Programmable disorder in random DNA tilings

Scaling up the complexity and diversity of synthetic molecular structures will require strategies that exploit the inherent stochasticity of molecular systems in a controlled fashion. Here we demonstrate a framework for programming random DNA tilings and show how to control the properties of global patterns through simple, local rules. We constructed three general forms of planar network—random loops, mazes and trees—on the surface of self-assembled DNA origami arrays on the micrometre scale with nanometre resolution. Using simple molecular building blocks and robust experimental conditions, we demonstrate control of a wide range of properties of the random networks, including the branching rules, the growth directions, the proximity between adjacent networks and the size distribution. Much as combinatorial approaches for generating random one-dimensional chains of polymers have been used to revolutionize chemical synthesis and the selection of functional nucleic acids, our strategy extends these principles to random two-dimensional networks of molecules and creates new opportunities for fabricating more complex molecular devices that are organized by DNA nanostructures

Stochastic Modeling and Optimal Control for Colloidal Organization, Navigation, and Machines

Colloidal suspensions consisting of particles undergoing Brownian motion are ubiquitous in scientific research and emerging technologies. Longstanding challenges in strategic control of complex colloidal systems are to investigate the principle of optimal control, overcome the curse of dimensionality, design efficient algorithms, and develop generalizable control strategies. In the first part of this dissertation, we present methods and results from three case studies to illustrate how these challenges are addressed from the perspectives of modeling and optimal control. Single-agent optimal navigation in complex mazes. We investigate the optimal navigation principle of a self-propelled colloidal particle in complex mazes. We construct approximate Markov chain model and use the Markov decision process framework to obtain the general principle of optimal navigation. Multiple-agent cooperation and coordination for colloidal machines. Using self-propelled Janus motors as the model system, we illustrate a new paradigm for cargo capture and transport based on multiple-agent feedback control. The control algorithm can coordinate multiple motors to cooperate on forming a reconfigurable machine for cargo capture and transport. Low-dimensional modeling and ensemble control. Optimal control in a high dimensional self-assembly processes with limited actuations presents a challenge in both modelling and controller design. We use colloidal crystallization in an electric field as a model system to illustrate the methodologies of low-dimensional modeling and control for self-assembly processes. We use a nonlinear machine learning algorithm to characterize the dimensionality and parametrize the low-dimension manifold on which the system evolves. A low-dimensional Smoluchowski model is constructed and calibrated to illustrate the dynamic pathways of the assembly process. The resulting model is further leveraged to perform optimal control of the assembly process. In the second part of dissertation, we report three additional relevant research projects on colloidal interaction, dynamics, and control. The first project extends ensemble control from finite-size systems to infinite-size systems using feedback control in sedimentation. The second project develops a computational method to model depletion interactions between general geometric objects The third project develops modified Stokesian dynamics methods to investigate the colloidal rod motion near a planar wall with hydrodynamic interactions

