Interacting single atoms with nanophotonics for chip-integrated quantum networks

Underlying matter and light are their building blocks of tiny atoms and photons. The ability to control and utilize matter-light interactions down to the elementary single atom and photon level at the nano-scale opens up exciting studies at the frontiers of science with applications in medicine, energy, and information technology. Of these, an intriguing front is the development of quantum networks where N >> 1 single-atom nodes are coherently linked by single photons, forming a collective quantum entity potentially capable of performing quantum computations and simulations. Here, a promising approach is to use optical cavities within the setting of cavity quantum electrodynamics (QED). However, since its first realization in 1992 by Kimble et al., current proof-of-principle experiments have involved just one or two conventional cavities. To move beyond to N >> 1 nodes, in this thesis we investigate a platform born from the marriage of cavity QED and nanophotonics, where single atoms at ~100 nm near the surfaces of lithographically fabricated dielectric photonic devices can strongly interact with single photons, on a chip. Particularly, we experimentally investigate three main types of devices: microtoroidal optical cavities, optical nanofibers, and nanophotonic crystal based structures. With a microtoroidal cavity, we realized a robust and efficient photon router where single photons are extracted from an incident coherent state of light and redirected to a separate output with high efficiency. We achieved strong single atom-photon coupling with atoms located ~100 nm near the surface of a microtoroid, which revealed important aspects in the atom dynamics and QED of these systems including atom-surface interaction effects. We present a method to achieve state-insensitive atom trapping near optical nanofibers, critical in nanophotonic systems where electromagnetic fields are tightly confined. We developed a system that fabricates high quality nanofibers with high controllability, with which we experimentally demonstrate a state-insensitive atom trap. We present initial investigations on nanophotonic crystal based structures as a platform for strong atom-photon interactions. The experimental advances and theoretical investigations carried out in this thesis provide a framework for and open the door to strong single atom-photon interactions using nanophotonics for chip-integrated quantum networks.

Developing peptide based capture agents for diagnostics and therapeutics

Iterative in situ click chemistry (IISCC) is a robust general technology for development of high throughput, inexpensive protein detection agents. In IISCC, the target protein acts as a template and catalyst, and assembles its own ligand from modular blocks of peptides. This process of ligand discovery is iterated to add peptide arms to develop a multivalent ligand with increased affinity and selectivity. The peptide based protein capture agents (PCC) should ideally have the same degree of selectivity and specificity as a monoclonal antibody, along with improved chemical stability. We had previously reported developing a PCC agent against bovine carbonic anhydrase II (bCAII) that could replace a polyclonal antibody. To further enhance the affinity or specificity of the PCC agent, I explore branching the peptide arms to develop branched PCC agents against bCAII. The developed branched capture agents have two to three fold higher affinities for the target protein. In the second part of my thesis, I describe the epitope targeting strategy, a strategy for directing the development of a peptide ligand against specific region or fragment of the protein. The strategy is successfully demonstrated by developing PCC agents with low nanomolar binding affinities that target the C-terminal hydrophobic motif of Akt2 kinase. One of the developed triligands inhibits the kinase activity of Akt. This suggests that, if targeted against the right epitope, the PCC agents can also influence the functional properties of the protein. The exquisite control of the epitope targeting strategy is further demonstrated by developing a cyclic ligand against Akt2. The cyclic ligand acts as an inhibitor by itself, without any iteration of the ligand discovery process. The epitope targeting strategy is a cornerstone of the IISCC technology and opens up new opportunities, leading to the development of protein detection agents and of modulators of protein functions.

A cocktail of thermally stable, chemically synthesized capture agents for the efficient detection of anti-gp41 antibodies from human sera and techniques

This thesis reports on a method to improve in vitro diagnostic assays that detect immune response, with specific application to HIV-1. The inherent polyclonal diversity of the humoral immune response was addressed by using sequential in situ click chemistry to develop a cocktail of peptide-based capture agents, the components of which were raised against different, representative anti-HIV antibodies that bind to a conserved epitope of the HIV-1 envelope protein gp41. The cocktail was used to detect anti-HIV-1 antibodies from a panel of sera collected from HIV-positive patients, with improved signal-to-noise ratio relative to the gold standard commercial recombinant protein antigen. The capture agents were stable when stored as a powder for two months at temperatures close to 60°C.

