Expanding the Toolkit for Synthetic Biology: Frameworks for Native-like Non-natural Gene Circuits

Synthetic biology combines biological parts from different sources in order to engineer non-native, functional systems. While there is a lot of potential for synthetic biology to revolutionize processes, such as the production of pharmaceuticals, engineering synthetic systems has been challenging. It is oftentimes necessary to explore a large design space to balance the levels of interacting components in the circuit. There are also times where it is desirable to incorporate enzymes that have non-biological functions into a synthetic circuit. Tuning the levels of different components, however, is often restricted to a fixed operating point, and this makes synthetic systems sensitive to changes in the environment. Natural systems are able to respond dynamically to a changing environment by obtaining information relevant to the function of the circuit. This work addresses these problems by establishing frameworks and mechanisms that allow synthetic circuits to communicate with the environment, maintain fixed ratios between components, and potentially add new parts that are outside the realm of current biological function. These frameworks provide a way for synthetic circuits to behave more like natural circuits by enabling a dynamic response, and provide a systematic and rational way to search design space to an experimentally tractable size where likely solutions exist. We hope that the contributions described below will aid in allowing synthetic biology to realize its potential.

Studies of response to earthquake ground motion

A study is made of the accuracy of electronic digital computer calculations of ground displacement and response spectra from strong-motion earthquake accelerograms. This involves an investigation of methods of the preparatory reduction of accelerograms into a form useful for the digital computation and of the accuracy of subsequent digital calculations. Various checks are made for both the ground displacement and response spectra results, and it is concluded that the main errors are those involved in digitizing the original record. Differences resulting from various investigators digitizing the same experimental record may become as large as 100% of the maximum computed ground displacements. The spread of the results of ground displacement calculations is greater than that of the response spectra calculations. Standardized methods of adjustment and calculation are recommended, to minimize such errors.

Studies are made of the spread of response spectral values about their mean. The distribution is investigated experimentally by Monte Carlo techniques using an electric analog system with white noise excitation, and histograms are presented indicating the dependence of the distribution on the damping and period of the structure. Approximate distributions are obtained analytically by confirming and extending existing results with accurate digital computer calculations. A comparison of the experimental and analytical approaches indicates good agreement for low damping values where the approximations are valid. A family of distribution curves to be used in conjunction with existing average spectra is presented. The combination of analog and digital computations used with Monte Carlo techniques is a promising approach to the statistical problems of earthquake engineering.

Methods of analysis of very small earthquake ground motion records obtained simultaneously at different sites are discussed. The advantages of Fourier spectrum analysis for certain types of studies and methods of calculation of Fourier spectra are presented. The digitizing and analysis of several earthquake records is described and checks are made of the dependence of results on digitizing procedure, earthquake duration and integration step length. Possible dangers of a direct ratio comparison of Fourier spectra curves are pointed out and the necessity for some type of smoothing procedure before comparison is established. A standard method of analysis for the study of comparative ground motion at different sites is recommended.

Distributed Optimal Control of Cyber-Physical Systems: Controller Synthesis, Architecture Design and System Identification

The centralized paradigm of a single controller and a single plant upon which modern control theory is built is no longer applicable to modern cyber-physical systems of interest, such as the power-grid, software defined networks or automated highways systems, as these are all large-scale and spatially distributed. Both the scale and the distributed nature of these systems has motivated the decentralization of control schemes into local sub-controllers that measure, exchange and act on locally available subsets of the globally available system information. This decentralization of control logic leads to different decision makers acting on asymmetric information sets, introduces the need for coordination between them, and perhaps not surprisingly makes the resulting optimal control problem much harder to solve. In fact, shortly after such questions were posed, it was realized that seemingly simple decentralized optimal control problems are computationally intractable to solve, with the Wistenhausen counterexample being a famous instance of this phenomenon. Spurred on by this perhaps discouraging result, a concerted 40 year effort to identify tractable classes of distributed optimal control problems culminated in the notion of quadratic invariance, which loosely states that if sub-controllers can exchange information with each other at least as quickly as the effect of their control actions propagates through the plant, then the resulting distributed optimal control problem admits a convex formulation.

