Laser Micromachining: An Enabling Technology for Functional Surfaces and Materials

L'abstract è presente nell'allegato / the abstract is in the attachmen

Computational physics of the mind

In the XIX century and earlier such physicists as Newton, Mayer, Hooke, Helmholtz and Mach were actively engaged in the research on psychophysics, trying to relate psychological sensations to intensities of physical stimuli. Computational physics allows to simulate complex neural processes giving a chance to answer not only the original psychophysical questions but also to create models of mind. In this paper several approaches relevant to modeling of mind are outlined. Since direct modeling of the brain functions is rather limited due to the complexity of such models a number of approximations is introduced. The path from the brain, or computational neurosciences, to the mind, or cognitive sciences, is sketched, with emphasis on higher cognitive functions such as memory and consciousness. No fundamental problems in understanding of the mind seem to arise. From computational point of view realistic models require massively parallel architectures

Application of polymeric microfluidic devices for separation of single-stranded DNA

Microsystems targeted for DNA sequencing, especially those focused on electrophoretic separations, are rapidly proving their viability to genomic research, mimicking the progress made when capillary electrophoresis developed from miniaturizing slab gel electrophoresis techniques. Being the more recent electrophoretic separation platform, the commercial availability of microchip electrophoresis devices remains relatively limited. To this extent, high-aspect ratio microstructures formed in thermo plastics have been developed using rapid fabrication methods from molding tools designed for mass replication of high-aspect ratio microfeatures. In this work, the choice and compatibility of poly(methylmethacrylate) (PMMA) – the primary substrate for DNA separations in this work – was investigated for use with our fluorescence lifetime detection instrument. The accuracy and precision of the fluorescence lifetime values of dye-labeled primers used for construction of single-stranded DNA (ssDNA) sequencing tracts was determined to discern the influence of PMMA as a substrate material to the discrimination method. The separation performance of ssDNA was evaluated for potential use of the polymer-based microchip electrophoresis devices as a platform for rapid, high-throughput DNA sequencing. To enhance these separations, a scheme to modify the surface of PMMA employing chemical and photochemical methods was developed. Once optimized, a linear polyacrylamide-modified PMMA surface demonstrated an electroosmotic flow, which varied from chip to chip, lowered by two orders of magnitude and demonstrated increased efficiencies for the separation of ssDNA fragments. As part of a modular system for the analysis of DNA material being developed in our labs, a purification device fabricated in polycarbonate was used to reversibly immobilize DNA sequencing fragments. The purified ssDNA was collected and analyzed by capillary electrophoresis to evaluate the device’s efficiency in removal of contaminants from fragments constructed with dye-labeled primers. One significant result showed the necessity for a down-stream concentration method. Thus, we have investigated the use of a thermally responsive polymer, poly-N-isopropylacrylamide (pNIPAAm) grafted onto the surface of PMMA to serve as a concentration medium for the purified fragments. Results suggest pNIPAAm will be effective in concentrating and releasing fragments when changing the temperature from above its critical temperature (32°), where it exhibits a hydrophobic nature, to below it where it becomes hydrophilic

FABRICATION OF MAGNETIC TWO-DIMENSIONAL AND THREE-DIMENSIONAL MICROSTRUCTURES FOR MICROFLUIDICS AND MICROROBOTICS APPLICATIONS

Micro-electro-mechanical systems (MEMS) technology has had an increasing impact on industry and our society. A wide range of MEMS devices are used in every aspects of our life, from microaccelerators and microgyroscopes to microscale drug-delivery systems. The increasing complexity of microsystems demands diverse microfabrication methods and actuation strategies to realize. Currently, it is challenging for existing microfabrication methods—particularly 3D microfabrication methods—to integrate multiple materials into the same component. This is a particular challenge for some applications, such as microrobotics and microfluidics, where integration of magnetically-responsive materials would be beneficial, because it enables contact-free actuation. In addition, most existing microfabrication methods can only fabricate flat, layered geometries; the few that can fabricate real 3D microstructures are not cost efficient and cannot realize mass production. This dissertation explores two solutions to these microfabrication problems: first, a method for integrating magnetically responsive regions into microstructures using photolithography, and second, a method for creating three-dimensional freestanding microstructures using a modified micromolding technique. The first method is a facile method of producing inexpensive freestanding photopatternable polymer micromagnets composed NdFeB microparticles dispersed in SU-8 photoresist. The microfabrication process is capable of fabricating polymer micromagnets with 3 µm feature resolution and greater than 10:1 aspect ratio. This method was used to demonstrate the creation of freestanding microrobots with an encapsulated magnetic core. A magnetic control system was developed and the magnetic microrobots were moved along a desired path at an average speed of 1.7 mm/s in a fluid environment under the presence of external magnetic field. A microfabrication process using aligned mask micromolding and soft lithography was also developed for creating freestanding microstructures with true 3D geometry. Characterization of this method and resolution limits were demonstrated. The combination of these two microfabrication methods has great potential for integrating several material types into one microstructure for a variety of applications