Development of protein-catalyzed capture (PCC) agents with application to the specific targeting of the E17K Point mutation of Akt1

This thesis describes the expansion and improvement of the iterative in situ click chemistry OBOC peptide library screening technology. Previous work provided a proof-of-concept demonstration that this technique was advantageous for the production of protein-catalyzed capture (PCC) agents that could be used as drop-in replacements for antibodies in a variety of applications. Chapter 2 describes the technology development that was undertaken to optimize this screening process and make it readily available for a wide variety of targets. This optimization is what has allowed for the explosive growth of the PCC agent project over the past few years.

These technology improvements were applied to the discovery of PCC agents specific for single amino acid point mutations in proteins, which have many applications in cancer detection and treatment. Chapter 3 describes the use of a general all-chemical epitope-targeting strategy that can focus PCC agent development directly to a site of interest on a protein surface. This technique utilizes a chemically-synthesized chunk of the protein, called an epitope, substituted with a click handle in combination with the OBOC in situ click chemistry libraries in order to focus ligand development at a site of interest. Specifically, Chapter 3 discusses the use of this technique in developing a PCC agent specific for the E17K mutation of Akt1. Chapter 4 details the expansion of this ligand into a mutation-specific inhibitor, with applications in therapeutics.

DNA-Mediated Charge Transport Devices for Protein Detection

Detection of biologically relevant targets, including small molecules, proteins, DNA, and RNA, is vital for fundamental research as well as clinical diagnostics. Sensors with biological elements provide a natural foundation for such devices because of the inherent recognition capabilities of biomolecules. Electrochemical DNA platforms are simple, sensitive, and do not require complex target labeling or expensive instrumentation. Sensitivity and specificity are added to DNA electrochemical platforms when the physical properties of DNA are harnessed. The inherent structure of DNA, with its stacked core of aromatic bases, enables DNA to act as a wire via DNA-mediated charge transport (DNA CT). DNA CT is not only robust over long molecular distances of at least 34 nm, but is also especially sensitive to anything that perturbs proper base stacking, including DNA mismatches, lesions, or DNA-binding proteins that distort the π-stack. Electrochemical sensors based on DNA CT have previously been used for single-nucleotide polymorphism detection, hybridization assays, and DNA-binding protein detection. Here, improvements to (i) the structure of DNA monolayers and (ii) the signal amplification with DNA CT platforms for improved sensitivity and detection are described.

First, improvements to the control over DNA monolayer formation are reported through the incorporation of copper-free click chemistry into DNA monolayer assembly. As opposed to conventional film formation involving the self-assembly of thiolated DNA, copper-free click chemistry enables DNA to be tethered to a pre-formed mixed alkylthiol monolayer. The total amount of DNA in the final film is directly related to the amount of azide in the underlying alkylthiol monolayer. DNA monolayers formed with this technique are significantly more homogeneous and lower density, with a larger amount of individual helices exposed to the analyte solution. With these improved monolayers, significantly more sensitive detection of the transcription factor TATA binding protein (TBP) is achieved.

Using low-density DNA monolayers, two-electrode DNA arrays were designed and fabricated to enable the placement of multiple DNA sequences onto a single underlying electrode. To pattern DNA onto the primary electrode surface of these arrays, a copper precatalyst for click chemistry was electrochemically activated at the secondary electrode. The location of the secondary electrode relative to the primary electrode enabled the patterning of up to four sequences of DNA onto a single electrode surface. As opposed to conventional electrochemical readout from the primary, DNA-modified electrode, a secondary microelectrode, coupled with electrocatalytic signal amplification, enables more sensitive detection with spatial resolution on the DNA array electrode surface. Using this two-electrode platform, arrays have been formed that facilitate differentiation between well-matched and mismatched sequences, detection of transcription factors, and sequence-selective DNA hybridization, all with the incorporation of internal controls.

For effective clinical detection, the two working electrode platform was multiplexed to contain two complementary arrays, each with fifteen electrodes. This platform, coupled with low density DNA monolayers and electrocatalysis with readout from a secondary electrode, enabled even more sensitive detection from especially small volumes (4 μL per well). This multiplexed platform has enabled the simultaneous detection of two transcription factors, TBP and CopG, with surface dissociation constants comparable to their solution dissociation constants.

With the sensitivity and selectivity obtained from the multiplexed, two working electrode array, an electrochemical signal-on assay for activity of the human methyltransferase DNMT1 was incorporated. DNMT1 is the most abundant human methyltransferase, and its aberrant methylation has been linked to the development of cancer. However, current methods to monitor methyltransferase activity are either ineffective with crude samples or are impractical to develop for clinical applications due to a reliance on radioactivity. Electrochemical detection of methyltransferase activity, in contrast, circumvents these issues. The signal-on detection assay translates methylation events into electrochemical signals via a methylation-specific restriction enzyme. Using the two working electrode platform combined with this assay, DNMT1 activity from tumor and healthy adjacent tissue lysate were evaluated. Our electrochemical measurements revealed significant differences in methyltransferase activity between tumor tissue and healthy adjacent tissue.