The identification of quadratic invariance as an appropriate means of "convexifying" distributed optimal control problems led to a renewed enthusiasm in the controller synthesis community, resulting in a rich set of results over the past decade. The contributions of this thesis can be seen as being a part of this broader family of results, with a particular focus on closing the gap between theory and practice by relaxing or removing assumptions made in the traditional distributed optimal control framework. Our contributions are to the foundational theory of distributed optimal control, and fall under three broad categories, namely controller synthesis, architecture design and system identification.

We begin by providing two novel controller synthesis algorithms. The first is a solution to the distributed H-infinity optimal control problem subject to delay constraints, and provides the only known exact characterization of delay-constrained distributed controllers satisfying an H-infinity norm bound. The second is an explicit dynamic programming solution to a two player LQR state-feedback problem with varying delays. Accommodating varying delays represents an important first step in combining distributed optimal control theory with the area of Networked Control Systems that considers lossy channels in the feedback loop. Our next set of results are concerned with controller architecture design. When designing controllers for large-scale systems, the architectural aspects of the controller such as the placement of actuators, sensors, and the communication links between them can no longer be taken as given -- indeed the task of designing this architecture is now as important as the design of the control laws themselves. To address this task, we formulate the Regularization for Design (RFD) framework, which is a unifying computationally tractable approach, based on the model matching framework and atomic norm regularization, for the simultaneous co-design of a structured optimal controller and the architecture needed to implement it. Our final result is a contribution to distributed system identification. Traditional system identification techniques such as subspace identification are not computationally scalable, and destroy rather than leverage any a priori information about the system's interconnection structure. We argue that in the context of system identification, an essential building block of any scalable algorithm is the ability to estimate local dynamics within a large interconnected system. To that end we propose a promising heuristic for identifying the dynamics of a subsystem that is still connected to a large system. We exploit the fact that the transfer function of the local dynamics is low-order, but full-rank, while the transfer function of the global dynamics is high-order, but low-rank, to formulate this separation task as a nuclear norm minimization problem. Finally, we conclude with a brief discussion of future research directions, with a particular emphasis on how to incorporate the results of this thesis, and those of optimal control theory in general, into a broader theory of dynamics, control and optimization in layered architectures.

Gerenciamento de resíduos químicos em ambientes hospitalares: necessidades e dificuldades - estudo de caso: Hospital Universitário Federal localizado no Estado do Rio de Janeiro.

O tema do presente estudo é o gerenciamento de resíduos químicos em ambientes hospitalares. Os resíduos químicos são gerados nas atividades auxiliares dos estabelecimentos prestadores de serviços de saúde, tais como hospitais, laboratórios, serviços de diagnóstico e tratamento, centros de saúde, clínicas, institutos de medicina legal e outros. Dentre todos, os hospitais, por suas características de atendimento, são, sem dúvida, os maiores geradores deste tipo de resíduo. Controlar e diminuir os riscos inerentes a este tipo de resíduos, além de ser uma exigência legal, passa a ser uma necessidade ambiental e um desafio a ser enfrentado pelos administradores de estabelecimentos assistenciais à saúde. O objetivo geral desta pesquisa passa então por avaliar o gerenciamento dos resíduos químicos gerados nos hospitais públicos da região metropolitana do Estado do Rio de Janeiro, abordando às necessidades e dificuldades enfrentadas por estes geradores que incluí aspectos políticos, administrativos, econômicos e em alguns casos físico-estruturais. Para atingir tal objetivo o método empregado foi dividido em duas etapas: I) Pesquisa Aplicada, onde foram visitados alguns hospitais públicos do Estado e utilizou-se um questionário para avaliar as questões relacionadas com o gerenciamento de resíduos químicos e II) Estudo de Caso, onde se considerou, através de observações e entrevistas, o gerenciamento de resíduos químicos de um hospital universitário de grande porte de maneira efetiva. Foram utilizadas como fontes secundárias informações obtidas em seminários relacionados ao tema, reportagens de jornais e entrevistas publicadas em fontes especializadas. Os resultados obtidos mostram que as dificuldades enfrentadas no gerenciamento de RSS, inclusos neste grupo os resíduos químicos, é uma realidade para a maioria dos hospitais da rede pública. Conclusão: o maior problema a ser enfrentado por estas instituições está diretamente ligado à conscientização, ou melhor, a falta de conscientização, de funcionários, médicos e gerência dos hospitais, quanto à importância da correta segregação, armazenagem e manuseio destes resíduos. Além disso, a falta de recursos financeiros e, em alguns casos, até de espaço físico também dificulta o efetivo gerenciamento deste tipo de resíduos. Problemas secundários relacionam-se com a falta de fiscalização dos órgãos sanitário-ambientais competentes e o descaso da própria população que não atenta para os problemas ambientais e de saúde e segurança, decorrentes de um incorreto gerenciamento não só dos resíduos químicos, mas de todos os resíduos de serviço de saúde. Como recomendação, pode-se dizer que se faz necessária uma maior mobilização por parte dos estabelecimentos hospitalares para a discussão e atendimento das legislações aplicáveis e também, o desenvolvimento de uma estrutura gerencial com responsabilidades definidas e ações planejadas, compatíveis com a realidade do serviço público, e que possam levar a alcançar os objetivos e metas de um gerenciamento dos resíduos de serviço de saúde.

