Redundant Unilaterally Actuated Kinematic Chains: Modeling and Analysis

Unilaterally Actuated Robots (UAR)s are a class of robots defined by an actuation that is constrained to a single sign. Cable robots, grasping, fixturing and tensegrity systems are certain applications of UARs. In recent years, there has been increasing interest in robotic and other mechanical systems actuated or constrained by cables. In such systems, an individual constraint is applied to a body of the mechanism in the form of a pure force which can change its magnitude but cannot reverse its direction. This uni-directional actuation complicates the design of cable-driven robots and can result in limited performance. Cable Driven Parallel Robot (CDPR)s are a class of parallel mechanisms where the actuating legs are replaced by cables. CDPRs benefit from the higher payload to weight ratio and increased rigidity. There is growing interest in the cable actuation of multibody systems. There are potential applications for such mechanisms where low moving inertia is required. Cable-driven serial kinematic chain (CDSKC) are mechanisms where the rigid links form a serial kinematic chain and the cables are arranged in a parallel configuration. CDSKC benefits from the dexterity of the serial mechanisms and the actuation advantages of cable-driven manipulators. Firstly, the kinematic modeling of CDSKC is presented, with a focus on different types of cable routings. A geometric approach based on convex cones is utilized to develop novel cable actuation schemes. The cable routing scheme and architecture have a significant effect on the performance of the robot resulting in a limited workspace and high cable forces required to perform a desired task. A novel cable routing scheme is proposed to reduce the number of actuating cables. The internal routing scheme is where, in addition to being externally routed, the cable can be re-routed internally within the link. This type of routing can be considered as the most generalized form of the multi-segment pass-through routing scheme where a cable segment can be attached within the same link. Secondly, the analysis for CDSKCs require extensions from single link CDPRs to consider different routings. The conditions to satisfy wrench-closure and the workspace analysis of different multi-link unilateral manipulators are investigated. Due to redundant and constrained actuation, it is possible for a motion to be either infeasible or the desired motion can be produced by an infinite number of different actuation profiles. The motion generation of the CDSKCs with a minimal number of actuating cables is studied. The static stiffness evaluation of CDSKCs with different routing topologies and isotropic stiffness conditions were investigated. The dexterity and wrench-based metrics were evaluated throughout the mechanism's workspace. Through this thesis, the fundamental tools required in studying cable-driven serial kinematic chains have been presented. The results of this work highlight the potential of using CDSKCs in bio-inspired systems and tensegrity robots

Modeling, Analysis, Force Sensing and Control of Continuum Robots for Minimally Invasive Surgery

This dissertation describes design, modeling and application of continuum robotics for surgical applications, specifically parallel continuum robots (PCRs) and concentric tube manipulators (CTMs). The introduction of robotics into surgical applications has allowed for a greater degree of precision, less invasive access to more remote surgical sites, and user-intuitive interfaces with enhanced vision systems. The most recent developments have been in the space of continuum robots, whose exible structure create an inherent safety factor when in contact with fragile tissues. The design challenges that exist involve balancing size and strength of the manipulators, controlling the manipulators over long transmission pathways, and incorporating force sensing and feedback from the manipulators to the user. Contributions presented in this work include: (1) prototyping, design, force sensing, and force control investigations of PCRs, and (2) prototyping of a concentric tube manipulator for use in a standard colonoscope. A general kinetostatic model is presented for PCRs along with identification of multiple physical constraints encountered in design and construction. Design considerations and manipulator capabilities are examined in the form of matrix metrics and ellipsoid representations. Finally, force sensing and control are explored and experimental results are provided showing the accuracy of force estimates based on actuation force measurements and control capabilities. An overview of the design requirements, manipulator construction, analysis and experimental results are provided for a CTM used as a tool manipulator in a traditional colonoscope. Currently, tools used in colonoscopic procedures are straight and exit the front of the scope with 1 DOF of operation (jaws of a grasper, tightening of a loop, etc.). This research shows that with a CTM deployed, the dexterity of these tools can be increased dramatically, increasing accuracy of tool operation, ease of use and safety of the overall procedure. The prototype investigated in this work allows for multiple tools to be used during a single procedure. Experimental results show the feasibility and advantages of the newly-designed manipulators

