Much of recent progress in medical research and diagnostics has been enabled through the advances in molecular analysis technologies, which now permit the detection and analysis of single molecules with high sensitivity and specificity. Assay sensitivity is fundamentally limited by the efficiency of the detection method used for read-out. Inefficient detection systems are usually compensated for by molecular amplification at the cost of elevated assay complexity. This thesis presents microfluidic automation and digital quantification of targeted nucleic acid detection methods based on padlock and selector probes and rolling circle amplification (RCA). In paper I, the highly sensitive, yet complex circle-to-circle amplification assay was automated on a digital microfluidic chip. In paper II, a new RCA product (RCP) sensing principle was developed based on resistive pulse sensing that allows label free digital RCP quantification. In paper III, a microfluidic chip for spatial RCP enrichment was developed, which enables the detection of RCPs with an unprecedented efficiency and allows for deeper analysis of enriched RCPs through next generation sequencing chemistry. In paper IV, a smart phone was converted into a multiplex fluorescent imaging device that enables imaging and quantification of RCPs on slides as well as within cells and tissues. KRAS point mutations were detected (i) in situ, directly in tumor tissue, and (ii) by targeted sequencing of extracted tumor DNA, imaged with the smart phone RCP imager. This thesis describes the building blocks required for the development of highly sensitive low-cost RCA-based nucleic acid analysis devices for utilization in research and diagnostics.

This thesis focuses on fundamental aspects of microfluidic systems and applies relevant findings to innovative designs for advanced particle manipulation applications. Computational Fluid Dynamics (CFD) is adopted for fluid modeling, based on the Finite Volume method. The accuracy of the solutions obtained is confirmed by grid sensitivity analysis and by comparisons with experimental work. Curved microchannel features and the induced Dean flow are studied through a parametric space exploration and simulations. The Lagrange-Euler coupling method – Surface Marker Point methodology – is applied to simulate large-size particles (of comparable size to the channel). Through this simulation approach, all the forces on such particles are directly derived through solving the governing equations and the influence of these particles on the flow is considered in a fully coupled manner. A new approach – the Frozen Flow & Flow Correction Coefficient method – is developed, making trans-relaxation-time simulations possible and improving computational efficiency significantly, for 3D simulations of arbitrary shape and size microparticles in complicated microfluidic channels. Detailed comparisons between simulation results and experiments involving particle sedimentation and particle equilibrium position have been conducted for methodology validation. Mechanisms of hydrodynamic particle manipulation are then studied, including hydrodynamic focusing and separation. It is found that the Tubular Pinch effect, Dean flow and the Radial Pressure Gradient effect interact to yield two distinct particle separation mechanisms. For advanced applications, particle focusing, non-magnetic and magnetic separation for neutrally buoyant particles are proposed, based on newly gained insight on the above-mentioned mechanisms. Appropriate channel designs have been proposed both for particle focusing and size-based particle separation, while the vertical-magnetic-Dean separation scheme is highlighted for magnetic separation. Finally, a new integrated system is proposed, that combines the above novel designs into a device-like ensemble. It promises to offer functionality for biomaterial separation and detection, including different types of cells, antigens and biomarkers.