梯度补偿法控温晶体的高功率绿光激光器

研究了平均功率超过30 W的稳定高效全固态绿光激光器,分析得出影响全固态腔内倍频激光器倍频效率和输出稳定性的主要因素是倍频晶体局部温升造成的相位失配和热透镜效应,采用温度梯度补偿控温法对大尺寸倍频晶体进行温度控制,降低激光器工作中倍频晶体内外温度梯度从而有效地克服因晶体局部温升造成的倍频相位匹配角失配和热透镜效应。采用三条60 W的半导体激光二极管阵列板条侧面抽运Nd:YAG激光增益介质棒,采用声光调Q,平凹直腔和腔内倍频结构配合温度梯度补偿控温法对大尺寸倍频晶体进行温度控制,得到了稳定高效的532 nm

Design and implementation of a cloud computing adoption decision tool: Generating a cloud road

Migrating to cloud computing is one of the current enterprise challenges. This technology provides a new paradigm based on "on-demand payment" for information and communication technologies. In this sense, the small and medium enterprise is supposed to be the most interested, since initial investments are avoided and the technology allows gradual implementation. However, even if the characteristics and capacities have been widely discussed, entry into the cloud is still lacking in terms of practical, real frameworks. This paper aims at filling this gap, presenting a real tool already implemented and tested, which can be used as a cloud computing adoption decision tool. This tool uses diagnosis based on specific questions to gather the required information and subsequently provide the user with valuable information to deploy the business within the cloud, specifically in the form of Software as a Service (SaaS) solutions. This information allows the decision makers to generate their particular Cloud Road. A pilot study has been carried out with enterprises at a local level with a two-fold objective: To ascertain the degree of knowledge on cloud computing and to identify the most interesting business areas and their related tools for this technology. As expected, the results show high interest and low knowledge on this subject and the tool presented aims to readdress this mismatch, insofar as possible. Copyright: © 2015 Bildosola et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Evaluación de dosis de radiación producida por una pérdida de refrigerante en reactor nuclear.

EN]This is a document done to try to see the effect of a nuclear power plant accident. In particular, it studies what would be the radiation doses delivered to the people in the close areas around the power plant of Garoña, if it had suffered from a loss of coolant accident during its normal functioning.

Welding of Al alloy plates using a novel high-average-power pulsed CO2 laser

A novel high-average-power pulsed CO2 laser with a unique electrode structure is presented. The operation of a 5-kW transverse-flow CO2 laser with the preionized pulse-train switched technique results in pulsation of the laser power, and the average laser power is about 5 kW. The characteristic of this technique is switching the preionized pulses into pulse trains so as to use the small preionized power (hundreds of watts) to control the large main-discharge power (tens of kilowatts). By this means, the cost and the complexity of the power supply are greatly reduced. The welding of LF2, LF21, LD2, and LY12 aluminum alloy plates has been successfully achieved using this laser. (c) 2005 Society of Photo-Optical Instrumentation Engineers.