Pedestrian Mobility Mining with Movement Patterns

In street-based mobility mining, pedestrian volume estimation receives increasing attention, as it provides important applications such as billboard evaluation, attraction ranking and emergency support systems. In practice, empirical measurements are sparse due to budget limitations and constrained mounting options. Therefore, estimation of pedestrian quantity is required to perform pedestrian mobility analysis at unobserved locations. Accurate pedestrian mobility analysis is difficult to achieve due to the non-random path selection of individual pedestrians (resulting from motivated movement behaviour), causing the pedestrian volumes to distribute non-uniformly among the traffic network. Existing approaches (pedestrian simulations and data mining methods) are hard to adjust to sensor measurements or require more expensive input data (e.g. high fidelity floor plans or total number of pedestrians in the site) and are thus unfeasible. In order to achieve a mobility model that encodes pedestrian volumes accurately, we propose two methods under the regression framework which overcome the limitations of existing methods. Namely, these two methods incorporate not just topological information and episodic sensor readings, but also prior knowledge on movement preferences and movement patterns. The first one is based on Least Squares Regression (LSR). The advantage of this method is the easy inclusion of route choice heuristics and robustness towards contradicting measurements. The second method is Gaussian Process Regression (GPR). The advantages of this method are the possibilities to include expert knowledge on pedestrian movement and to estimate the uncertainty in predicting the unknown frequencies. Furthermore the kernel matrix of the pedestrian frequencies returned by the method supports sensor placement decisions. Major benefits of the regression approach are (1) seamless integration of expert data and (2) simple reproduction of sensor measurements. Further advantages are (3) invariance of the results against traffic network homeomorphism and (4) the computational complexity depends not on the number of modeled pedestrians but on the traffic network complexity. We compare our novel approaches to state-of-the-art pedestrian simulation (Generalized Centrifugal Force Model) as well as existing Data Mining methods for traffic volume estimation (Spatial k-Nearest Neighbour) and commonly used graph kernels for the Gaussian Process Regression (Squared Exponential, Regularized Laplacian and Diffusion Kernel) in terms of prediction performance (measured with mean absolute error). Our methods showed significantly lower error rates. Since pattern knowledge is not easy to obtain, we present algorithms for pattern acquisition and analysis from Episodic Movement Data. The proposed analysis of Episodic Movement Data involve spatio-temporal aggregation of visits and flows, cluster analyses and dependency models. For pedestrian mobility data collection we further developed and successfully applied the recently evolved Bluetooth tracking technology. The introduced methods are combined to a system for pedestrian mobility analysis which comprises three layers. The Sensor Layer (1) monitors geo-coded sensor recordings on people’s presence and hands this episodic movement data in as input to the next layer. By use of standardized Open Geographic Consortium (OGC) compliant interfaces for data collection, we support seamless integration of various sensor technologies depending on the application requirements. The Query Layer (2) interacts with the user, who could ask for analyses within a given region and a certain time interval. Results are returned to the user in OGC conform Geography Markup Language (GML) format. The user query triggers the (3) Analysis Layer which utilizes the mobility model for pedestrian volume estimation. The proposed approach is promising for location performance evaluation and attractor identification. Thus, it was successfully applied to numerous industrial applications: Zurich central train station, the zoo of Duisburg (Germany) and a football stadium (Stade des Costières Nîmes, France)

A Contribution to the Design of Highly Redundant Compliant Aerial Manipulation Systems