Engineering evolutionary control for real-world robotic systems

Evolutionary Robotics (ER) is the field of study concerned with the application of evolutionary computation to the design of robotic systems. Two main issues have prevented ER from being applied to real-world tasks, namely scaling to complex tasks and the transfer of control to real-robot systems. Finding solutions to complex tasks is challenging for evolutionary approaches due to the bootstrap problem and deception. When the task goal is too difficult, the evolutionary process will drift in regions of the search space with equally low levels of performance and therefore fail to bootstrap. Furthermore, the search space tends to get rugged (deceptive) as task complexity increases, which can lead to premature convergence. Another prominent issue in ER is the reality gap. Behavioral control is typically evolved in simulation and then only transferred to the real robotic hardware when a good solution has been found. Since simulation is an abstraction of the real world, the accuracy of the robot model and its interactions with the environment is limited. As a result, control evolved in a simulator tends to display a lower performance in reality than in simulation. In this thesis, we present a hierarchical control synthesis approach that enables the use of ER techniques for complex tasks in real robotic hardware by mitigating the bootstrap problem, deception, and the reality gap. We recursively decompose a task into sub-tasks, and synthesize control for each sub-task. The individual behaviors are then composed hierarchically. The possibility of incrementally transferring control as the controller is composed allows transferability issues to be addressed locally in the controller hierarchy. Our approach features hybridity, allowing different control synthesis techniques to be combined. We demonstrate our approach in a series of tasks that go beyond the complexity of tasks where ER has been successfully applied. We further show that hierarchical control can be applied in single-robot systems and in multirobot systems. Given our long-term goal of enabling the application of ER techniques to real-world tasks, we systematically validate our approach in real robotic hardware. For one of the demonstrations in this thesis, we have designed and built a swarm robotic platform, and we show the first successful transfer of evolved and hierarchical control to a swarm of robots outside of controlled laboratory conditions.A Robótica Evolutiva (RE) é a área de investigação que estuda a aplicação de computação evolutiva na conceção de sistemas robóticos. Dois principais desafios têm impedido a aplicação da RE em tarefas do mundo real: a dificuldade em solucionar tarefas complexas e a transferência de controladores evoluídos para sistemas robóticos reais. Encontrar soluções para tarefas complexas é desafiante para as técnicas evolutivas devido ao bootstrap problem e à deception. Quando o objetivo é demasiado difícil, o processo evolutivo tende a permanecer em regiões do espaço de procura com níveis de desempenho igualmente baixos, e consequentemente não consegue inicializar. Por outro lado, o espaço de procura tende a enrugar à medida que a complexidade da tarefa aumenta, o que pode resultar numa convergência prematura. Outro desafio na RE é a reality gap. O controlo robótico é tipicamente evoluído em simulação, e só é transferido para o sistema robótico real quando uma boa solução tiver sido encontrada. Como a simulação é uma abstração da realidade, a precisão do modelo do robô e das suas interações com o ambiente é limitada, podendo resultar em controladores com um menor desempenho no mundo real. Nesta tese, apresentamos uma abordagem de síntese de controlo hierárquica que permite o uso de técnicas de RE em tarefas complexas com hardware robótico real, mitigando o bootstrap problem, a deception e a reality gap. Decompomos recursivamente uma tarefa em sub-tarefas, e sintetizamos controlo para cada subtarefa. Os comportamentos individuais são então compostos hierarquicamente. A possibilidade de transferir o controlo incrementalmente à medida que o controlador é composto permite que problemas de transferibilidade possam ser endereçados localmente na hierarquia do controlador. A nossa abordagem permite o uso de diferentes técnicas de síntese de controlo, resultando em controladores híbridos. Demonstramos a nossa abordagem em várias tarefas que vão para além da complexidade das tarefas onde a RE foi aplicada. Também mostramos que o controlo hierárquico pode ser aplicado em sistemas de um robô ou sistemas multirobô. Dado o nosso objetivo de longo prazo de permitir o uso de técnicas de RE em tarefas no mundo real, concebemos e desenvolvemos uma plataforma de robótica de enxame, e mostramos a primeira transferência de controlo evoluído e hierárquico para um exame de robôs fora de condições controladas de laboratório.This work has been supported by the Portuguese Foundation for Science and Technology (Fundação para a Ciência e Tecnologia) under the grants SFRH/BD/76438/2011, EXPL/EEI-AUT/0329/2013, and by Instituto de Telecomunicações under the grant UID/EEA/50008/2013

Programmable disorder in random DNA tilings

Scaling up the complexity and diversity of synthetic molecular structures will require strategies that exploit the inherent stochasticity of molecular systems in a controlled fashion. Here we demonstrate a framework for programming random DNA tilings and show how to control the properties of global patterns through simple, local rules. We constructed three general forms of planar network—random loops, mazes and trees—on the surface of self-assembled DNA origami arrays on the micrometre scale with nanometre resolution. Using simple molecular building blocks and robust experimental conditions, we demonstrate control of a wide range of properties of the random networks, including the branching rules, the growth directions, the proximity between adjacent networks and the size distribution. Much as combinatorial approaches for generating random one-dimensional chains of polymers have been used to revolutionize chemical synthesis and the selection of functional nucleic acids, our strategy extends these principles to random two-dimensional networks of molecules and creates new opportunities for fabricating more complex molecular devices that are organized by DNA nanostructures

(Do Not) Overlook. Room 237 and the Dismemberment of The Shining

Few movies in the history of cinema have been as enigmatic and thought-provoking as Kubrick's horror masterpiece The Shining (1980). The movie's maze structure and archetypical background of mythical reminiscence have challenged many film scholars and cinephiles to unravel the intricate pattern that Kubrick created. In 2012, the young filmmaker Rodney Ascher made Room 237,a documentary not so much about The Shining itself as about the many interpretations generated from Kubrick's movie. Assembled from movies' excerpts and archival materials, and with commentary by five people with different interests but united by an authentic obsession with The Shining, Room 237 is an enlightening journey into the most obscure regions of cinephilia, where repeated viewings of movies and overlap between cinema and everyday life confuse different levels of reality, causing an interpretation of the world mediated by cinema. Furthermore, the fragmentary structure of Room 237, constituted by a wide variety of material (from found footage to the visual analysis of The Shining's most compelling scenes), embodies and represents the progress of cinematographic spectatorship, from the movie theater to the home video years, and the Internet era with its digital streaming services. The article's main goal is to show how Kubrick's The Shining is particularly suitable for repeated compulsive viewing that encourages sensory overload and a potentially infinite cycle of interpretations. Furthermore, analysis of Room 237 will highlight the distinctive traits of contemporary remix aesthetic, which Ascher seems to choose as a vehicle for a reflection on the different ways of modern cinephilia