Contact region fidelity, sensitivity, and control in roll-based soft lithography

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 341-349).Soft lithography is a printing process that uses small features on an elastomeric stamp to transfer micron and sub-micron patterns to a substrate. Translating this lab scale process to a roll-based manufacturing platform allows precise control of the stamp contact region and the potential for large area, high rate surface patterning. In this manner, emerging devices can be produced economically, including flexible displays, distributed sensor networks, transparent conductors, and bio-inspired surfaces. Achieving and maintaining collapse-free contact of the soft stamp features is a necessary condition for printing. In the first part of the thesis, stamp behavior is examined at two length scales. First, microfeature collapse is examined across a range of dimensionless aspect ratios and pattern ratios to determine the collapse mode and the feature stiffness. Second, behavior of roll-mounted stamps is investigated on the macroscopic scale. The results of these analyses, simulations, and experiments show that contact is prohibitively sensitive as the feature scale shrinks to single microns or below. In the second part of the thesis, methods are developed to reduce the contact sensitivity. A compliant stamp architecture is introduced to tune the mechanical response of the stamp. Next, a new process for manufacturing cylindrical stamps is developed that removes limitations of planar stamp templates. The third part of the thesis addresses process control. A parallel kinematic stage is designed to manipulate the height and pitch of a roll over a substrate with submicron precision. A hybrid state-space / classical feedback control approach is used to achieve high bandwidth servo control in the presence of coupling and unmodeled dynamics. Using optical instrumentation, the stamp contact pattern is monitored and can be controlled using camera images as a control variable. Ultimately, a practical method of impedance control is implemented that demonstrates excellent disturbance rejection. The results of this thesis provide models for stamp behavior at the local microscale and the roll-based macroscale. These results illustrate the high sensitivity of contact to displacement disturbances in roll-based lithography, but also provide valuable design insight towards designing stamps and processing machinery that are robust to these inherent disturbances.by Joseph Edward Petrzelka.Ph.D

Case Retrieval Nets as a Model for Building Flexible Information Systems

Im Rahmen dieser Arbeit wird das Modell der Case Retrieval Netze vorgestellt, das ein Speichermodell für die Phase des Retrievals beim fallbasierten Schliessen darstellt. Dieses Modell lehnt sich an Assoziativspeicher an, insbesondere wird das Retrieval als Rekonstruktion des Falles betrachtet anstatt als eine Suche im traditionellen Sinne. Zwei der wesentlichen Vorteile des Modells sind Effizienz und Flexibilität: Effizienz beschreibt dabei die Fähigkeit, mit grossen Fallbasen umzugehen und dennoch schnell ein Resultat des Retrievals liefern zu können. Im Rahmen dieser Arbeit wird dieser Aspekt formal untersucht, das Hauptaugenmerk ist aber eher pragmatisch motiviert insofern als der Retrieval-Prozess so schnell sein sollte, dass der Benutzer möglichst keine Wartezeiten in Kauf nehmen muss. Flexibilität betrifft andererseits die allgemeine Anwendbarkeit des Modells in Bezug auf veränderte Aufgabenstellungen, auf alternative Formen der Fallrepräsentation usw. Hierfür wird das Konzept der Informationsvervollständigung diskutiert, welches insbesondere für die Beschreibung von interaktiven Entscheidungsunterstützungssystemen geeignet ist. Traditionelle Problemlöseverfahren, wie etwa Klassifikation oder Diagnose, können als Spezialfälle von Informationsvervollständigung aufgefasst werden. Das formale Modell der Case Retrieval Netze wird im Detail erläutert und dessen Eigenschaften untersucht. Anschliessend werden einige möglich Erweiterungen beschrieben. Neben diesen theoretischen Aspekten bilden Anwendungen, die mit Hilfe des Case Retrieval Netz Modells erstellt wurden, einen weiteren Schwerpunkt. Diese lassen sich in zwei grosse Richtungen einordnen: intelligente Verkaufsunterstützung für Zwecke des E-Commerce sowie Wissensmanagement auf Basis textueller Dokumente, wobei für letzteres der Aspekt der Wiederbenutzung von Problemlösewissen essentiell ist. Für jedes dieser Gebiete wird eine Anwendung im Detail beschrieben, weitere dienen der Illustration und werden nur kurz erläutert. Zuvor wird allgemein beschrieben, welche Aspekte bei Entwurf und Implementierung eines Informationssystems zu beachten sind, welches das Modell der Case Retrieval Netze nutzt.In this thesis, a specific memory structure is presented that has been developed for the retrieval task in Case-Based Reasoning systems, namely Case Retrieval Nets (CRNs). This model borrows from associative memories in that it suggests to interpret case retrieval as a process of re-constructing a stored case rather than searching for it in the traditional sense. Tow major advantages of this model are efficiency and flexibility: Efficiency, on the one hand, is concerned with the ability to handle large case bases and still deliver retrieval results reasonably fast. In this thesis, a formal investigation of efficiency is included but the main focus is set on a more pragmatic view in the sense that retrieval should, in the ideal case, be fast enough such that for the users of a related system no delay will be noticeable. Flexibility, on the other hand, is related to the general applicability of a case memory depending on the type of task to perform, the representation of cases etc. For this, the concept of information completion is discussed which allows to capture the interactive nature of problem solving methods in particular when they are applied within a decision support system environment. As discussed, information completion, thus, covers more specific problem solving types, such as classification and diagnosis. The formal model of CRNs is presented in detail and its properties are investigated. After that, some possible extensions are described. Besides these more theoretical aspects, a further focus is set on applications that have been developed on the basis of the CRN model. Roughly speaking, two areas of applications can be recognized: electronic commerce applications for which Case-Based Reasoning may provide intelligent sales support, and knowledge management based on textual documents where the reuse of problem solving knowledge plays a crucial role. For each of these areas, a single application is described in full detail and further case studies are listed for illustration purposes. Prior to the details of the applications, a more general framework is presented describing the general design and implementation of an information system that makes uses of the model of CRNs

