Within the realm of biosensing, DNA analysis has become an indispensable research tool in medicine, enabling the investigation of relationships among genes, proteins, and drugs. Conventional DNA microarray technology uses multiple lasers and complex optics, resulting in expensive and bulky systems which are not suitable for point-of-care medical diagnostics. The immobilization of DNA probes across the microarray substrate also results in substantial spatial variation. To mitigate the above shortcomings, this thesis presents a set of techniques developed for the CMOS image sensor for point-of-care spectrally-multiplexed fluorescent DNA sensing and other fluorescence biosensing applications. First, a CMOS tunable-wavelength multi-color photogate (CPG) sensor is presented. The CPG exploits the absorption property of a polysilicon gate to form an optical filter, thus the sensor does not require an external color filter. A prototype has been fabricated in a standard 0.35μm digital CMOS technology and demonstrates intensity measurements of blue (450nm), green (520nm), and red (620nm) illumination. Second, a wide dynamic range CMOS multi-color image sensor is presented. An analysis is performed for the wide dynamic-range, asynchronous self-reset with residue readout architecture where photon shot noise is taken into consideration. A prototype was fabricated in a standard 0.35μm CMOS process and is validated in color light sensing. The readout circuit achieves a measured dynamic range of 82dB with a peak SNR of 46.2dB. Third, a low-power CMOS image sensor VLSI architecture for use with comparator based ADCs is presented. By eliminating the in-pixel source follower, power consumption is reduced, compared to the conventional active pixel sensor. A 64×64 prototype with a 10μm pixel pitch has been fabricated in a 0.35μm standard CMOS technology and validated experimentally. Fourth, a spectrally-multiplexed fluorescence contact imaging microsystem for DNA analysis is presented. The microsystem has been quantitatively modeled and validated in the detection of marker gene sequences for spinal muscular atropy disease and the E. coli bacteria. Spectral multiplexing enables the two DNA targets to be simultaneously detected with a measured detection limit of 240nM and 210nM of target concentration at a sample volume of 10μL for the green and red transduction channels, respectively.

Un système microfluidique à onde élastique de surface a été développé dans le but de réaliser une réaction d'amplification de brins d'ADN par PCR. Nous avons principalement étudié la température et l'uniformité de l'échauffement des gouttes irradiées par des ondes de type Rayleigh. Ces dernières sont générées à la surface d'un substrat piézoélectrique de Niobate de Lithium (LiNbO3). Nous avons pensé un système consommant le moins d'énergie électrique possible pour atteindre les températures désirées et permettant une meilleure uniformité de la température des gouttes. Pour cela, un dispositif à transducteur enterré a été réalisé sous une couche isolante de silice. Les gouttes sont ainsi directement posées sur le transducteur ce qui limite les pertes et améliore la répartition de la chaleur au sein des gouttes. Nous avons ensuite vérifié que les réactifs de la PCR ne sont pas affectés par les ondes de Rayleigh ce qui laisse présager que la PCR peut être réalisée à l'aide d'un système d'échauffement par ondes de Rayleigh. Par ailleurs, le déplacement de goutte sur ce type de substrat de LiNbO3 est important pour des applications de type laboratoire sur puce. Ce substrat ayant des propriétés hydrophiles, des revêtements ont été développés afin de minimiser la force nécessaire à l'actionnement des gouttes. Dans ces travaux, nous proposons un nouveau type de couche à base de copolymère P(VDF-TrFe) dont la fabrication est simplement réalisée par dissolution et étalement par spin-coating. Nous avons montré que ce type de couche n'affecte que très peu la propagation des ondes de Rayleigh et les propriétés hydrophobes sont équivalentes à d'autres revêtements / In this work, a microfluidic system based on surface acoustic wave has been developed in order to achieve the amplification of DNA strands by temperature cycling (PCR). We studied mainly the temperature and the heat uniformity of microdroplets irradiated by Rayleigh waves. These waves are generated at the surface of a lithium niobate substrate. We propose a system allowing better temperature uniformity within microdroplets with an optimal energy consumption. For this, a device with buried transducer has been developed under an insulating layer (Silice). The droplets are then placed directly on the transducer which limits losses and improves the distribution of heat within the microdroplets. We then verified that the PCR reagents are not affected by the Rayleigh waves which suggests that PCR can be performed using a heating system by Rayleigh waves. Moreover, the move of microdroplets on this kind of LiNbO3 substrate is important for lab on chip applications. This substrate having hydrophilic properties, some coatings have been developed to minimize the required force to actuate the microdroplets. In this work, we developed a new hydrophobic layer based on copolymer P(VDF-TrFe) whose production is simply made by dissolving and spreading by spin-coating. We have shown that this kind of layer is compatible with Rayleigh waves and that the hydrophobic properties are equivalent to other coatings