“Lab on a Chip” technologies have revolutionized the field of bio-chemical analytics. The crucial role of optical techniques in this revolution resulted in the emergence of a field by itself, which is popularly termed as “optofluidics”. The miniaturization and integration of the optical parts in the majority of optofluidic devices however still remains a technical challenge. The works described in this thesis focuses on developing integration methods to combine various optical techniques with microfluidics in an alignment-free geometry, which could lead to the development of portable analytical devices, suitable for field applications. The integration approach was applied to implement an alignment-free optofluidic chip for optical chromatography; a passive optical fractionation technique fractionation for cells or colloids. This system was realized by embedding large mode area photonic crystal fiber into a microfluidic chip to achieve on-chip laser beam delivery. Another study on passive sorting envisages an optofluidic device for passive sorting of cells using an optical potential energy landscape, generated using an acousto-optic deflector based optical trapping system. On the analytical side, an optofluidic chip with fiber based microfluidic Raman spectroscopy was realized for bio-chemical analysis. A completely alignment-free optofluidic device was realized for rapid bio-chemical analysis in the first generation by embedding a novel split Raman probe into a microfluidic chip. The second generation development of this approach enabled further miniaturization into true microfluidic dimensions through a technique, termed Waveguide Confined Raman Spectroscopy (WCRS). The abilities of WCRS for online process monitoring in a microreactor and for probing microdroplets were explored. Further enhanced detection sensitivity of WCRS with the implementation of wavelength modulation based fluorescent suppression technique was demonstrated. WCRS based microfluidic devices can be an optofluidic analogue to fiber Raman probes when it comes to bio-chemical analysis. This allows faster chemical analysis with reduced required sample volume, without any special sample preparation stage which was demonstrated by analyzing and classifying various brands of Scotch whiskies using this device. The results from this study also show that, along with Raman spectroscopic information, WCRS picks up the fluorescence information as well, which might enhance the classification efficiency. A novel microfabrication method for fabricating polymer microlensed fibers is also discussed. The microlensed fiber, fabricated with this technique, was combined with a microfluidic gene delivery system to achieve an integrated system for optical transfection with localized gene delivery.

In this thesis, microelectrode arrays of micropumps have been designed, fabricated and characterized for transporting microfluid by AC electro-osmosis (ACEO). In particular, the 3D stepped electrode design which shows superior performance to others in literature is adopted for making micropumps, and the performance of such devices has been studied and explored. A novel fabrication process has also been developed in the work, realizing 3D stepped electrodes on a flexible substrate, which is suitable for biomedical use, for example glaucoma implant. There are three major contributions to ACEO pumping in the work. First, a novel design of 3D “T-shaped” discrete electrode arrays was made using PolyMUMPs® process. The breakthrough of this work was discretizing the continuous 3D stepped electrodes which were commonly seen in the past research. The “T-shaped” electrodes did not only create ACEO flows on the top surfaces of electrodes but also along the side walls between separated electrodes. Secondly, four 3D stepped electrode arrays were designed, fabricated and tested. It was found from the experiment that PolyMUMPs® ACEO electrodes usually required a higher driving voltage than gold electrodes for operation. It was also noticed that a simulation based on the modified model taking into account the surface oxide of electrodes showed a better agreement with the experimental results. It thus demonstrated the possibility that the surface oxide of electrodes had impact on fluidic pumping. This methodology could also be applied to metal electrodes with a native oxide layer such as titanium and aluminum. Thirdly, a prototype of the ACEO pump with 3D stepped electrode arrays was first time realized on a flexible substrate using Kapton polyimide sheets and packaged with PDMS encapsulants. Comprehensive experimental testing was also conducted to evaluate the mechanical properties as well as the pumping performance. The experimental findings indicated that this fabrication process was a promising method to create flexible ACEO pumps that can be used as medical implants and wearable devices. / Thesis (Ph.D, Mechanical and Materials Engineering) -- Queen's University, 2013-05-06 10:57:48.077