Es ist vorhersehbar, dass die Luftmanipulatoren in den nächsten Jahrzehnten für viele Aufgaben eingesetzt werden, die entweder zu gefährlich oder zu teuer sind, um sie mit herkömmlichen Methoden zu bewältigen. In dieser Arbeit wird eine neuartige Lösung für die Gesamtsteuerung von hochredundanten Luftmanipulationssystemen vorgestellt. Die Ergebnisse werden auf eine Referenzkonfiguration angewendet, die als universelle Plattform für die Durchführung verschiedener Luftmanipulationsaufgaben etabliert wird. Diese Plattform besteht aus einer omnidirektionalen Drohne und einem seriellen Manipulator. Um den modularen Regelungsentwurf zu gewährleisten, werden zwei rechnerisch effiziente Algorithmen untersucht, um den virtuellen Eingang den Aktuatorbefehlen zuzuordnen. Durch die Integration eines auf einem künstlichen neuronalen Netz basierenden Diagnosemoduls und der rekonfigurierbaren Steuerungszuordnung in den Regelkreis, wird die Fehlertoleranz für die Drohne erzielt. Außerdem wird die Motorsättigung durch Rekonfiguration der Geschwindigkeits- und Beschleunigungsprofile behandelt. Für die Beobachtung der externen Kräfte und Drehmomente werden zwei Filter vorgestellt. Dies ist notwendig, um ein nachgiebiges Verhalten des Endeffektors durch die achsenselektive Impedanzregelung zu erreichen. Unter Ausnutzung der Redundanz des vorgestellten Luftmanipulators wird ein Regler entworfen, der nicht nur die Referenz der Endeffektor-Bewegung verfolgt, sondern auch priorisierte sekundäre Aufgaben ausführt. Die Wirksamkeit der vorgestellten Lösungen wird durch umfangreiche Tests überprüft, und das vorgestellte Steuerungssystem wird als sehr vielseitig und effektiv bewertet.:1 Introduction 2 Fundamentals 3 System Design and Modeling 4 Reconfigurable Control Allocation 5 Fault Diagnostics For Free Flight 6 Force and Torque Observer 7 Trajectory Generation 8 Hybrid Task Priority Control 9 System Integration and Performance Evaluation 10 ConclusionIn the following decades, aerial manipulators are expected to be deployed in scenarios that are either too dangerous for human beings or too expensive to be accomplished by traditional methods. This thesis presents a novel solution for the overall control of highly redundant aerial manipulation systems. The results are applied to a reference configuration established as a universal platform for performing various aerial manipulation tasks. The platform consists of an omnidirectional multirotor UAV and a serial manipulator. To ensure modular control design, two computationally efficient algorithms are studied to allocate the virtual input to actuator commands. Fault tolerance of the aerial vehicle is achieved by integrating a diagnostic module based on an artificial neural network and the reconfigurable control allocation into the control loop. Besides, the risk of input saturation of individual rotors is minimized by predicting and reconfiguring the speed and acceleration responses. Two filter-based observers are presented to provide the knowledge of external forces and torques, which is necessary to achieve compliant behavior of the end-effector through an axis-selective impedance control in the outer loop. Exploiting the redundancy of the proposed aerial manipulator, the author has designed a control law to achieve the desired end-effector motion and execute secondary tasks in order of priority. The effectiveness of the proposed designs is verified with extensive tests generated by following Monte Carlo method, and the presented control scheme is proved to be versatile and effective.:1 Introduction 2 Fundamentals 3 System Design and Modeling 4 Reconfigurable Control Allocation 5 Fault Diagnostics For Free Flight 6 Force and Torque Observer 7 Trajectory Generation 8 Hybrid Task Priority Control 9 System Integration and Performance Evaluation 10 Conclusio

A centrifugal microfluidic platform for capturing, assaying and manipulation of beads and biological cells

