A Design of Digital Microfluidic Biochip along with Structural and Behavioural Features in Triangular Electrode Based Array

AbstractDigital microfluidic based biochip manoeuvres on the theory of microfluidic technology, having a broad variety of applications in chemistry, biology, environmental monitoring, military etc. Being concerned about the technological advancement in this domain, we have focused on equilateral triangular electrodes based DMFB systems. Accepting the associated design issues, here, we have addressed many facets of such electrodes regarding their structural and behavioural issues in comparison to the existing square electrodes. As the requisite voltage reduction is a key challenging design issues, to implement all the tasks using triangular electrodes that are possible in square electrode arrays as well, is a tedious job. Furthermore, to deal with this new design deploying triangular electrodes, we have analyzed all the necessary decisive factors including fluidic constraints to ensure safe droplet movements and other modular operations together with mixing and routing. Moreover, an algorithm has been developed to find a route for a given source and destination pair in this newly designed DMFB. Finally, we have included a comparative study between this new design and the existing one while encountering the above mentioned issues

Design and Optimization Methods for Pin-Limited and Cyberphysical Digital Microfluidic Biochips

<p>Microfluidic biochips have now come of age, with applications to biomolecular recognition for high-throughput DNA sequencing, immunoassays, and point-of-care clinical diagnostics. In particular, digital microfluidic biochips, which use electrowetting-on-dielectric to manipulate discrete droplets (or "packets of biochemical payload") of picoliter volumes under clock control, are especially promising. The potential applications of biochips include real-time analysis for biochemical reagents, clinical diagnostics, flash chemistry, and on-chip DNA sequencing. The ease of reconfigurability and software-based control in digital microfluidics has motivated research on various aspects of automated chip design and optimization.</p><p>This thesis research is focused on facilitating advances in on-chip bioassays, enhancing the automated use of digital microfluidic biochips, and developing an "intelligent" microfluidic system that has the capability of making on-line re-synthesis while a bioassay is being executed. This thesis includes the concept of a "cyberphysical microfluidic biochip" based on the digital microfluidics hardware platform and on-chip sensing technique. In such a biochip, the control software, on-chip sensing, and the microfluidic operations are tightly coupled. The status of the droplets is dynamically monitored by on-chip sensors. If an error is detected, the control software performs dynamic re-synthesis procedure and error recovery.</p><p>In order to minimize the size and cost of the system, a hardware-assisted error-recovery method, which relies on an error dictionary for rapid error recovery, is also presented. The error-recovery procedure is controlled by a finite-state-machine implemented on a field-programmable gate array (FPGA) instead of a software running on a separate computer. Each state of the FSM represents a possible error that may occur on the biochip; for each of these errors, the corresponding sequence of error-recovery signals is stored inside the memory of the FPGA before the bioassay is conducted. When an error occurs, the FSM transitions from one state to another, and the corresponding control signals are updated. Therefore, by using inexpensive FPGA, a portable cyberphysical system can be implemented.</p><p>In addition to errors in fluid-handling operations, bioassay outcomes can also be erroneous due the uncertainty in the completion time for fluidic operations. Due to the inherent randomness of biochemical reactions, the time required to complete each step of the bioassay is a random variable. To address this issue, a new "operation-interdependence-aware" synthesis algorithm is proposed in this thesis. The start and stop time of each operation are dynamically determined based on feedback from the on-chip sensors. Unlike previous synthesis algorithms that execute bioassays based on pre-determined start and end times of each operation, the proposed method facilitates "self-adaptive" bioassays on cyberphysical microfluidic biochips.</p><p>Another design problem addressed in this thesis is the development of a layout-design algorithm that can minimize the interference between devices on a biochip. A probabilistic model for the polymerase chain reaction (PCR) has been developed; based on the model, the control software can make on-line decisions regarding the number of thermal cycles that must be performed during PCR. Therefore, PCR can be controlled more precisely using cyberphysical integration.</p><p>To reduce the fabrication cost of biochips, yet maintain application flexibility, the concept of a "general-purpose pin-limited biochip" is proposed. Using a graph model for pin-assignment, we develop the theoretical basis and a heuristic algorithm to generate optimized pin-assignment configurations. The associated scheduling algorithm for on-chip biochemistry synthesis has also been developed. Based on the theoretical framework, a complete design flow for pin-limited cyberphysical microfluidic biochips is presented.</p><p>In summary, this thesis research has led to an algorithmic infrastructure and optimization tools for cyberphysical system design and technology demonstrations. The results of this thesis research are expected to enable the hardware/software co-design of a new class of digital microfluidic biochips with tight coupling between microfluidics, sensors, and control software.</p>Dissertatio