As differential activity was observed between colorectal tumor tissue and healthy adjacent tissue, ten tumor sets were subsequently analyzed for DNMT1 activity both electrochemically and by tritium incorporation. These results were compared to expression levels of DNMT1, measured by qPCR, and total DNMT1 protein content, measured by Western blot. The only trend detected was that hyperactivity was observed in the tumor samples as compared to the healthy adjacent tissue when measured electrochemically. These advances in DNA CT-based platforms have propelled this class of sensors from the purely academic realm into the realm of clinically relevant detection.

Distributed Control and Optimization for Communication and Power Systems

We are at the cusp of a historic transformation of both communication system and electricity system. This creates challenges as well as opportunities for the study of networked systems. Problems of these systems typically involve a huge number of end points that require intelligent coordination in a distributed manner. In this thesis, we develop models, theories, and scalable distributed optimization and control algorithms to overcome these challenges.

This thesis focuses on two specific areas: multi-path TCP (Transmission Control Protocol) and electricity distribution system operation and control. Multi-path TCP (MP-TCP) is a TCP extension that allows a single data stream to be split across multiple paths. MP-TCP has the potential to greatly improve reliability as well as efficiency of communication devices. We propose a fluid model for a large class of MP-TCP algorithms and identify design criteria that guarantee the existence, uniqueness, and stability of system equilibrium. We clarify how algorithm parameters impact TCP-friendliness, responsiveness, and window oscillation and demonstrate an inevitable tradeoff among these properties. We discuss the implications of these properties on the behavior of existing algorithms and motivate a new algorithm Balia (balanced linked adaptation) which generalizes existing algorithms and strikes a good balance among TCP-friendliness, responsiveness, and window oscillation. We have implemented Balia in the Linux kernel. We use our prototype to compare the new proposed algorithm Balia with existing MP-TCP algorithms.

Our second focus is on designing computationally efficient algorithms for electricity distribution system operation and control. First, we develop efficient algorithms for feeder reconfiguration in distribution networks. The feeder reconfiguration problem chooses the on/off status of the switches in a distribution network in order to minimize a certain cost such as power loss. It is a mixed integer nonlinear program and hence hard to solve. We propose a heuristic algorithm that is based on the recently developed convex relaxation of the optimal power flow problem. The algorithm is efficient and can successfully computes an optimal configuration on all networks that we have tested. Moreover we prove that the algorithm solves the feeder reconfiguration problem optimally under certain conditions. We also propose a more efficient algorithm and it incurs a loss in optimality of less than 3% on the test networks.

Second, we develop efficient distributed algorithms that solve the optimal power flow (OPF) problem on distribution networks. The OPF problem determines a network operating point that minimizes a certain objective such as generation cost or power loss. Traditionally OPF is solved in a centralized manner. With increasing penetration of volatile renewable energy resources in distribution systems, we need faster and distributed solutions for real-time feedback control. This is difficult because power flow equations are nonlinear and kirchhoff's law is global. We propose solutions for both balanced and unbalanced radial distribution networks. They exploit recent results that suggest solving for a globally optimal solution of OPF over a radial network through a second-order cone program (SOCP) or semi-definite program (SDP) relaxation. Our distributed algorithms are based on the alternating direction method of multiplier (ADMM), but unlike standard ADMM-based distributed OPF algorithms that require solving optimization subproblems using iterative methods, the proposed solutions exploit the problem structure that greatly reduce the computation time. Specifically, for balanced networks, our decomposition allows us to derive closed form solutions for these subproblems and it speeds up the convergence by 1000x times in simulations. For unbalanced networks, the subproblems reduce to either closed form solutions or eigenvalue problems whose size remains constant as the network scales up and computation time is reduced by 100x compared with iterative methods.