In most applications concerning a fluid flowing over a solid surface, the no-slip velocity condition was widely used because it is simple and produces the results in agreement with experiments. However, this dynamical boundary condition is not appropriate when the flow under consideration is at a micro or nano length scale.In order to model this effect at the macroscopic scale, the Navier boundary conditions have been introduced, with the slip length as a parameter. When the fluid is a gas, this length is related to the tangential momentum accommodation coefficient (TMAC) and the mean free path, according to the Maxwell model. The aim of this work is to systematically address this model using a multi-scale approach and to extend it by incorporating both the morphology and the anisotropy of a surface. The thesis consists of five chapters. In Chapter 1, the basics of the kinetic theory of gases, the Boltzmann equation and related solutions (Navier-Stokes-Fourier, Burnett, Grad, Direct Simulation Monte Carlo ...) are briefly presented. The models of gas-wall interaction and slip models introduced in the fluid mechanics are also recalled. The chapter ends with a description of the computational method used for the molecular dynamics simulations performed in this work. Chapter 2 is dedicated to the development of a simple technique to simulate the pressure driven flows. The principle is to rely on the atomistic formulas of the stress tensor (Irving Kirkwood, Method of Plane, Virial Stress) and to modify the periodic conditions by maintaining the difference between the kinetic energy of the ingoing and outgoing particles of the simulation domain. Several types of channels are studied with this technique. The results (temperature, velocity ...) are discussed and compared. Chapter 3 deals with the study of the gas-wall interaction potential by the ab-initio method. The code CRYSTAL 09 is used to obtain the potential between an atom of argon (Ar) and a surface of platinum (Pt) <111> as a function of distance. Then the gas-wall potential is decomposed into binary potential and approached by an analytic function. This function is then implemented in a MD code to simulate the gas-wall collisions and determine the TMAC coefficient. In Chapter 4, the effect of morphology is studied. The multi-body Quantum Sutton Chen (QSC) potential is used for Pt <100> solid and the binary potential proposed in the previous chapter for the Ar-Pt couple is employed. The QSC potential is needed to reproduce the surface effects that affect the final results. Different surfaces are treated : smooth, nanostructured surface and, random surface obtained by Chemical vapor deposition (CVD). The TMAC is determined using a generalized approach, i.e. depending on the angle of incident flux of gas atoms on the surface. The surface anisotropy and the scattering kernel are also examined. In Chapter 5, we propose a model of anisotropic slip for fluids based on accommodation tensor. The model is obtained by the analytical approximate calculations developed in the framework of the kinetic theory. We thus generalize Maxwell's equation by showing that the slip length tensor is directly related to the accommodation tensor. The model is in good agreement with the MD results. Thanks to our MD simulations, we develop a suitable technique for reproducing the anisotropy of the accommodation tensor. The thesis ends with a conclusion section in which we suggest some perspectives for a continuation of this work

1-Microevaporation - Microfluidics is the branch of fluid mechanics dedicated to the study of flows in the channel withdimensions between 1 micron and 100 micron. The object of this chapter is to illustrate the basicprinciples and possible applications of microfluidic chip, called microevaporator. In the first part ofthe chapter, we present a detailed description of the physics of microevaporators using analyticalarguments, and describe some applications. In the second part of the chapter, we present theexperimental protocol of engineering of micro evaporator and different type of microfluidics device.2- On-chip microspectroscopy - The object of this chapter is to illustrate a method to measure absorption spectra during theprocess of growth of our materials in our microfluidic tools. The aim is to make an opticalcharacterization of our micro materials and to carry-out a spatio-temporal study of kineticproperties of our dispersion under study. This instrumental chapter presents the theoretical basis !of the method we used.3-Role of colloidal stability in the growth of micromaterials - We used combined microspectroscopy and videomicroscopy to follow the nucleation and growth ofmaterials made of core-shell Ag@SiO2 NPs in micro evaporators.!We evidence that the growth is actually not always possible, and instead precipitation may occurduring the concentration process. This event is governed by the concentration of dispersion in thereservoir and we assume that its origin come from ionic species that are concentrated all togetherwith the NPs and may alter the colloidal stability en route towards high concentration. 4-Microfluidic-induced growth and shape-up of three-dimensional extended arrays of denselypacked nano particles - In this chapter I present in details microfluidic evaporation experiments to engineer various denselypacked 3D arrays of NPs.5-Bulk metamaterials assembled by microfluidic evaporation - In this chapter I introduced the technique we used (microspot ellipsometry) in close collaborationswith V.Kravets and A.Grigorenko(University of Manchester) and with A.Aradian, P.Barois, A.Baron,K.Ehrhardt(CRPP, Pessac) to characterized the solids made of densely packed NPs. I describe theconstraints that emerge from the coupling between the small size of our materials and the opticalrequirements, the analysis and interpretation of the ellipsometry experiments show that for thematerial with high volume fraction of metal exists the strong electrical coupling between the NPsand the materials display an extremely high refraction index in the near infra-red regime.