Microfluidics is deemed a field with great opportunities, especially for applications in medical diagnostics. The vision is to miniaturize processes typically performed in a central clinical lab into small, simple to use devices - so called lab-on-a-chip (LOC) systems. A wide variety of concepts for liquid actuation have been developed, including pressure driven flow, electro-osmotic actuation or capillary driven methods. This work is based on the centrifugal platform (lab-on-a-disc). Fluid actuation is performed by the forces induced due to the rotation of the disc, thus eliminating the need for external pumps since only a spindle motor is necessary to rotate the disc and propel the liquids inside of the micro structures. Lab-on-a-disc systems are especially promising for point-of-care applications involving particles or cells due to the centrifugal force present in a rotating system. Capturing, assaying and identification of biological cells and microparticles are important operations for lab-on-a-disc platforms, and the focus of this work is to provide novel building blocks towards an integrated system for cell and particle based assays. As a main outcome of my work, a novel particle capturing and manipulation scheme on a centrifugal microfluidic platform has been developed. To capture particles (biological cells or micro-beads) I designed an array of V-shaped micro cups and characterized it. Particles sediment under stagnant flow conditions into the array where they are then mechanically trapped in spatially well-defined locations. Due to the absence of flow during the capturing process, i.e. particle sedimentation is driven by the artificial gravity field on the centrifugal platform, the capture efficiency of this approach is close to 100% which is notably higher than values reported for typical pressure driven systems. After capturing the particles, the surrounding medium can easily be exchanged to expose them to various conditions such as staining solutions or washing buffers, and thus perform assays on the captured particles. By scale matching the size of the capturing elements to the size of the particles, sharply peaked single occupancy can be achieved. Since all particles are arrayed in the same focal plane in spatially well defined locations, operations such as counting or fluorescent detection can be performed easily. The application of this platform to perform multiplexed bead-based immunoassays as well as the discrimination of various cell types based on intra cellular and membrane based markers using fluorescently tagged antibodies is demonstrated. Additionally, methods to manipulate captured particles either in batch mode or on an individual particle level have been developed and characterized. Batch release of captured particles is performed by a novel magnetic actuator which is solely controlled by the rotation frequency of the disc. Furthermore, the application of this actuator to rapidly mix liquids is shown. Manipulation of individual particles is performed using an optical tweezers setup which has been developed as part of this work. Additionally, this optical module also provides fluorescence detection capabilities. This is the first time that optical tweezers have been combined with a centrifugal microfluidic system. This work presents the core technology for an integrated centrifugal platform to perform cell and particle based assays for fundamental research as well as for point-of- care applications. The key outputs of my specific work are: 1. Design, fabrication and characterization of a novel particle capturing scheme on a centrifugal microfluidic platform (V-cups) with very high capture efficiency (close to 100%) and sharply peaked single occupancy (up to 99.7% single occupancy). 2. A novel rotation frequency controlled magnetic actuator for releasing captured particles as well as for rapidly mixing liquids has been developed, manufactured and characterized. 3. The V-cup platform has successfully been employed to capture cells and perform multi-step antibody staining assays for cell discrimination. 4. An optical tweezers setup has been built and integrated into a centrifugal teststand, and successful manipulation of individual particles trapped in the V-cup array is demonstrated

Design and analysis of integrated waveguide structures and their coupling to silicon-based light emitters