In der vorliegenden Arbeit wird eine integrierbare Pumpentechnologie für polymerbasierte mikrofluidische Systeme entwickelt. Ausgehend von den Anforderungen für die Durchführung molekulardiagnostischer Nachweise kommen dabei Fertigungsverfahren zum Einsatz, die sich auch für Einweg-Anwendungen eignen. Das genutzte Aktorprinzip für die integrierten Mikropumpen basiert auf der Elektrolyse von Wasser. Zur besseren technologischen Integrierbarkeit wird das Wasser in Form eines Hydrogels appliziert. Der Elektrolyt wird dabei mit einer Polymermembran mit geringer Wasserdampfdurchlässigkeit verschlossen. Die Membran wird in ihrem plastischen Verformbereich genutzt. Zur Dimensionierung der Mikropumpen und des mikrofluidischen Systems werden analytische und numerische Modelle entwickelt, die eine gute Übereinstimmung mit den Messwerten zeigen. Die Funktionsfähigkeit wird anhand zweier vollständig integriert ablaufender Immunoassays demonstriert. Dabei kommt ein polymerbasierter, optischer Biosensor zum Einsatz.

The rise of superbugs, including antibiotic-resistant bacteria, and virus outbreaks, such as the recent coronavirus scare, illustrate the need for rapid detection of disease pathogens. Widespread availability of rapid disease identification would facilitate outbreak prevention and specific treatment. The ARROW biosensor microchip can directly detect single molecules through fluorescence-based optofluidic interrogation. The nature of the microfluidic channels found on optofluidic sensor platforms sets some of the ultimate sensitivity and accuracy limits and can result in false negative test results. Yet higher sensitivity and specificity is desired through hydrodynamic focusing. Novel 3D hydrodynamic focusing designs were developed and implemented on the ARROW platform, an optofluidic lab-on-a-chip single-molecule detector device. Microchannels with cross-section dimensions smaller than 10 μm were formed using sacrificial etching of photoresist layers covered with plasma-enhanced chemical-vapor-deposited silicon dioxide on a silicon wafer. Buffer fluid carried to the focusing junction enveloped an intersecting sample fluid, resulting in 3D focusing of the sample stream. The designs which operate across a wide range of fluid velocities through pressure-driven flow were integrated with optical waveguides in order to interrogate fluorescing particles and confirm 3D focusing, characterize diffusion, and quantify optofluidic detection enhancement of single viruses on chip.

Nanopore technology has introduced new techniques for single particle detection and analysis. A nanopore consists of a small opening in a membrane on the nanometer scale. Nanopores are found in nature and are utilized for transporting molecules through biological membranes. Researchers have been able to mimic naturally forming biological nanopores and utilize them for a variety of sensing applications. Nanopores, fabricated either organically or inorganically, can be used for detecting biomarkers such as proteins, nucleic acids, and metabolites that translocate the membrane by way of the nanopore. Constant ionic current flow is measured through the nanopore by way of a sensitive ammeter. In the presence of a biomarker, the ionic current flow will be impeded, causing the electrical signal to drop. This drop uniquely corresponds to the type of particle passing through the nanopore. In this work, the thin membrane on which the nanopore resides is created through a newly developed meniscus shaped sacrificial technique. The sacrificial polymer material starts as a liquid and is confined to the microfluidic channel through the capillary effect, giving it the meniscus profile. It is used as a structural support on which a thin silicon dioxide layer is grown. The layer of oxide takes on the same natural meniscus shape as the sacrificial material. The polymer is subsequently etched, resulting in a hollow core liquid channel with a suspended meniscus membrane. This process allows a thin membrane to be fabricated on top of a microfluidic channel that ranges from 50-200 nm in thickness. The meniscus membrane is crucial to the success of nanopore formation. The nanoscale membrane allows for smaller, more precise nanopores to be created. Reduced nanopore dimensions are advantageous for the detection of smaller biomarkers. The platform described in this dissertation integrates solid-state naturally forming meniscus membranes with solid-core and optofluidic waveguides for nanopore detection applications. The waveguides allow for a particle trap to be introduced to the system. The ability to trap particles directly under the nanopore is critical to the speed of which the nanopore can operate. This dissertation focuses on the fabrication, characterization, and testing of an optofluidic platform that features a nanopore for rapid single molecule detection and analysis.