Une capsule est une goutte de liquide enveloppée par une membrane fine et déformable. Les propriétés mécaniques de la membrane sont essentielles pour le mouvement de la capsule. L’analyse de l’écoulement d’une suspension de capsules dans un canal microfluidique au moyen d’un modèle mécanique est une technique permettant de déterminer les propriétés élastiques de la membrane. Un modèle numérique tridimensionnel a été développé pour résoudre ce problème d’interaction fluide-structure en écoulement confiné. Il couple une méthode des intégrales de frontières pour les écoulements des fluides et une méthode éléments finis pour la déformation de la membrane. Le modèle est utilisé pour étudier l’écoulement d’une capsule initialement sphérique dans des canaux de différentes sections. Dans un canal cylindrique, on montre que l’effet de confinement du canal conduit à la compression de la capsule. Cela engendre la formation de plis sur la membrane autour de l’axe de l’écoulement, phénomène également observé expérimentalement. Dans un canal de section carrée, les effets de la loi constitutive de la membrane, du rapport de taille et du débit d’écoulement sur la déformation de la capsule sont systématiquement étudiés. La comparaison entre les résultats expérimentaux et numériques nous permet de déduire les propriétés mécaniques de la membrane d’une population de capsules artificielles. Ce travail démontre la faisabilité de la mesure de propriétés mécaniques d’une membrane en utilisant une technique microfluidique en canal carré. Il pourrait être étendu par l’étude d’écoulements instationnaires dans un canal de section variable ou avec bifurcations. / A capsule is a liquid droplet enclosed by a thin and deformable membrane. The membrane mechanical properties are critical for the deformation and motion of capsules. The flow of a capsule suspension through a microfluidic channel with dimensions comparable to those of the suspended particles can be used to infer the membrane elastic properties. However a mechanical model of the process is necessary. We present a three-dimensional numerical model to simulate such fluid-structure interaction problem. We use a novel numerical model that couples a boundary integral method for the internal and external fluid flows and a finite element method for the membrane deformation. The model is applied to study the flow of an initially spherical capsule in channels with different cross-sections. In a cylindrical channel with circular cross-section, we show that the confinement effect leads to the compression of the capsule in the hoop direction. The membrane tends to buckle and to fold as observed experimentally. In a microfluidic channel with a square cross-section, the effects of the membrane constitutive law, size ratio and flow strength on the capsule deformation are systematically studied. The comparison between experimental and numerical results allows us to deduce the membrane mechanical properties of a population of artificial capsules. The present work shows that it is possible to measure the membrane mechanical properties by using a microfluidic channel with a square cross-section. It can be extended to unsteady capsule flows in a channel with variable cross-sections or bifurcations.

Microfluidics covers the science of manipulating small quantities of fluids using microscale devices with great potential in analysis, multiplexing, automation and high-throughput screening. Compared to conventional systems, microfluidics benefits from miniaturization resulting in shortened time of experiments, decreased sample and reagent consumptions as well as reduced overall costs. For microfluidic devices where further weight and cost reduction is additionally required, stimuli-responsive hydrogels are particularly interesting materials since they can convert an environmental stimulus directly to mechanical work without any extra power source. Hydrogels are used as chemostats, micropumps, and chemo-mechanical valves in microfluidics. Existing studies about hydrogels for flow control reported on hydrogels responsive to only one stimulus, including temperature, pH value, and solvent. Combining temperature and pH stimuli within one material is an interesting approach, which allows internal as well as external flow control and broadens potential applications. Among the variety of temperature- and pH-responsive monomers, N-isopropylacrylamide (NiPAAm) and acrylic acid (AA) are considered as ideal building blocks to obtain a hydrogel with pronounced stimuli response. There are different architectures for realizing a temperature- and pH-responsive hydrogel with NiPAAm and AA (e.g. copolymer gels, interpenetrating polymer networks (IPNs), semi-IPNs, or graft copolymer