Efficacy and safety of autologous platelet rich plasma for the treatment of vascular ulcers in primary care: Phase III study

Background: Vascular ulcers are commonly seen in daily practice at all levels of care and have great impact at personal, professional and social levels with a high cost in terms of human and material resources. Given that the application of autologous platelet rich plasma has been shown to decrease healing times in various different studies in the hospital setting, we considered that it would be interesting to assess the efficacy and feasibility of this treatment in primary care. The objectives of this study are to assess the potential efficacy and safety of autologous platelet rich plasma for the treatment of venous ulcers compared to the conventional treatment (moist wound care) in primary care patients with chronic venous insufficiency (C, clinical class, E, aetiology, A, anatomy and P, pathophysiology classification C6). Design: We will conduct a phase III, open-label, parallel-group, multicentre, randomized study. The subjects will be 150 patients aged between 40 and 100 years of age with an at least 2-month history of a vascular venous ulcer assigned to ten primary care centres. For the treatment with autologous platelet rich plasma, all the following tasks will be performed in the primary care setting: blood collection, centrifugation, separation of platelet rich plasma, activation of coagulation adding calcium chloride and application of the PRP topically after gelification. The control group will receive standard moist wound care. The outcome variables to be measured at baseline, and at weeks 5 and 9 later include: reduction in the ulcer area, Chronic Venous Insufficiency Quality of Life Questionnaire score, and percentage of patients who require wound care only once a week. Discussion: The results of this study will be useful to improve the protocol for using platelet rich plasma in chronic vascular ulcers and to favour wider use of this treatment in primary care.

El pintor navarro Juan Ochoa de Arín (1600-1652) y su producción en Gipuzkoa

Investigación realizada dentro del Programa de Formación y Perfeccionamiento de Personal Investigador del Gobierno Vasco (2010-2013).

Centro de gestión de contenido en RDF

La primera idea de la realización de este proyecto, fue concebida por la necesidad de tener un sistema por el cual se pudieran cambiar datos de una aplicación, en un sistema móvil, a través de una página web. Sin embargo al conocer la potencia que tiene RDF para ser muy escalable terminó siendo un sistema de gestión de contenido general en RDF. Este sistema de gestión se ha realizado para ser lo más simple posible para un usuario, de tal manera que con solo 2 click en la página web y rellenando un formulario simple, pudiera tener una base de datos sin muchos conocimientos sobre la gestión de las mismas. Aunque claramente no es un sistema potente como si fuera una base de datos en Oracle, por citar un ejemplo, sirve para poder agregar, modificar y eliminar datos con sencillez. Así este sistema de gestión da una posibilidad muy sencilla de realizar tus propias bases de datos. Además aunque tiene un motor SQL para la gestión interna de almacenamiento, la salida de los datos es en RDF/XML con lo que podría ser compatible con un sistema más amplio como Oracle Database Semantic Technologies. Este CMS también tendrá un sistema de seguridad basado en usuario y contraseña. Para que la edición del contenido sea accesible solo a usuarios con acceso, mientras que la exportación de los datos será pública, y podrá ser accesible por cualquier usuario mediante una URI.

Desarrollo de un gestor de conexión con facebook para aplicación de mensajeria instantanea.

[EN]Until May 2015, an application for Linux KDE desktops called KDE-Telepathy had the possibility of adding Facebook accounts in order to talk to friends through an XMPP Gateway. After Facebook’s announcement of the closure of this Gateway, this project will try to explain the development process of a new connection manager. This fact generates the need of an unofficial alternative which Facebook does not provide. Along the different sections, there will be explained how to implement the most basic functions a connection manager must have, like: a contact list, sending or receiving messages. Meanwhile, there will be involved different solutions part of the Facebook’s official infrastructure, but also, some that are not.

Colaboración en las prestaciones y la documentación de Kdenlive.

[Es]Con el paso de los años, el uso de tecnologías de edición de vídeo ha ido cobrando protagonismo, tanto dentro del mundo del arte cinematográfico, como en reportajes, o, en los últimos años, en vídeos subidos por usuarios a redes sociales. Por otra parte, el software libre se ha ido expandiendo en todos los sectores, proporcionando a los usuarios código de calidad sin tener que pagar las licencias de otros programas similares. Por ello, se decide por optar por la colaboración en Kdenlive, un editor de vídeo de código libre desarrollado en KDE. Este programa cuenta con una multitud de potentes herramientas, y está basado en torno a una comunidad de desarrolladores, que trabajan con el objetivo de crear el editor de vídeo no lineal más avanzado de GNU/Linux. Mediante este trabajo, se pretende contribuir a dicho programa mediante el diseño y codificación de una nueva funcionalidad para el programa, a la vez que colaborar con la documentación ofrecida por los desarrolladores del programa con el objetivo de ayudar a nuevos desarrolladores a incorporarse al desarrollo de la aplicación de una manera más sencilla.