<p dir="ltr">Pancreatic ductal adenocarcinoma (PDAC) remains one of the most deadliest cancer and despite advancements in cancer therapy, remain highly refractory to treatment, largely due to its desmoplastic tumor microenvironment (TME) characterized by complex interactions among cancer cells and stromal components. Particularly, the PDAC associated coagulation system due to leaky tumor vasculatures plays a pivotal role in reshaping the PDAC stroma and its pathogenesis. Understanding the intricate interplay between tumor cells, stromal cells, and the elevated coagulation pathway elements, including tissue factor, thrombin, and fibrin, is essential for developing effective therapeutic strategies. To address these challenges, this research proposes the engineering of a novel PDAC-associated coagulation system using a microfluidic technology, known as coagulation-on-tumor-microenvironment-on-chip (cT-MOC). The study aims to integrate key coagulation pathways in cT-MOC to investigate pivotal interactions in the PDAC stroma: <i>i)</i> thrombin-protease-activated receptors (PARs) mediated promotion of PDAC fibrosis via activation of cancer-fibroblast cross-talk; <i>ii)</i> in-depth analysis of transport and mechanical properties of collagen-fibrin microstructure; <i>iii)</i> inhibited drug delivery in reprogrammed PDAC stroma due to pronounced fibrin deposition on collagen. By leveraging innovative microfluidic technologies and comprehensive experimental approaches, the research endeavors to provide a novel platform that bridges traditional <i>in vitro</i> and <i>in vivo</i> models to overcome the challenges posed by the desmoplastic TME and enhance therapeutic strategies for treatment by targeting the coagulation at the PDAC TME.</p>

By implementing the rolled-up microfabrication method based on strain engineering, several systems are investigated within the contents of this thesis. The structural morphing of planar geometries into three-dimensional structures opens up many doors for the creation of unique material configurations and devices. An exploration into several novel microsystems, encompassing various scientific subjects, is made and methods for on-chip integration of these devices are presented. The roll-up of a metal and oxide allows for a cylindrical hollow-core structure with a cladding layer composed of a multilayer stack, plasmonic metamaterial. This structure can be used as a platform for a number of optical metamaterial devices. By guiding light radially through this structure, a theoretical investigation into the system makeup of a rolled-up hyperlens, is given. Using the same design, but rather propagating light parallel to the cylinder, a novel device known as a metamaterial optical fiber is defined. This fiber allows light to be guided classically and plasmonically within a single device. These fibers are developed experimentally and are integrated into preexisting on-chip structures and characterized. A system known as lab-in-a-tube is introduced. The idea of lab-in-a-tube combines various rolled-up components into a single all-encompassing biosensor that can be used to detect and monitor single bio-organisms. The first device specifically tailored to this system is developed, flexible split-wall microtube resonator sensors. A method for the capturing of embryonic mouse cells into on-chip optical resonators is introduced. The sensor can optically detect, via photoluminescence, living cells confined within the resonator through the compression and expansion of a nanogap built within its walls. The rolled-up fabrication method is not limited to the well-investigated systems based on the roll-up from semiconductor material or from a photoresist layer. A new approach, relying on the delamination of polymers, is presented. This offers never-before-realized microscale structures and configurations. This includes novel magnetic configurations and flexible fluidic sensors which can be designed for on-chip and roving detector applications.

Within healthcare there is a market pull for biomedical devices that can rapidly perform laboratory processes, such as diagnostic testing, in a hand-held format. For this reason, biomedical devices must become smaller, more sophisticated, and easier to use for a reasonable cost. However, despite the accelerating academic research on biomedical microdevices, and especially plastic-based microfluidic chips, there is still a gap between the inventions in academia and their benefit to society. To bridge this gap there is a need for new materials which both exhibit similar properties as industrial thermoplastics, and that enable rapid prototyping in academia. In this thesis, thiol-ene and thiol-ene-epoxy thermosets are evaluated both in terms of their suitability for rapid prototyping of biomedical microdevices and their potential for industrial manufacturing of “lab-on-chips”. The first part of the thesis focuses on material development of thiol-ene and thiol-ene-epoxy thermosets. Chemical and mechanical properties are studied, as well as in vitro biocompatibility with cells. The second part of the thesis focuses on microfabrication methods for both thermosets. This includes reaction injection molding, photostructuring, and surface modification. It is demonstrated how thiol-ene and thiol-ene-epoxy both provide advantageous thermo-mechanical properties and versatile surface modifications via “thiol-click chemistry”. In the end of the thesis, two applications for both polymer platforms are demonstrated. Firstly, thiol-ene is used for constructing nanoliter well arrays for liquid storage and on-demand electrochemical release. Secondly, thiol-ene-epoxy is used to enhance the biocompatibility of neural probes by tuning their flexibility. It is concluded that both thiol-ene and thiol-ene-epoxy thermosets exhibit several properties that are highly suitable for rapid prototyping as well as for scalable manufacturing of biomedical microdevices. / <p>QC 20171003</p>