A major focus is on integrated Silicon-based optoelectronics for the creation of low-cost photonics for mass-market applications. Especially, the growing demand for sensitive and portable optical sensors in the environmental control and medicine follows in the development of integrated high resolution sensors [1]. In particular, since 2013 the quick onsite verification of pathogens, like legionella in drinking water pipes, is becoming increasingly important [2, 3]. The essential questions regarding the establishment of portable biochemical sensors are the incorporation of electronic and optical devices as well as the implementations of fundamental cross-innovations between biotechnology and microelectronics. This thesis describes the design, fabrication and analysis of high-refractive-index-contrast photonic structures. Besides silicon nitride (Si3N4) strip waveguides, lateral tapers, bended waveguides, two-dimensional photonic crystals (PhCs) the focus lies on monolithically integrated waveguide butt-coupled Silicon-based light emitting devices (Sibased LEDs) [4, 5] for use as bioanalytical sensor components. Firstly, the design and performance characteristics as single mode regime, confinement factor and propagation losses due to the geometry and operation wavelength (1550 nm, 541 nm) of single mode (SM), multi mode (MM) waveguides and bends are studied and simulated. As a result, SM operation is obtained for 1550 nm by limiting the waveguide cross-section to 0.5 μm x 1 μm resulting in modal confinement factors of 87 %. In contrast, for shorter wavelengths as 541 nm SM propagation is excluded if the core height is not further decreased. Moreover, the obtained theoretical propagation losses for the lowestorder TE/TM mode are in the range of 0.3 - 1.3 dB/cm for an interface roughness of 1 nm. The lower silicon dioxide (SiO2) waveguide cladding should be at least 1 μm to avoid substrate radiations. These results are in a good correlation to the known values for common dielectric structures. In the case of bended waveguides, an idealized device with a radius of 10 μm was developed which shows a reflection minimum (S11 = - 22 dB) at 1550 nm resulting in almost perfect transmission of the signal. Additionally, tapered waveguides were investigated for an optimized light coupling between high-aspect-ratio devices. Here, adiabatic down-tapered waveguides were designed for the elimination of higher-order modes and perfect signal transmission. Secondly, fabrication lines including Electron-beam (E-beam) lithography and reactive ion etching (RIE) with an Aluminum (Al) mask were developed and lead to well fabricated optical devices in the (sub)micrometer range. The usage of focused ion beam (FIB) milling is invented for smoother front faces which were analyzed by scanning electron microscopy (SEM) and atomic force microscopy (AFM). As a result, the anisotropy of the RIE process was increased, but the obtained surface roughness parameters are still too high (10 – 20 nm) demonstrating a more advanced lithography technique is needed for higher quality structures. Moreover, this study presents an alternative fabrication pathway for novel designed waveguides with free-edge overlapping endfaces for improving fiber-chipcoupling. Thirdly, the main focus lies on the development of a monolithic integration circuit consisting of the Si-based LED coupled to an integrated waveguide. The light propagation between high-aspect-ratio devices is enabled through low-loss adiabatic tapers. This study shows, that the usage of CMOS-related fabrication technologies result in a monolithic manufacturing pathway for the successful implementation of fully integrated Si-based photonic circuits. Fourth, transmission loss measurements of the fabricated photonic structures as well as the waveguide butt-coupled Si-based LEDs were performed with a generated setup. As a result, free-edge overlapping MM waveguides show propagation loss coefficients of ~ 65 dB/cm in the range of the telecommunication wavelength. The high surface roughness parameters (~ 150 nm) and the modal dispersion in the core are one of the key driving factors. These facts clearly underline the improvement potential of the used fabrication processes. However, electroluminescence (EL) measurements of waveguide butt-coupled Si-based LEDs due to the implanted rare earth (RE) ion (Tb3+, Er3+) and the host material (SiO2/SiNx) were carried out. The detected transmission spectra of the coupled Tb:SiO2 systems show a weak EL signal at the main transition line of the Tb3+-ion (538 nm). A second emission line was detected in the red region of the spectrum either corresponding to a further optical transition of Tb3+ or a Non Bridging Oxygen Hole Center (NBOHC) in SiO2. Unfortunately, no light emission in the infrared range was established for the Er3+-doped photonic circuits caused by the low external quantum efficiencies (EQE) of the Er3+ implanted Si-based LEDs. Nevertheless, transmission measurements between 450 nm – 800 nm lead again to the result that an emission at 650 nm is either caused by an optical transition of the Er3+-ion or initialized by the NBOHC in the host. Overall, it is difficult to assess whether or not these EL signals are generated from the implanted ions, thus detailed statements about the coupling efficiency between the LED and the integrated waveguide are quite inadequate. Nevertheless, the principle of a fully monolithically integrated photonic circuit consisting of a Si-based LED and a waveguide has been successfully proven in this study