gels). Each approach has its inherent benefits and disadvantages. Grafted hydrogels with a temperature-responsive backbone and pH-responsive graft chains are a promising architecture overcoming drawbacks of copolymer gels (loss of thermoresponsive behavior due to the comonomer), interpenetrating polymer networks (IPNs, difficult fabrication of structured particles via soft lithography), and semi-IPNs (leakage of penetrating polymer). However, studies about multi-responsive grafted hydrogels for flow control in microfluidics are comparatively rare and further research is needed to emphasize their real potential. For this reason, the overall aim of this work was the synthesis of temperature- and pH-responsive grafted hydrogels based on NiPAAm and AA for flow control in microfluidics. This required the synthesis of a pH-responsive macromonomer by RAFT polymerization. As a suitable chain transfer agent with a carboxylic acid group for an end-group functionalization, 2-(dodecyl-thiocarbonothioylthio)-2-methylpropionic (DTP) acid was employed. The approach towards the synthesis of the pH-responsive macromonomer based on two key steps: (i) attaching a functional group, which retains during RAFT polymerization, and (ii) conducting the RAFT polymerization to synthesize the pH-responsive macromonomer. In total, four functionalizations for the macromonomer were investigated, including allyl, unconjugated vinyl, acrylamide, and styrene. End-group analysis and solubility tests revealed that macromonomers with a styrene functionalization are suitable for the synthesis of graft copolymer gels. A series of grafted net-PNiPAAm-g-PAA-styrene hydrogels with a PNiPAAm backbone and PAA-styrene graft chains (Mn = 4200 g/mol, Mw/Mn = 1.6) were prepared and characterized. The main goal was to identify suitable stimuli for an application as a chemo-mechanical valve and to show reversibility of the swelling and shrinking process. Importantly, the temperature sensitivity should be retained, while a pH response needs to be introduced. Equilibrium swelling studies quantified with the response ratio revealed that a grafting density of PAA-styrene between 0.25 and 1 mol-% provides a suitable response towards temperature, pH, salt, and solvent. Furthermore, the swelling and shrinking process is highly reproducible over four consecutive cycles for all four stimuli. In order to evaluate the swelling kinetics of grafted net-PNiPAAm-g-PAA-styrene hydrogels, the collective diffusion model extended by a volume specific surface was applied. The determined cooperative diffusion coefficients of net-PNiPAAm-g-PAA-styrene indicated faster response time with increasing PAA-styrene content. Remarkably, net-PNiPAAm-g-PAA-styrene containing 1 mol-% PAA-styrene exhibited an accelerated swelling rate by a factor of 9 compared to pure net-PNiPAAm. Rheological analysis of net-PNiPAAm-g-PAA-styrene showed that an increasing graft density leads to decreasing mechanical stability. The photopolymerization experiments showed that the gelation time linearly increases with the grafting density. Grafted net-PNiPAAm-g-PAA-styrene hydrogels were tested in two fluidic setups for flow control. A straightforward fluidic platform was developed consisting of a fluid reservoir, an inlet channel, an actuator chamber and an outlet channel. The actuator chamber was filled with crushed hydrogel particles. Accordingly, the fluid flow was directed by the active resistance of the hydrogel particles in the actuator chamber (i.e. swelling degree) and allowed flow control by the local environmental conditions. Flow rate studies showed that the fluid flow throttles when the inlet channel was provided with a solution in which the hydrogel swells (pH 9 buffer solution at room temperature). In contrast, the hydrogel-based valve opens immediately when a solution was used in which the hydrogel collapses. The advantageous properties of net-PNiPAAm-g-PAA-styrene were highlighted by using pH, salt and solvent stimulus in one experiment. Remarkably, the opening and closing function was reversible over six consecutive cycles. As part of a collaboration project with the chair of polymeric microsystems within the Cluster of Excellence Center for Advancing Electronics Dresden (A. Richter and P. Frank), membrane assures hydraulic coupling in a chemo-fluidic membrane transistor (CFMT) and grafted net-PNiPAAm-g-PAA-styrene hydrogels were combined to emphasize the potential of both systems. Flow rate studies showed that 4 different stimuli can be used to control the opening and closing state of the CFMT. Multiple opening and closing cycles revealed no considerable changes in the valve function emphasizing a high potential for an application in microfluidics.