In novel drug delivery system, the encapsulation of therapeutic cells in microparticles has great promises for the treatment of a range of health con- ditions. Therefore, the encapsulation material and technology are of great importance to the validity and efficiency of the advanced medical therapy. Several unsolved challenges in regards to versatile microparticle synthesis ma- terials and methods form the main obstacle for a translation of novel cell therapy concepts from research to clinical practice. Thiol-ene based polymer systems have emerged and gained great popular- ity in material development in general and in biomedical applications specif- ically. The thiol-ene platform is broad and therefore of interest for a variety of applications. At the same time, many aspects of this material platform are largely unexplored, for example material and manufacturing technology developments for microfluidic applications . In this Ph.D. thesis, thiol-ene materials are explored for use in cell encap- sulation. The marriage of these two technology fields breeds the possibility for a novel microfluidic cell encapsulation approach using a novel encapsulation material. To this end, several new manufacturing technologies for thiol-ene and thiol-ene-epoxy droplet microfluidic devices were developed. Moreover, core-shell microparticle synthesis for cell encapsulation based on a novel co- synthesis concept using a thiol-ene based material was developed and inves- tigated. Finally, a thiol-ene-epoxy system was also used for the formation of microwells and microchannels that improve protein analysis on microarrays. The first part of the thesis presents the background and state-of-the-art technologies in regards to cell therapy, microfluidics, and thiol-ene based ma- terials. In the second part of the thesis, a novel manufacturing approach of thiol-ene-epoxy material as well as core-shell particle co-synthesis in micro- fluidics using thiol-ene based material are presented and characterized. The third part of the thesis presents the cell viability studies of encapsulated cells using the novel encapsulation material and method. In the final part of the thesis, two applications of thiol-ene-epoxy gaskets for protein detection mi- croarrays are presented. / Inkapsling av levande celler i mikrokapslar för terapeutiska ändamål är mycket lovande för frmatida behandling av många olika sjukdomar. Emeller- tid är en behandlings effektivitet i hög grad beroende av vilka material som används för inkapsling och vilken teknisk lösning som används för att ska- pa mikrokapslarna. För närvarande återstår det många utmaningar för att omvandla grundforskningresultat till klinisk verklighet, vilken kräver mer än- damålsenliga tillvägagångssätt för att tillverka mikrokapslar i material som är kompatibla med användningsområdena. De senaste åren har tiol-en baserade polymerer har blivit mycket använda för materialutveckling i stort och för biomedicinska tillämpningar i synnerhet. Med tiol-en kemi kan en mycket stor mängd helt olika syntetiska material framställas, vilket gör tiol-ener intressanta för en mängd applikationer. För närvarande är dock mycket inom denna materialklass outforskat, t.ex. inom material och tillverkningmetodik för mikrofluidiktillämpningar. I denna avhandling används tiol-ener för cellinkapsling. Sammanslagning av dessa teknologier möjliggör en ny typ av cellinkapsling med nya materi- alegenskaper. En mängd olika tillverkningssätt där tiol-en eller tiol-en-epoxi används för droplet-mikrofluidiksystem utvecklades. Core-shell mikrokapsel- syntes för cell-inkapsling baserat på en ny metod för samtidig syntes av både core och shell utvecklades och karaktäriserades. Slutligen utvecklades ett tiol- en-epoxi system för enkel integrering med proteinmikroarrayer på objektsglas. I avhandlingens första del presenteras bakgrund och dagens bästa teknolo- gier för terapeutisk cellinkapsling, mikrofluidik och tiol-en baserade material. I avhandlingens andra del presenteras en ny tillverkningsmetod för mikro- strukturerade tiol-en-epoxi artiklar och samtidig syntes av core och shell för mikrokapslar med användande av mikrofluidik. I den tredje delen presenteras cellöverlevandsstudier för de celler som inkapslats med de nya materialen och de nyutvecklade metoderna. I den avslutande delen beskrivs två specifika fall där tiol-en-epoxi komponenter används för proteindetektion och mikroarrayer. / <p>QC 20171122</p>