Welding of Al alloy plates using a novel high-average-power pulsed CO2 laser

A novel high-average-power pulsed CO2 laser with a unique electrode structure is presented. The operation of a 5-kW transverse-flow CO2 laser with the preionized pulse-train switched technique results in pulsation of the laser power, and the average laser power is about 5 kW. The characteristic of this technique is switching the preionized pulses into pulse trains so as to use the small preionized power (hundreds of watts) to control the large main-discharge power (tens of kilowatts). By this means, the cost and the complexity of the power supply are greatly reduced. The welding of LF2, LF21, LD2, and LY12 aluminum alloy plates has been successfully achieved using this laser. (c) 2005 Society of Photo-Optical Instrumentation Engineers.

Valuation of Wind Energy Projects: A Real Options Approach

We address the valuation of an operating wind farm and the finite-lived option to invest in it under different reward/support schemes: a constant feed-in tariff, a premium on top of the electricity market price (either a fixed premium or a variable subsidy such as a renewable obligation certificate or ROC), and a transitory subsidy, among others. Futures contracts on electricity with ever longer maturities enable market-based valuations to be undertaken. The model considers up to three sources of uncertainty: the electricity price, the level of wind generation, and the certificate (ROC) price where appropriate. When analytical solutions are lacking, we resort to a trinomial lattice combined with Monte Carlo simulation; we also use a two-dimensional binomial lattice when uncertainty in the ROC price is considered. Our data set refers to the UK. The numerical results show the impact of several factors involved in the decision to invest: the subsidy per MWh generated, the initial lump-sum subsidy, the maturity of the investment option, and electricity price volatility. Different combinations of variables can help bring forward investments in wind generation. One-off policies, e.g., a transitory initial subsidy, seem to have a stronger effect than a fixed premium per MWh produced.

Análise dinâmica e controle de vibrações de passarelas de pedestres submetidas ao caminhar humano.

Passarelas de pedestres mistas (aço-concreto) e de aço são frequentemente submetidas a ações dinâmicas de magnitude variável, devido à travessia de pedestres sobre a laje de concreto. Estas ações dinâmicas podem produzir vibrações excessivas e dependendo de sua magnitude e intensidade, estes efeitos adversos podem comprometer a confiabilidade e a resposta do sistema estrutural e, também, podem levar a uma redução da expectativa de vida útil da passarela. Por outro lado, a experiência e o conhecimento dos engenheiros estruturais em conjunto com o uso de novos materiais e tecnologias construtivas têm produzido projetos de passarelas mistas (aço-concreto) bastante arrojados. Uma consequência direta desta tendência de projeto é um aumento considerável das vibrações estruturais. Com base neste cenário, esta dissertação visa investigar o comportamento dinâmico de três passarelas de pedestres mistas (aço-concreto) localizadas no Rio de Janeiro, submetidas ao caminhar humano. Estes sistemas estruturais são constituídos por uma estrutura principal de aço e laje em concreto e são destinados à travessia de pedestres. Deste modo, foram desenvolvidos modelos numérico-computacionais, adotando-se as técnicas tradicionais de refinamento presentes em simulações do método de elementos finitos, com base no uso do software ANSYS. Estes modelos numéricos permitiram uma completa avaliação dinâmica das passarelas investigadas, especialmente em termos de conforto humano. As respostas dinâmicas foram obtidas em termos de acelerações de pico e comparadas com valores limites propostas por diversos autores e normas de projeto. Os valores de aceleração de pico e aceleração rms encontrados na presente investigação indicaram que as passarelas analisadas apresentaram problemas relacionados com o conforto humano. Assim sendo, considerando-se que foi detectado que estas estruturas poderiam atingir níveis elevados de vibração que possam vir a comprometer o conforto dos usuários, foi verificado que uma estratégia para o controle estrutural era necessária, a fim de reduzir as vibrações excessivas nas passarelas. Finalmente, uma investigação foi realizada com base em alternativas de controle estrutural objetivando atenuar vibrações excessivas, a partir do emprego de sistemas de atenuadores dinâmicos sintonizados (ADS).

Construção e operação de wetland como polimento de lixiviado de aterro de resíduos sólidos urbanos.