Formulation and aerosol delivery of nano-sized biomaterials

The aim of this research has been to study and develop the engineering principles associated with the impact of formulation and device parameters on the safe delivery of nano-sized biomaterials such as plasmid DNA. In the present investigation, Omron U22 and U03 mesh nebulisers operating at frequencies of ~175 kHz and ~65 kHz respectively were used. Since the U22 device is a recently introduced mesh nebuliser for respiratory drug delivery, detailed characterisation, experimentation, modelling and analysis was carried out for this device. Plasmids of size 5.7, 8.7, 13 and 20 kb were purified from Escherichia coli cells and used for nebulisation experiments. Experiments on the nebulisation of plasmid DNA using the U22 device in a bio-safety cabinet showed no damage to the sc structure of the 5.7 kb plasmid, but almost complete damage to the 20 kb plasmid in the condensed aerosols collected using a fabricated aerosol collection apparatus. The damage to the sc structure of plasmid DNA was analysed using gel electrophoresis, PicoGreen assay and atomic force microscope (AFM). Engineering analysis was performed using computational fluid dynamics (CFD) modelling to determine the shear and elongational strain rates in the mesh nozzle of nebuliser. The estimated maximum hydrodynamic force on plasmid DNA based on the Ryskin equation was calculated in picoNewton (PN) from the actual molecular size of the sc structure and predicted strain rates. Optimisation of the formulation and device parameters were carried out using Design of Experiments (DOE) to predict damage to the sc structure. Formulation of the 20 kb plasmid with polyethyleneimine (PEI) resulted in safe aerosol delivery using the mesh nebuliser. In vitro transfection studies in suspension-adapted Chinese Hamster Ovary (CHO-S) cells resulted in successful integration of Green Fluorescent Protein (GFP) from the 5.7 kb plasmid after nebulisation. The commercially available U22 mesh nebuliser promises to be a useful pulmonary device for the successful delivery of plasmid DNA for non-viral gene therapy. Realisation of this promise however will require both innovations in the design of experiments, formulation and methods of studying plasmid DNA damage as demonstrated in this thesis

The development of a warhead into an integrated weapon system to provide an advanced battlefield capability

This thesis addresses the topic of integration of weapons systems into communication networks to provide an advanced battlefield capability, with particular application to air launched and long range crew served weapon systems which may also be vehicle mounted. It considers the use of 'Military off-the-shelf' seeker, navigation and communication systems coupled with a novel tandem warhead system. This combination of 'low risk' technologies and a novel warhead system is intended to demonstrate a greater flexibility in weapon systems which could be exploited to reduce development risk, integration risk, qualification costs and increase target defeat capability across the wider more current target set. The use of a suitable communication and navigation system enabling integration of such a weapon system into a networked force was also investigated. This thesis is based on one area of research; Multiple Effects Weapons. Research is being undertaken by several nations on Multiple Effects Weapons. The aim of this research is not to provide a one weapon fits all solution, a panacea, the aim is to widen the utility of one system which could be employed in many roles. As yet no warhead system has achieved the types of effects that are being sought, although research and product development – particularly in the United States of America - continues. Therefore the United Kingdom government has sought to understand what technologies would be required to achieve a truly flexible warhead system which would enable defeat of large Main Battle Tanks, heavily armoured Infantry Fighting Vehicles, Soft Skinned Vehicles, infantry and urban structures. To this end numerical modelling, design and a demonstration programme of a MEW warhead system was performed. MEW systems are not only reliant on 'Smart' warhead systems, the application of sensors, fuzing and communication systems are crucial to enable suitable employment of a 'one size fits most' approach. The other important sub-systems which provide the link to the battlefield network are also discussed in this thesis, the inclusion of these well developed low risk technologies make it is possible to bring such systems into service in the near term with increased system flexibility. The integration of such a system relies on the current United States Department of Defense procurement strategy which includes development of the Joint Tactical Radio System radio system which will allow Ad-Hoc networking between platforms, weapons systems and commanders. Airframe and propulsion technologies are not discussed; they are outside of the scope of this thesis. The use of proprietary data from suppliers other than QinetiQ has been avoided as suitable permissions are not in place, this has limited the systems engineering aspects of this thesis to high level block diagrams which provide guidance on integration issues