The field of organ-on-chip is a relatively new area of research and builds upon the principle of engineering microfluidic systems to mimic the body’s internal environment as precisely as possible. Eventually these models could hopefully simulate whole organ-systems and enable the examination of the cell’s or organ’s reaction to foreign substances like new pharmaceuticals in a better way than current models. Previously this has been done with in vitro models such as petri dishes that only offer static culturing conditions. These are not very realistic environments compared to the human body where the cells are exposed to both variations in pressure and flows among other things. The purpose of this bachelor’s thesis project has been to evaluate and improve the design of an organ-on-chip system developed by the EMBLA-group at Ångströmslaboratoriet, Uppsala university. This has been done by evaluating the manufacturing process to find areas of improvements of the current chip design, as well as conducting a literature study to understand key components of similar organ-on-chip systems and see if it is possible to implement relevant parts to the organ-on-chip of this project. One of these important parts is a so-called bubble trap. A bubble trap is a construction that enables the capturing and elimination of bubbles in the system since the bubbles can harm the chips components, kill the cells, and compromise measurements.  A first prototype of the bubble trap was developed in Polydimethylsioxane (PDMS) and integrated on the EMBLA-group’s chip design. The principle behind the bubble trap was to use the natural buoyancy of the bubbles to trap them. This was done by introducing an upwards going slope before the inlets to the chip. In this manner the bubbles would float up to the top of the slope and accumulate at the roof as the liquid moved on into the chip without bubbles. To make the bubbles leave the chip a low-pressure chamber was added on top of the bubble trap to help the process of the bubble’s diffusion through the roof and out of the chip. The development of an improved chip design turned out to be a time-consuming endeavor and the time left for evaluation the functionality of the chip became too short. One test was performed which showed that the bubbles did accumulate at the top of the slope as expected, but it rapidly became full and thus started to let bubbles through to the microfluidic chip. The bubbles did not diffuse as efficiently as required and the removal of the bubbles became inefficient. To understand and correct the problem areas of this bubble trap design further tests and experiments will have to be conducted. / Organ-på-chip (Organ-on-chip eller OoC) är ett relativt nytt forskningsområde som bygger på att mikrofluidiksystem utvecklas till att efterlikna människokroppen i så stor utsträckning som möjligt. Detta då det är attraktivt att kunna undersöka cellers/organs beteende vid tillförsel av vissa substanser, till exempel nya läkemedel. I tidigare in vitro modeller har det endast observerats och utförts tester på celler odlade i statiska förhållanden vilket inte är likt den omgivning cellerna har i människokroppen där de tex utsätts för olika vätskeflöden och tryckförändringar.    Syftet med detta examensarbete har varit att utvärdera och förbättra designen på ett OoC system utvecklat av EMBLA-gruppen på Ångströmlaboratoriet vid Uppsala universitet. Detta har gjorts genom att studera den nuvarande tillverkningsprocessen för att hitta relevanta förbättringsområden samt att genom en litteraturstudie undersöka viktiga delar som bör ingå i dessa typer av system. En av dessa delar är en bubbelfälla (bubble trap eller BT) vilket innebär att det i chippet bör finnas ett sätt att eliminera/fånga upp bubblor. Detta eftersom bubblorna kan orsaka stor skada på både chipet, cellerna och mätningarna som skall utföras. En första prototyp av en BT design i Polydimetylsiloxan (PDMS) utvecklades och integrerades på EMBLA-gruppens OoC design. Principen bakom BT-designen var att utnyttja bubblornas flytkraft vilket gjordes genom att introducera en uppåtgående backe innan ingångskanalen. Bubblorna kan därmed flyta upp till toppen av lutningen och vätskan kan fortsätta in i mikrochipset utan bubblor. För att bubblorna ska ta sig ut ur chippet integrerades en tryckkammare ovanpå BT-designen för att få bubblorna att diffundera ut genom taket i den uppåtgående kammaren och ut ur chippet. Utvecklingen av den förbättrade chip-designen visade sig var tidskrävande och tiden för att utvärdera designens funktionalitet blev för kort. Ett test gjordes på den nya chip-designen vilket visade att den utvecklade BT som väntat fångade upp bubblor men att den snabbt blev full i och med att bubblorna inte diffunderade ut genom taket i den takt som behövdes. Vidare undersökningar och experiment behövs för att evaluera vad som orsakade detta och rätta till eventuella felkällor i design och experimentuppställning.