Droplet routing for digital microfluidic biochips based on microelectrode dot array architecture

A digital microfluidic biochip (DMFB) is a device that digitizes fluidic samples into tiny droplets and operates chemical processes on a single chip. Movement control of droplets can be realized by using electrowetting-on-dielectric (EWOD) technology. DMFBs have high configurability, high sensitivity, low cost and reduced human error as well as a promising future in the applications of point-of-care medical diagnostic, and DNA sequencing. As the demands of scalability, configurability and portability increase, a new DMFB architecture called Microelectrode Dot Array (MEDA) has been introduced recently to allow configurable electrodes shape and more precise control of droplets. The objective of this work is to investigate a routing algorithm which can not only handle the routing problem for traditional DMFBs, but also be able to route different sizes of droplets and incorporate diagonal movements for MEDA. The proposed droplet routing algorithm is based on 3D-A* search algorithm. The simulation results show that the proposed algorithm can reduce the maximum latest arrival time, average latest arrival time and total number of used cells. By enabling channel-based routing in MEDA, the equivalent total number of used cells can be significantly reduced. Compared to all existing algorithms, the proposed algorithm can achieve so far the least average latest arrival time

Single-Molecule Detection of Unique Genome Signatures: Applications in Molecular Diagnostics and Homeland Security

Single-molecule detection (SMD) offers an attractive approach for identifying the presence of certain markers that can be used for in vitro molecular diagnostics in a near real-time format. The ability to eliminate sample processing steps afforded by the ultra-high sensitivity associated with SMD yields an increased sampling pipeline. When SMD and microfluidics are used in conjunction with nucleic acid-based assays such as the ligase detection reaction coupled with single-pair fluorescent resonance energy transfer (LDR-spFRET), complete molecular profiling and screening of certain cancers, pathogenic bacteria, and other biomarkers becomes possible at remarkable speeds and sensitivities with high specificity. The merging of these technologies and techniques into two different novel instrument formats has been investigated. (1) The use of a charge-coupled device (CCD) in time-delayed integration (TDI) mode as a means for increasing the throughput of any single molecule measurement by simultaneously tracking and detecting single-molecules in multiple microfluidic channels was demonstrated. The CCD/TDI approach allowed increasing the sample throughput by a factor of 8 compared to a single-assay SMD experiment. A sampling throughput of 276 molecules s-1 per channel and 2208 molecules s-1 for an eight channel microfluidic system was achieved. A cyclic olefin copolymer (COC) waveguide was designed and fabricated in a pre-cast poly(dimethylsiloxane) stencil to increase the SNR by controlling the excitation geometry. The waveguide showed an attenuation of 0.67 dB/cm and the launch angle was optimized to increase the depth of penetration of the evanescent wave. (2) A compact SMD (cSMD) instrument was designed and built for the reporting of molecular signatures associated with bacteria. The optical waveguides were poised within the fluidic chip at orientation of 90° with respect to each other for the interrogation of single-molecule events. Molecular beacons (MB) were designed to probe bacteria for the classification of Gram +. MBs were mixed with bacterial cells and pumped though the cSMD which allowed S. aureus to be classified with 2,000 cells in 1 min. Finally, the integration of the LDR-spFRET assay on the cSMD was explored with the future direction of designing a molecular screening approach for stroke diagnostics