Development of a Microfluidic Based Portable Analyzer for Continuous Monitoring of Glutamate and other Amino Acid Neurotransmitters

The amino acid glutamate (Glu) is one of the most ubiquitous neurotransmitters in the brain and the chief excitatory neurotransmitter. As a neurotransmitter, Glu is integral to the normal workings of the brain and is involved in many functions, such as memory formation and long-term potentiation, via action on multiple receptors. Two primary classes of Glu receptors, metabotropic and ionotropic respond to the concentration of Glu in the extracellular space of the brain in a dose dependent manner. Large excesses of Glu have been shown to produce an excitotoxic effect, which can lead to the long-term neuronal damage seen in many neurological disorders including stroke and traumatic brain injury (TBI). Following an event such as these, methods for continuous monitoring of Glu concentrations in the brain can be very useful to clinicians for determining the best timing for pharmacological intervention, provided the acquisition of that information can itself be performed in a timely manner. With that in mind, this thesis focuses on the development of analytical methods that will provide information on the extracellular concentration of glutamate and other amino acids in a timely manner and thereby providing actionable information for a clinician. Microdialysis (MD) is an in vivo sampling method that can be used to monitor multiple analytes simultaneously while also enabling the delivery of a pharmaceutical intervention directly to the site of the probe This technique can provide a powerful window into tissue function and health when combined with a separation-based analytical method. However, due to the need for very low flow rates, a trade off exists with regard to sample concentration and time. In order to maximize the concentration and minimize the time required, sensitive methods of detection must be used such as laser induced fluorescence (LIF) detection. To minimize the time required for sample analysis (and make point of care analysis possible), a portable fluorescence detection system for use with microchip electrophoresis was developed. With this system, six neuroactive amines commonly found in brain dialysate (arginine, citrulline, taurine, histamine, glutamate, and aspartate) were derivatized offline with naphthalene-2,3-dicarboxaldehyde/cyanide, separated electrophoretic ally, and detected by fluorescence. It was found that this system was able to detect these analytes of interest within a range of 250 nM – 1.3 µM, which was adequate for subsequent detection in a microdialysis sample collected from the brain of an anesthetized rat. Finally, the design and evaluation of a microfluidic device for coupling microdialysis to microchip electrophoresis with on-line derivatization (MD-ME) is discussed. By coupling sampling directly to the microchip, elements that would otherwise delay analysis such as the need to transport volumes to the analysis system or the wait for the generation of larger sample volumes can be avoided. The MD-ME device was modeled first using COMSOL Multiphysics™ in an effort to optimize the device geometry, allowing on-line sampling with minimal back pressure, but with complete sample derivatization prior to analysis. Following this, the device was evaluated experimentally to detect Glu samples collected via microdialysis over an extended time period. While the limits of detection for Glu were found to be slightly high for immediate use for in vivo brain sampling, it is hoped that modifications to materials used to construct the microchip may eliminate this problem