Genetic Analysis and Cell Manipulation on Microfluidic Surfaces

Personalized cancer medicine is a cancer care paradigm in which diagnostic and therapeutic strategies are customized for individual patients. Microsystems that are created by Micro-Electro-Mechanical Systems (MEMS) technology and integrate various diagnostic and therapeutic methods on a single chip hold great potential to enable personalized cancer medicine. Toward ultimate realization of such microsystems, this thesis focuses on developing critical functional building blocks that perform genetic variation identification (single-nucleotide polymorphism (SNP) genotyping) and specific, efficient and flexible cell manipulation on microfluidic surfaces. For the identification of genetic variations, we first present a bead-based approach to detect single-base mutations by performing single-base extension (SBE) of SNP specific primers on solid surfaces. Successful genotyping of the SNP on exon 1 of HBB gene demonstrates the potential of the device for simple, rapid, and accurate detection of SNPs. In addition, a multi-step solution-based approach, which integrates SBE with mass-tagged dideoxynucleotides and solid-phase purification of extension products, is also presented. Rapid, accurate and simultaneous detection of 4 loci on a synthetic template demonstrates the capability of multiplex genotyping with reduced consumption of samples and reagents. For cell manipulation, we first present a microfluidic device for cell purification with surface-immobilized aptamers, exploiting the strong temperature dependence of the affinity binding between aptamers and cells. Further, we demonstrate the feasibility of using aptamers to specifically separate target cells from a heterogeneous solution and employing environmental changes to retrieve purified cells. Moreover, spatially specific capture and selective temperature-mediated release of cells on design-specified areas is presented, which demonstrates the ability to establish cell arrays on pre-defined regions and to collect only specifically selected cell groups for downstream analysis. We also investigate tunable microfluidic trapping of cells by exploiting the large compliance of elastomers to create an array of cell-trapping microstructures, whose dimensions can be mechanically modulated by inducing uniform strain via the application of external force. Cell trapping under different strain modulations has been studied, and capture of a predetermined number of cells, from single cells to multiple cells, has been achieved. In addition, to address the lack of aptamers for targets of interest, which is a major hindrance to aptamer-based cell manipulation, we present a microfluidic device for synthetically isolating cell-targeting aptamers from a randomized single-strand DNA (ssDNA) library, integrating cell culturing with affinity selection and amplification of cell-binding ssDNA. Multi-round aptamer isolation on a single chip has also been realized by using pressure-driven flow. Finally, some perspectives on future work are presented, and strategies and notable issues are discussed for further development of MEMS/microfluidics-based devices for personalized cancer medicine

Mechanisms of Vegetation-Induced Channel Narrowing on an Unregulated Canyon-Bound River

The processes and interactions that determine the width of a river channel remain a fundamental area of investigation in geomorphology. An increasing appreciation of the capacity of riparian vegetation to alter fluvial processes, and thus influence channel form, has highlighted the need to include vegetation in these analyses. However, a disconnect exists between the small spatial and temporal scales over which the linkages among flow patterns, sediment, and plants are evaluated and the larger spatial and temporal scales in which river systems operate. In this dissertation, I strove to identify some of the key mechanisms by which vegetation affects channel width. I worked to reconcile the issue of scale by developing a novel tool that resolves patch-scale (sub-meter) patterns of hydraulic roughness over the reach scale. While the approach can be generalized to evaluate any vegetated floodplain, the multi-scalar model was specifically applied to stands dominated by the non-native riparian shrub, tamarisk, that invaded the riparian corridor of southwestern US rivers during the past century. I focused my analyses on the lower Yampa River in western Colorado. Tamarisk colonized the Yampa in the absence of other environmental perturbations. As a result, adjustments to channel form may be linked to an altered vegetation community. From a careful geomorphic and vegetation reconstruction of the Yampa, I determined that tamarisk was the driving force in channel narrowing. Application of the multi-scalar model of vegetation resistance to the Yampa enabled me to reconstruct the changing hydraulic conditions as tamarisk established and the channel narrowed over time. This hydraulic reconstruction furthered our understanding of the interactions among vegetation recruitment patterns, the increased hydraulic resistance, and the changing flow and sediment transport field. Positive feedbacks between vegetation and geomorphic change created additional areas within the channel where tamarisk could establish, and thus accelerated the rate of channel narrowing. However, these feedbacks also changed the importance of common and large floods for vegetation establishment and sediment transport. Application of this process-based understanding to future flow regimes will help managers anticipate locations along the channel that are susceptible to vegetation encroachment and changes to channel width