Browsing by Subject "assembly"
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Item Open Access Molecular Computing with DNA Self-Assembly(2009) Majumder, UrmiSynthetic biology is an emerging technology field whose goal is to use biology as a substrate for engineering. Self-assembly is one of the many methods for fabricating such synthetic biosystems.
Self-assembly is a process where components spontaneously arrange themselves into organized aggregates by the selective affinity of substructures. DNA is an excellent candidate for making synthetic biological systems using self-assembly because of its modular structure and simple chemistry. This thesis describes several
techniques which use DNA as a nano-construction material and
explores the computational capabilities of DNA self-assembly.
For this dissertation, I set out to build a biomolecular computing device with several
useful properties, including compactness, robustness, high degrees of complexity, flexibility, scalability and easily characterized yields
and convergence rates. However, a unified device that satisfies all these properties is still many years away. Instead, this thesis presents designs, simulations,
and experimental results for several distinct DNA nano-systems, as
well as experimental protocols, each of which satisfies a subset of the above-mentioned properties. The hope is that the lessons learned from building all these biomolecular computational devices would bring us closer to our ultimate goal and would eventually pave the path for a computing device that satisfies all the properties. We experimentally demonstrate how we can reduce errors in tiling assembly using an optimized set of physical parameters. We propose a novel DNA tile design
which enforces directionality of growth, reducing assembly errors. We build simulation models to characterize damage in fragile nanostructures under the impact of various external forces. Furthermore, we investigate reversible computation as a means to provide self-repairability to such damaged structures.
We suggest two modifications of an existing DNA computing device,
called Whiplash PCR machine, which allow it to operate robustly outside of controlled laboratory conditions and allow it to implement a simple form of inter-device communication. We present analysis techniques which characterize the yields and time convergence of self-assembled DNA nanostructures. We also present an experimental demonstration of a novel DNA nanostructure which is capable of tiling the plane and could prove to be a way of building 3D DNA assemblies.
Item Open Access Self-assembled DNA Nanostructures: from Structural Material to Biomedical Nanodevices(2008-08-08) Li, HanyingIn addition to being the natural genetic information carrier, DNA can also serve as a versatile material for construction of nanoscale objects. By using the base-pairing properties of DNA, we have been able to mass-produce nano-scale structures in a variety of different shapes, upon which patterns of other molecules can be further specified. The diversity of molecules and materials that can be attached to DNA and the capability of providing precise spatial positioning considerably enhance the attractiveness of DNA for nano-scale construction. A further challenge remains to use these DNA based structures for biomedical applications.
As proof-of-concept, a DNA-based nanodevice for multivalent thrombolytic delivery is designed, which intends to employ DNA nanostructures as carriers for the delivery of tissue plasminogen activator (tPA) and plasminogen. Universal modular adapter molecules that can simultaneously bind "down" to the DNA structures and "up" to these thrombolytic drugs are further proposed. We begin with exploring the molecular recognition properties provided by biotin-avidin and aptamer-ligand pairs, and are able to achieve site-specific display of certain protein targets along the DNA nanostructure scaffold. Yet for both of these approaches, only biotinylated or specially selected proteins can be patterned. We further propose to develop single-chain diabodies (scDb) as the adapter molecules. This scDb approach is highly modular and can be extended to assemble virtually any proteins and therapeutic molecules of interests, which at the same time will greatly enhance our molecular toolbox for nanoscale construction.
Item Open Access Structures, Circuits and Architectures for Molecular Scale Integrated Sensing and Computing(2009) Pistol, ConstantinNanoscale devices offer the technological advances to enable a new era in computing. Device sizes at the molecular-scale have the potential to expand the domain of conventional computer systems to reach into environments and application domains that are otherwise impractical, such as single-cell sensing or micro-environmental monitoring.
New potential application domains, like biological scale computing, require processing elements that can function inside nanoscale volumes (e.g. single biological cells) and are thus subject to extreme size and resource constraints. In this thesis we address these critical new domain challenges through a synergistic approach that matches manufacturing techniques, circuit technology, and architectural design with application requirements. We explore and vertically integrate these three fronts: a) assembly methods that can cost-effectively provide nanometer feature sizes, b) device technologies for molecular-scale computing and sensing, and c) architectural design techniques for nanoscale processors, with the goal of mapping a potential path toward achieving molecular-scale computing.
We make four primary contributions in this thesis. First, we develop and experimentally demonstrate a scalable, cost-effective DNA self-assembly-based fabrication technique for molecular circuits. Second, we propose and evaluate Resonance Energy Transfer (RET) logic, a novel nanoscale technology for computing based on single-molecule optical devices. Third, we design and experimentally demonstrate selective sensing of several biomolecules using RET-logic elements. Fourth, we explore the architectural implications of integrating computation and molecular sensors to form nanoscale sensor processors (nSP), nanoscale-sized systems that can sense, process, store and communicate molecular information. Through the use of self-assembly manufacturing, RET molecular logic, and novel architectural techniques, the smallest nSP design is about the size of the largest known virus.
Item Open Access The Street Must Be Defended: Towards a Theory of Assembly on Hong Kong’s Avenida de la Revolución(2020) Tran, Andrew ChiFrom North Africa and the Middle East to Europe, the Americas, and East Asia, the social movements of the past decade have, without being in explicit dialogue with one another, resembled the same march into the public street. Despite the breadth of the cultural, political, and topographical variations in the spaces and places that these movements cover, even in a city like Hong Kong, where the development of urban space has taken a trajectory and assumed a quality of unique status, protest seems to march to the beat of the same drum in Hong Kong’s tropical, urban financial center as it does in St. Louis’ suburban neighborhoods. Why, despite the obvious differences from city-to- city and street-to-street, does protest seem to look the same across societies, cultures, and regimes?
This paper explores the theoretical matrix by which discourses of the street have emerged alongside the imperialisms of the nineteenth century to take inventory of the ways in which the street speaks and is spoken about in the city, in politics, in poetry and literature. While these discourses illuminate the coordinates and mediations in the implicit conception of the street, they only complement the very real emergence and mutations of urban space in Hong Kong in the twentieth century driven by finance capital. I chart the contours of the history of the street in Hong Kong and the ways of capturing the assemblies that have always taken place on it in a step towards understanding how social movement and political assembly can be made effective in contemporary urban space.