O presente trabalho tem o objetivo de avaliar a metodologia de construção, de plantio, de manutenção, de operação e a eficiência de um sistema de tratamento por wetland construído como etapa de polimento da Estação de Tratamento de Lixiviado (ETC) de Aterro já encerrado de Resíduos Sólidos Urbanos na Região Metropolitana do Rio de Janeiro. Parte do efluente tratado por lodos ativados na ETC foi direcionado e tratado no wetland construído. Foi escolhido o projeto de Fluxo Horizontal Subsuperficial e a vegetação selecionada foi a taboa (Typha latifolia) que é nativa da área do aterro. Em média, foram feitas três amostragens mensais do afluente e do efluente do wetland, de maio a outubro de 2013. A eficiência do sistema foi avaliada por meio de parâmetros físico-químicos e de parâmetros coletivos específicos. A eficiência de remoção de Demanda Química de Oxigênio (DQO) foi de 60%, nitrogênio amoniacal de 67%, nitrito de 72% e nitrato de 57%. Outro parâmetro avaliado foi a toxicidade aguda, foram utilizados os organismos teste Danio rerio (peixe), a Daphnia similis (microcrustáceo) e a Aliivibrio fischeri (bactéria luminescente). Durante o período foram coletados diariamente as vazões de entrada e saída, a condutividade elétrica e o índice pluviométrico. Os resultados mostraram que o uso de wetland como etapa de polimento pode ser uma alternativa para o tratamento de lixiviado.

水稻对大气二氧化碳浓度及温度升高的光合适应的研究

基于长期观测资料，众多大气环流模型预测在二十一世纪末大气中二氧化碳浓度将达到700μmolmol'I，地球表面年平均温度也将升高1.5-4.OoC。水稻是亚洲的主要粮食作物，为世界近三分之一的人口提供食物能源。这项工作的目的，是利用人工模拟环境，预测在未来全球气候变化，二氧化碳及温度升高的条件下，水稻的光合生理反应及随之而来的对其产量的影响。本研究是美国环境署( EPA)与国际水稻研究所(IRRI)合作研究项目“Effects of UV-B and Global Climate Change on Rice”的一部分． 在这项研究中，采用了特殊设计并直接建立在水稻田间的开顶式气室（open-top chambers）。在此之前还没有这样大规模的在水稻主产区的此类模拟研究，水稻在气室中渡过了从萌发到收获的整个生长过程。模拟环境条件有三个浓度的二氧化碳（包括现有大气浓度，在此基础上升高200及300 μmolmol-l）和两个温度（即：现有大气温度及升高4度）共六个处理。供试水稻品种四个：IR72，IR65598-112-2，IR65600-42-5-2-BSI-313和N22。在实验中我们发现，水稻品种（如：1R72）单叶光合速率（以二氧化碳气体交换速率计）受二氧化碳浓度促进，在水稻营养生长期，二氧化碳及温度对其光合有协同促进作用．然而，随着花期的到来，在高温条件下，叶片光合能力（photosynthetic capacity）下降，出现光合适应现象（Photosynthetic acclirnation）.水稻群体光合作用同样受到二氧化碳浓度促进，但在后期(Grain fill stage)这种促进作用消失;在高浓度二氧化碳下生长的大多数水稻品种的叶片中有较多的碳水化和物（可溶性糖和淀粉）积累．耐高温品种N22叶片中淀粉积累较少：叶片中氮素含量降低，同时发现Rubisco总活性相应降低，这与NCi曲线所示光合效率降低相吻合;通过叶片叶绿素荧光动力学测定，没有发现光系统光能转化效率的变化;水稻籽粒产量随二氧化碳浓度升高而增加，但温度升高使产量降低12.8-36.8%;不同品种对二氧化碳浓度的反应没有显著差别;在高温条件下，耐高温品生长在高二氧化碳浓度下表现良好。 本文系统地研究了水稻光合作用在二氧化碳及温度条件影响下，对二氧化碳浓度及光强变化的反应曲线，初次对水稻单叶与群体光合对二氧化碳浓度变化的反应做了实验性对比;讨论了温度升高对水稻在高浓度二氧化碳下发生光合适应的影响，对光合适应现象的可能机制做了探讨，并提出对未来大气二氧化碳浓度及温度升高条件下水稻适应品种筛选的可能方向。