The development of microfluidic platforms for environmental analysis

There is currently a gap in the use of centrifugal microfluidics in the field environmental sensing. The purpose of this thesis was to develop new and innovative centrifugal microfluidic platforms, which could enhance current environmental monitoring strategy limitations; portability and in-situ capability, cost-effectiveness, generical design for multi-analyte detectability, and the minimal required end-user interaction. Included in the main body of the thesis will be a review article, providing the theoretical perspectives which have been demonstrated for microfluidic applications in other domains and recommendations for adaptation towards environmental sensing using centrifugal microfluidics, and three novel papers on the staged development of a multi- toxin detection platform aimed to be incorporated within the fully deployable MariaBox (Marine environmental in-situ assessment and monitoring toolBox, co-funded by the European Commission: contract no.614088) system. The aspects covered across these three original articles includes the development of a centrifugal microfluidic platform with complementary fluorescence detection system as an initial test bed for toxin bio- assay integration on-disc, progression of current centrifugally-automatable pneumatic microvalve mechanisms for increased actuation predictability, and the further combination of both of these detection and microvalve mechanisms for a complete on- disc, multi-toxin detection platform which has been designed specifically to be compatible with the deployable MariaBox platform

A unified platform for experimental and computational biology

PhD ThesisIn natural sciences, the correct engineering of a system’s chemical, biological and physical properties may allow it to sustain life. Bioengineering cells is probably one of the most complex challenges of biological research; yet, the little we do know about the nature of life is sufficient to guide scientific research, and to explore the elements beyond the apparent simple proliferation of living cells. Although Mendel first characterised the concept of genetic heredity over 150 years ago, we only recently became able to perform tailored genetic modification of living organisms. The development of digital technologies, in particular, has positively influenced the quality and reproducibility of experimental results emerging from biological assays. However, the use of any equipment may require the need for a specific expertise in order to perform a given experimental procedure. Therefore, multidisciplinary research can bring benefits to all fields of science by helping the development of analytical methods that cross the boundaries of individual disciplines. This emerges as a systematic view of scientific problems, and relies on the adequation and integration of results from different research areas. Nevertheless, there is a complex interface between hard sciences that often creates a gap between experimental and theoretical models. In this thesis, we explored synthetic biology approaches and created a unified platform to fill this gap. We propose the first barcoding platform (Bac2code) that allows the identification and the tracking of bacterial strains. In order to facilitate communication between researchers, we developed a barcode system in DNA that physically links bacteria to their genetic description. We designed DNA barcodes as bioorthogonal elements, elaborated a universal cloning strategy to integrate these sequences in Gram-negative and Gram-positive bacteria, and demonstrated their stability over time. Through a generic protocol, any barcoded strain can later be identified via a single sequencing read. With the engineering of a synthetic circuit library, we built a biorepository of genetic constructs for our barcoding platform. These biological devices were optimised based on the closest achievable interface between experimental biology and viii computational results. Following their characterisation, and in the context of intercellular communication, we studied the behaviour of small cohorts of bioengineered cells at the microscale in microfluidics. We pushed the biological and physical boundaries of engineering techniques to the maximum, in order to observe physiological changes between bacteria separated by distances down to 20µm. However, we also showed that we reached a technological barrier, where even the use of nanoscale features was found insufficient to maintain cells isolated under high cellular density. Yet, microfluidics remains a remarkable technology, and we propose the expansion of barcoding methods to automated systems, which would allow serial barcode integration and documentation retrieval at any one time. Here, we developed and tested a barcoding method to ensure the cohesion of experimental and computational biology resources. We demonstrated its use by the in vitro assembly and the in vivo or in silico characterisation of a series of genetic circuits via different techniques. The research output of this thesis is realised as a step forward in interdisciplinary studies, and is now being adapted to reach a larger community of users as a startup companyEngineering and Physical Sciences Research Council and Newcastle University’s School of Computing Science

SCREEN: Learning a Flat Syntactic and Semantic Spoken Language Analysis Using Artificial Neural Networks

In this paper, we describe a so-called screening approach for learning robust processing of spontaneously spoken language. A screening approach is a flat analysis which uses shallow sequences of category representations for analyzing an utterance at various syntactic, semantic and dialog levels. Rather than using a deeply structured symbolic analysis, we use a flat connectionist analysis. This screening approach aims at supporting speech and language processing by using (1) data-driven learning and (2) robustness of connectionist networks. In order to test this approach, we have developed the SCREEN system which is based on this new robust, learned and flat analysis. In this paper, we focus on a detailed description of SCREEN's architecture, the flat syntactic and semantic analysis, the interaction with a speech recognizer, and a detailed evaluation analysis of the robustness under the influence of noisy or incomplete input. The main result of this paper is that flat representations allow more robust processing of spontaneous spoken language than deeply structured representations. In particular, we show how the fault-tolerance and learning capability of connectionist networks can support a flat analysis for providing more robust spoken-language processing within an overall hybrid symbolic/connectionist framework.Comment: 51 pages, Postscript. To be published in Journal of Artificial Intelligence Research 6(1), 199