a CMOS (complementary metal-oxide semiconductor) biosensor based on CMFET (Charge-Modulated Field Effect Transistor) able to measure kinetics of DNA replication and telomerase reaction was developed. The sensor can be functionalized by immobilizing single strands of DNA that contain the telomeric sequence, used as probes. If telomerase is present, the probes will be elongated by the enzyme and the charge on the sensing area will change, which reflects in a variation of the output current or voltage. The chip includes three different readout schemes (voltage, current- and time-based), each of which has different measuring ranges and operating conditions. The measured data is then digitized, stored, and can be sent off-chip through SPI (Serial Peripheral Interface) protocol. A total of 1024 biosensors have been integrated in a single chip with a size of 10x10 mm2. Each sensor can be independently addressed and functionalized by an electrochemical procedure using an integrated potentiostat, thus requiring no external equipment. Although the sensors have been tailored and optimized to perform telomerase detection, the sensing areas can be functionalized to be used with different analytes. This feature turns the chip into a complete bioassay platform. The second part of this work rises from the idea that bacteria, like Escherichia coli, can detect analytes in solution even at extremely low concentrations and change their movement through a process called chemotaxis, to move towards chemical gradients in the solution. E. coli moves by rotating its flagella either clockwise (for random tumbles) or counterclockwise (for straight runs, when it senses a chemical it is attracted to). Therefore, observing bacteria flagellar rotation can give enough information on the presence of a specific analyte in the solution. To electronically detect bacteria movement, an active surface covered in electrodes has been designed. By measuring the impedance between each pair of electrodes through an integrated LIA (lock-in amplifier), it is possible to know how a single bacterium is moving. By that, the presence or absence of the analyte can be deduced, thus effectively turning bacteria into chemical sensors

Low-Power and Programmable Analog Circuitry for Wireless Sensors

Embedding networks of secure, wirelessly-connected sensors and actuators will help us to conscientiously manage our local and extended environments. One major challenge for this vision is to create networks of wireless sensor devices that provide maximal knowledge of their environment while using only the energy that is available within that environment. In this work, it is argued that the energy constraints in wireless sensor design are best addressed by incorporating analog signal processors. The low power-consumption of an analog signal processor allows persistent monitoring of multiple sensors while the device\u27s analog-to-digital converter, microcontroller, and transceiver are all in sleep mode. This dissertation describes the development of analog signal processing integrated circuits for wireless sensor networks. Specific technology problems that are addressed include reconfigurable processing architectures for low-power sensing applications, as well as the development of reprogrammable biasing for analog circuits

Low-Power and Programmable Analog Circuitry for Wireless Sensors

Embedding networks of secure, wirelessly-connected sensors and actuators will help us to conscientiously manage our local and extended environments. One major challenge for this vision is to create networks of wireless sensor devices that provide maximal knowledge of their environment while using only the energy that is available within that environment. In this work, it is argued that the energy constraints in wireless sensor design are best addressed by incorporating analog signal processors. The low power-consumption of an analog signal processor allows persistent monitoring of multiple sensors while the device\u27s analog-to-digital converter, microcontroller, and transceiver are all in sleep mode. This dissertation describes the development of analog signal processing integrated circuits for wireless sensor networks. Specific technology problems that are addressed include reconfigurable processing architectures for low-power sensing applications, as well as the development of reprogrammable biasing for analog circuits

Digital CMOS ISFET architectures and algorithmic methods for point-of-care diagnostics