Towards a smartphone-connected point-of-care test for HIV

The devastation caused by HIV is driving the development of new point-of-care diagnostics. The work presented in this thesis aims to help develop a new generation of smartphone- connected HIV tests designed to address the very high levels of undiagnosed HIV-infected individuals, by widening access to HIV testing to doctors surgeries, pharmacies and developing countries. The biosensor is based on mass manufacturable surface acoustic wave (SAW) devices, and uses piezoelectricity to transduce the binding of biomarkers on the surface of the device into a measurable electric signal, making the test low cost, easy to use and reliable. In addition, the SAW biosensor presented here has the ability to wirelessly and securely transmit results to healthcare providers to potentially offer follow-up appointments at local clinics, or virtually. This thesis begins with the theory behind SAW biosensors. A more focussed characterisation of the specific device developed is then presented, followed by the details of the work done to optimise the biosensor in order to make it a good candidate for a point-of-care test for HIV. Key results include the proof of concept detection of different biomarkers of HIV infection, as well as a demonstration of the ability of the SAW biosensor to deliver a fast response. Different pilot studies are then presented, demonstrating the performance of the device as a diagnostic test, highlighting 100% sensitivity and 100% specificity. These were conducted with more than 30 confirmed HIV positive patient samples and more than 100 healthy volunteers. The following chapter then examines the fundamental mechanisms underpinning the SAW biosensor output and an empirical method to ultimately design more sensitive devices in future antigen detection. This thesis concludes with a summary of the main results and future work, including the potential for larger clinical studies, and field trials in developing countries

Biosensors

A biosensor is defined as a detecting device that combines a transducer with a biologically sensitive and selective component. When a specific target molecule interacts with the biological component, a signal is produced, at transducer level, proportional to the concentration of the substance. Therefore biosensors can measure compounds present in the environment, chemical processes, food and human body at low cost if compared with traditional analytical techniques. This book covers a wide range of aspects and issues related to biosensor technology, bringing together researchers from 11 different countries. The book consists of 16 chapters written by 53 authors. The first four chapters describe several aspects of nanotechnology applied to biosensors. The subsequent section, including three chapters, is devoted to biosensor applications in the fields of drug discovery, diagnostics and bacteria detection. The principles behind optical biosensors and some of their application are discussed in chapters from 8 to 11. The last five chapters treat of microelectronics, interfacing circuits, signal transmission, biotelemetry and algorithms applied to biosensing

Self-contained microfluidic platform for general purpose lab-on-chip using pcb-mems technology.