Droplet microfluidics is an emerging technology for analysis of single cells and biomolecules at high throughput. The controlled encapsulation of particles along with the surrounding microenvironment in discrete droplets, which acts as miniaturized reaction vessels, allows millions of particles to be screened in parallel. By utilizing the unit operations developed to generate, manipulate and analyze droplets, this technology platform has been used to miniaturize a wide range of complex biological assays including, but not limited to, directed evolution, rare cell detection, single cell transcriptomics, rare mutation detection and drug screening. The aim of this thesis is to develop droplet microfluidics based methods for analysis of single cells and nucleic acids. In Paper I, a method for time-series analysis of mammalian cells, using automated fluorescence microscopy and image analysis technique is presented. The cell-containing droplets were trapped on-chip and imaged continuously to assess the viability of hundreds of isolated individual cells over time. This method can be used for studying the dynamic behavior of cells. In Paper II, the influence of droplet size on cell division and viability of mammalian cell factories during cultivation in droplets is presented. The ability to achieve continuous cell division in droplets will enable development of mammalian cell factory screening assays in droplets. In Paper III, a workflow for detecting the outcome of droplet PCR assay using fluorescently color-coded beads is presented. This workflow was used to detect the presence of DNA biomarkers associated with poultry pathogens in a sample. The use of color-coded detection beads will help to improve the scalability of the detection panel, to detect multiple targets in a sample. In Paper IV, a novel unit operation for label-free enrichment of particles in droplets using acoustophoresis is presented. This technique will be useful for developing droplet-based assays that require label-free enrichment of cells/particles and removal of droplet content. In general, droplet microfluidics has proven to be a versatile tool for biological analysis. In the years to come, droplet microfluidics could potentially be used to improve clinical diagnostics and bio-based production processes. / <p>QC 20160926</p>

Les ARN (Acide RiboNucléique) remplissent de nombreuses fonctions clés dans le vivant. Ils peuvent être support de l'information génétique, régulateurs de celle-ci. Visualiser ces molécules au sein d'une cellule représenterait une étape importante vers une meilleure compréhension de la régulation de l'expression des gènes. Les ARN fluorogènes tels que Spinach et Mango sont des outils extrêmement prometteurs pour atteindre cet objectif. Cependant ces deux ARN fluorogènes présentent une brillance limitée. La Compartimentation in vitro assistée par microfluidique (µCIV) est un outil très prometteur dont notre groupe a démontré l’efficacité pour l’évolution d’ARN. Dans le cadre de cette thèse, la µCIV a été adaptée à la sélection d'aptamères d'ARN fluorogènes pour en améliorer les propriétés (surtout la brillance). De plus, l’utilisation conjointe du séquençage haut débit a permis l’optimisation très rapide et semi-automatisée à la fois d’aptamères mais aussi de biosenseurs fluorogènes. Ainsi, cette thèse a permis de mettre en place et d’exploiter des technologies de criblage robustes pour la découverte de nouveaux aptamères d'ARN et de biosenseurs. / RNA is a key molecule in gene expression and its regulation. Therefore, being able to monitor RNA through live-cell imaging would represent an important step toward a better understanding of gene expression regulation. RNA-based fluorogenic modules are extremely promising tools to reach this goal. To this end, two light-up RNA aptamers (Spinach and Mango) display attractive properties but they suffer from a limited brightness. Since previous work in the group demonstrated the possibility to evolve RNA using microfluidic-assisted in vitro compartmentalization (µIVC), this technology appeared to be well suited to improve light-up aptamers properties by an evolution strategy. Therefore, the µIVC procedure was adapted to fluorogenic RNA aptamers to improve their properties (especially the brightness). Finally, using µIVC in tandem with high-throughput sequencing (NGS) allowed further developing the technology into a more integrated and semi-automatized approach in which RNAs and biosensors are selected by µIVC screening and the best variants identified by a bioinformatics process upon NGS analysis. To summarize, this thesis allowed establishing robust µIVC screening workflows for the discovery of novel efficient light-up RNA aptamers as well as metabolites biosensors.