Over the past decade, the surge of infectious diseases outbreaks across the globe is redefining how healthcare is provided and delivered to patients, with a clear trend towards distributed diagnosis at the Point-of-Care (PoC). In this context, Ion-Sensitive Field Effect Transistors (ISFETs) fabricated on standard CMOS technology have emerged as a promising solution to achieve a precise, deliverable and inexpensive platform that could be deployed worldwide to provide a rapid diagnosis of infectious diseases. This thesis presents advancements for the future of ISFET-based PoC diagnostic platforms, proposing and implementing a set of hardware and software methodologies to overcome its main challenges and enhance its sensing capabilities. The first part of this thesis focuses on novel hardware architectures that enable direct integration with computational capabilities while providing pixel programmability and adaptability required to overcome pressing challenges on ISFET-based PoC platforms. This section explores oscillator-based ISFET architectures, a set of sensing front-ends that encodes the chemical information on the duty cycle of a PWM signal. Two initial architectures are proposed and fabricated in AMS 0.35um, confirming multiple degrees of programmability and potential for multi-sensing. One of these architectures is optimised to create a dual-sensing pixel capable of sensing both temperature and chemical information on the same spatial point while modulating this information simultaneously on a single waveform. This dual-sensing capability, verified in silico using TSMC 0.18um process, is vital for DNA-based diagnosis where protocols such as LAMP or PCR require precise thermal control. The COVID-19 pandemic highlighted the need for a deliverable diagnosis that perform nucleic acid amplification tests at the PoC, requiring minimal footprint by integrating sensing and computational capabilities. In response to this challenge, a paradigm shift is proposed, advocating for integrating all elements of the portable diagnostic platform under a single piece of silicon, realising a ``Diagnosis-on-a-Chip". This approach is enabled by a novel Digital ISFET Pixel that integrates both ADC and memory with sensing elements on each pixel, enhancing its parallelism. Furthermore, this architecture removes the need for external instrumentation or memories and facilitates its integration with computational capabilities on-chip, such as the proposed ARM Cortex M3 system. These computational capabilities need to be complemented with software methods that enable sensing enhancement and new applications using ISFET arrays. The second part of this thesis is devoted to these methods. Leveraging the programmability capabilities available on oscillator-based architectures, various digital signal processing algorithms are implemented to overcome the most urgent ISFET non-idealities, such as trapped charge, drift and chemical noise. These methods enable fast trapped charge cancellation and enhanced dynamic range through real-time drift compensation, achieving over 36 hours of continuous monitoring without pixel saturation. Furthermore, the recent development of data-driven models and software methods open a wide range of opportunities for ISFET sensing and beyond. In the last section of this thesis, two examples of these opportunities are explored: the optimisation of image compression algorithms on chemical images generated by an ultra-high frame-rate ISFET array; and a proposed paradigm shift on surface Electromyography (sEMG) signals, moving from data-harvesting to information-focused sensing. These examples represent an initial step forward on a journey towards a new generation of miniaturised, precise and efficient sensors for PoC diagnostics.Open Acces

LTCC packaging for Lab-on-a-chip application

LTCC -pakkaus Lab-on-a-chip -sovellukseen. Tiivistelmä. Tässä työssä suunniteltiin, valmistettiin ja testattiin uusi pakkaustekniikka ”Lab-on-a-chip” (LOC) -sovellukseen. Pakkaus tehtiin pii-mikrosirulle, jolla voidaan mitata solujen kiinnittymistä sirun pintaan solujen elinkelpoisuuden indikaattorina. Luotettavuustestaukset tehtiin daisy-chain -resistanssimittauksilla solunkasvatusolosuhteissa. Lisäksi työssä selvitettiin LTCC- ja ”Lab-on-a-chip” -teknologioiden perusteet teoreettiselta pohjalta. Mikrosirun pakkauksessa käytettiin joustavaa LTCC-teknologiaa. Sähköisiin kontakteihin ja niiden suojauksiin käytettiin sekä johtavia että eristäviä epoksi-liimoja. LOC-sovelluksiin on tärkeää kehittää uusia pakkausmenetelmiä jotta näiden laitteiden kaikki ominaisuudet saadaan toimimaan luotettavasti. Pakkaus testattiin samoissa olosuhteissa missä sitä tullaan käyttämään ja pakkaus kesti kaikki nämä haasteet. Lisäksi esitetty valmistusprosessi on sellainen, että sitä voidaan käyttää myös muihin ”Lab-on-a-chip” -sovelluksiin.Abstract. This work presents design, manufacturing and testing of new packaging method for Lab-on-a-chip (LOC) application. Packaging was made for silicon microchip which can measure cell adhesion on chips surface as indication of cell viability. Reliability testing was done with daisy-chain resistance measurement in real conditions. Moreover basic theory of LTCC and Lab-on-a-chip technology is presented. Resilient LTCC technology was used for packaging material and conductive/insulating epoxies were applied for electrical contacts and barriers against the environment. It is fundamentally important to develop new packaging methods for LOC applications, so all the properties can be utilized reliably. Packaging was tested under the cell growth conditions and the package showed to withstand all these challenges. Moreover the presented packaging method is possible to use also in other Lab-on-a-chip applications