El presente trabajo está centrado en la investigación de una nueva plataforma microfluídica autónoma para propósito general fabricada en PCBMEMS. En la vista de la proliferación en los últimos años de los sistemas microfluídicos Lab on Chip (LoC) y la multitud de aplicaciones en las que tienen cabida, surge la necesidad de creación de un sistema portable, autónomo y con una fabricación orientada hacia la producción masiva. En este contexto, se presenta el trabajo de esta tesis dentro de los proyectos de investigación de financiación nacional ISILAB (TEC2011-29045-C04-02) y BIOLOP (TEC2014-54449-C3-2- R). La tesis se encuentra organizada para cubrir los aspectos previamente propuestos. Primeramente, se presenta una introducción donde se explican los motivos para el desarrollo de este trabajo y cuáles son los objetivos específicos que se quieren cumplir. Seguidamente, se hace un breve estudio del arte. En este estudio se presenta la tecnología MEMS, los principios básicos de la microfluídica, que son los fundamentos de los sistemas LOCs y por último, se detalla un estudio de los principales elementos activos en la literatura que componen una plataforma microfluídica. Después de la introducción y revisión literaria del marco de esta tesis, se explican los resultados obtenidos. Esta tesis está desarrollada en dos fases principales: el desarrollo de todos los componentes que hacen un lab on chip autónomo de propósito general y el desarrollo de una tecnología basada en estándares para una producción masiva. En la primera fase se detallan los principales componentes que forman parte de una plataforma autónoma multifunción: microválvula, sistema de impulsión, circuito microfluídico y plataforma de sensado. Todos estos componentes son diseñados como un prototipo y están fabricados en SU-8 y PCBMEMS. El PCB permanece como sustrato y los canales y cámaras microfluídicas están fabricados en SU-8. La microválvula diseñada presenta una activación termoeléctrica, es de un solo uso y tiene una rápida activación y un consumo bajo de energía. Además, el diseño está pensado para ser altamente integrable en una plataforma microfluídica. El siguiente componente descrito es una sistema de impulsión basado en cámaras presurizadas, este sistema está integrado con la microválvula y su principal característica es la activación en el momento de uso, asegurando la ausencia de pérdidas. Para probar la validez de los componentes anteriores, se desarrolla un circuito microfluídico de propósito general. El circuito está diseñado para mezclar dos muestras y transportarlas a una cámara de detección. Finalmente, se desarrolla una plataforma para la detección de glucosa, integrable en el circuito microfluídico. Una vez desarrollado el prototipo, el siguiente objetivo de la tesis es el paso de la tecnología de prototipado hacía una de producción masiva. Para ello los materiales utilizados son el PMMA y el PCB. La tecnología PCBMEMS es conocida por su versatilidad para la integración de la electrónica, por lo que lo hace idóneo para la conexión con el exterior. El PMMA es un material también muy extendido en las aplicaciones microfluídicas, debido a su transparencia, bio compatibilidad y su fácil modelado. La unión de los dos componentes representa un desafío en el desarrollo de la tesis, debido a sus diferentes propiedades químicas. El proceso de fabricación se desarrolla integrando la microválvula y el sistema de impulsión, como partes de una plataforma microfluídica. Para terminar, se ha diseñado un pequeño circuito microfluídico para probar la viabilidad del sistema propuesto hacia una tecnología de gran escala. Finalmente, se exponen las conclusiones de la investigación, las posibles líneas futuras de este trabajo y los apéndices que complementan el trabajo de la tesis.The work presented is focused on the investigation of a new autonomous microfluidic platform manufactured using PCBMEMS technology for general purpose. With the proliferation of the microfluidic platforms, Lab on Chip (LoC), and the multitude of applications which have placed in the market, there is a need to create a self-contained microfluidic platform for general purpose with mass production-oriented manufacturing. Within this framework, the work of this thesis is presented. This is part of two national research project ISILAB (TEC2011-29045-C04-02) and BIOLOP (TEC2014-54449-C3-2- R). The thesis is organized to cover the aspects previously explained. Firstly, an introduction is presented with the motivation and objectives of this work. Subsequently, a study of the art is done. This study presents theMEMS technology, the basics principles of microfluidics, which are the pillars of the lab on chips and finally, a study of the main active elements presented in the literature. After the introduction and the literary revision of the framework of this thesis, the results obtained are presented. This thesis is developed in two main phases: the development of all components that make an autonomous general purpose lab on chip and the development of a standards-based technology for mass production. The first phase details the main components of an autonomous multifunction platform: microvalve, impulsion system, microfluidic circuit and sensing platform. All of these components are designed as a prototype and are manufactured in SU- 8 and PCBMEMS. The PCB remains as a substrate, and the microfluidic channels and chambers are manufactured in SU-8. The microvalve developed is a single use thermoelectrical microvalve with fast activation and low power consumption. In addition, the design is thought to be highly integrable in a microfluidic plat-form. The next component is a impulsion system based on pressurized chambers. The system is integrated with the microvalve and its main characteristic is the activation at the moment of use, ensuring the absence of losses. To test the validity of the above components, a general purpose microfluidic circuit is developed. The circuit is designed to mix two samples and transport those to a detection chamber. Finally, a platform for the detection of glucose, integrable in the microfluidic circuit, is developed. Once the prototype is achieved, the next objective of the thesis is the migration from prototyping technology to mass production. To this end, the materials used are PMMA and PCB. PCBMEMS technology is known for its versatility for the integration of electronics, making it suitable for electrical connection. PMMA is also widely used in microfluidic applications due to its transparency, bio compatibility and easy modeling. The union of the two components represents a challenge in the development of the thesis due to its different chemical properties. The manufacturing process is developed by integrating the microvalve and the drive system, as parts of a microfluidic platform. In conclusion, a small microfluidic circuit is designed by testing the feasibility of the proposed system towards large-scale technology. Finally, the conclusions of the research, the possible future lines of this work and the appendices that complement the work of the thesis are presented