Thinking Through Consciousness

Consciousness is difficult to pin down. Most human beings go about their days with full and more or less uninterrupted consciousness, without contemplating their own (or other peoples’) conscious states. To be in the world, and accomplish great acts takes little metaawareness of consciousness, but in the study of consciousness our inability to think outside of our conscious states creates controversies at the conceptual and methodological levels. As Victor Lamme states (2006), even when we set aside the more difficult (or more poorly defined) questions about conscious experience to focus on finding the neural correlates of consciousness (NCC), we face immense difficulties (Lamme, 2006, p. 494). Experiments designed to find the NCC often involve the manipulation of conscious states through anesthesia, the study of sleep, or brain lesion studies (Lamme, 2006, p. 494). However, even in the case of anesthesia, where we can voluntarily induce a reversible altered state of consciousness there does not seem to be a clear dividing line between consciousness and unconsciousness with any of the processed electroencephalogram (EEG) signals (Guzeldere, 1998, p. 1) such that the conscious and unconscious states are still confirmed behaviorally (Lamme, 2006, p. 494). This leads to a problem, as it must be decided what behavioral measures \u27count\u27 as evidence for the subject having conscious experience (p. 494) a problem that is not so simple as the ability to speak and respond, as will be more clear in a later discussion of intraoperative awareness. Furthermore, Guven Guzeldere points to the difficulty of defining what the problem of consciousness is, within and across disciplinary boundaries (Guzeldere, p. 7). The problems that philosophers of consciousness, cognitive scientists and neuroscientists address when they study consciousness are not inevitably going to be identical, but are shaped by disciplinary perspectives, methods and technologies. Therefore, in this paper I am going to contrast two similar models of consciousness, Giulio Tononi’s Integrated Information Theory and Daniel Dennett’s Multiple Drafts Model, and evaluate them against the mechanisms of several anesthetics (Propofol, ketamine, and the inhalation anesthetics, including xenon), which will be summarized by a review of the literature. I have two goals in mind with this project: first, I have chosen two very similar models in order to demonstrate how small differences- such as Tononi’s engagement with the concept of qualia and Dennett’s deconstruction of it-- have large implications for what types of knowledge are possible when these models are applied; second, I am summarizing the literature concerning the study of anesthetics to show both that anesthetics are useful for the elucidation of the neural correlates of consciousness, and that there is a danger of conflating the neural correlates of unconsciousness with a full description of how consciousness arises, or what consciousness is. Moreover, I will argue that because Dennett’s model specifically addresses the importance of language in shaping human consciousness, despite the distance between his model and a full neurobiological approach, his model is more useful going forward. It must be emphasized that I am not arguing that Dennett’s model is the correct model of consciousness, but that he is thinking about consciousness in the right ways

Advances in Reinforcement Learning

Reinforcement Learning (RL) is a very dynamic area in terms of theory and application. This book brings together many different aspects of the current research on several fields associated to RL which has been growing rapidly, producing a wide variety of learning algorithms for different applications. Based on 24 Chapters, it covers a very broad variety of topics in RL and their application in autonomous systems. A set of chapters in this book provide a general overview of RL while other chapters focus mostly on the applications of RL paradigms: Game Theory, Multi-Agent Theory, Robotic, Networking Technologies, Vehicular Navigation, Medicine and Industrial Logistic

The Digital Affect: A Rhetorical Hermeneutic for Reading, Writing, and Understanding Narrative in Contemporary Literature and New Media

The Digital Affect is an exploration of ways to improve the teaching of reading and writing using digital media and technology. This requires a fundamental reexamination of digital narratives, building on and updating Espen Aarseth's seminal work in Cybertext and N. Katherine Hayles' recent work in Writing Machines. It also requires a critical appraisal of the technology of the personal computer as an environment in which writers compose - an environment that introduces possibilities while imposing constraints that materially influence the writer's efforts. This exploration is best undertaken, I argue, from the perspective of literacy studies, not literary theory. Rather than assuming the literary nature of digital narratives, my examination of the literacy requirements and effects of digital media and digital environments allows for the construction of a more nuanced and precise typology and genealogy of digital narrative. Focusing on the hermeneutical demands of digital media and environments reveals a narrative tradition that extends back to the earliest days of oral storytelling and that manifests itself not as a generic or historical formation, but rather as a poetical and rhetorical mode in which the narrative material is fragmented and distributed across media and throughout the virtual space of the story. Probing the hermeneutical act of interpreting digital narratives suggests the operation of what I term the "distributed mode" of composing narrative, an authorial mode I examine in works as varied as Stuart Moulthrop's hypermedia story Reagan Library, Italo Calvino's novel If on a winter's night a traveler, Godfrey Reggio's film Koyaanisqatsi, and Laurence Sterne's novel Tristram Shandy. This attention to the hermeneutical requirements of works composed in the distributed mode reveals two important features: first, the inadequacy of the widely-used term "digital literacy" to describe the range of activities undertaken by the interpreter of such works; and second, the inextricability and simultaneity of "reading" and "writing" during the interpretation of digital and non-digital works alike. Throughout The Digital Affect, I argue that digital media disrupts and reconfigures our standard literacy practices, presenting an invaluable opportunity to make those practices visible and teachable in literature and composition classrooms