Modificação química do poli(cloreto de vinila) com nucleófilos nitrogenados assistida por micro-ondas

Nesse trabalho foram realizadas reações de substituição nucleofílica (SN2), utilizando aquecimento térmico convencional e por irradiação de micro-ondas (MO), de alguns átomos cloro em amostras comerciais de poli(cloreto de vinila) (PVC), por grupos nitrila e também por grupos azida. Os grupos nitrila e azida foram substituidos na matriz em diferentes teores (10% e 20%). As reações do PVC com azida foram eficazes, apresentado percentuais de derivatização muito próximos dos valores desejados. Já no estudo com a nitrila não foi obtido o resultado esperado. Os copolímeros PVC azido substituídos foram modificados com propargilato de etila, sob catálise de iodeto de cuproso (CuI), para a obtenção de heterocíclicos do tipo triazólicos. Todos os copolímeros obtidos foram caracterizados por espectroscopia na região do infravermelho (FTIR) e os teores de nitrogênio incorporado foram determinados por análise elementar (AE). Através da análise dos dados obtidos, foi comprovado que a utilização da irradiação micro-ondas, quando comparada ao aquecimento convencional, é um processo mais seletivo e diminui, significativamente, os tempos de reação

Proyecto Akeko: sistema de gestión de accesos de estudiantes en servidores

El propósito fundamental de éste trabajo fin de grado es la creación de una herramienta que permita a un profesor poder gestionar los distintos servicios a los que puede acceder un alumno. Entendemos como servicios, aquellas herramientas que permiten desarrollar de forma efectiva las competencias necesarias en cada asignatura. Por ejemplo, servicios como bases de datos “MySQL” o servicios de control de versiones como “GIT”. Éste trabajo fin de grado ha consistido en la consecución del estudio de 3 lenguajes de programación diferentes, del aprendizaje de nuevas formas distintas de programar, de saber hacer una búsqueda de información, de escuchar al usuario para obtener una mejor adaptación visual, de encontrar los diferentes caminos que llevan a una solución, de entender que cada lenguaje tiene su forma de pensar y de hacer y sobre todo, de la dificultad que acarrea integrar una aplicación compleja en varios entornos operativos con distintos tipos de arquitecturas.

Efficient Synthesis of Single-Chain Polymer Nanoparticles via Amide Formation

Single-chain technology (SCT) allows the transformation of individual polymer chains to folded/collapsed unimolecular soft nanoparticles. In this work we contribute to the enlargement of the SCT toolbox by demonstrating the efficient synthesis of single-chain polymer nanoparticles (SCNPs) via intrachain amide formation. In particular, we exploit cross-linking between active methylene groups and isocyanate moieties as powerful "click" chemistry driving force for SCNP construction. By employing poly(methyl methacrylate)- (PMMA-) based copolymers bearing beta-ketoester units distributed randomly along the copolymer chains and bifunctional isocyanate cross-linkers, SCNPs were successfully synthesized at r.t. under appropriate reaction conditions. Characterization of the resulting SCNPs was carried out by means of a combination of techniques including size exclusion chromatography (SEC), infrared (IR) spectroscopy, proton nuclear magnetic resonance (H-1 NMR) spectroscopy, dynamic light scattering (DLS), and elemental analysis (EA).

Determinação de posicionamento de nós roteadores em redes sem fio utilizando redes imunológicas.

A tecnologia sem fio (wireless) vem tomando conta do mundo. A cada dia mais pessoas estão trocando seus equipamentos com fio por equipamentos com a tecnologia wireless. Isso vem crescendo, devido as suas vantagens, tais como: facilidade de instalação e manutenção, redução de tempo de instalação de dispositivos, inexistência de estrutura de cabeamento, economia no custo de projetos, economia em infraestrutura, flexibilidade de configuração de dispositivos, economia no custo de montagem, flexibilidade na alteração de arquiteturas existentes e outros. Por essas facilidades supracitadas a área de automação industrial está também aumentando o seu interesse nessa tecnologia wireless. Nessa área, a segurança, confiabilidade e robustez dos dados são de suma importância. Então, para minimizar os efeitos das interferências geradas nesse meio são usadas técnicas de espalhamento em frequência e topologia em malha ou árvore para transmissão dos dados enviados pelos sensores aos nós roteadores até chegar ao gateway. Sendo assim, o posicionamento dos nós roteadores na rede em malha garantirá a menor influência dessas interferências. Esse trabalho propõe uma ferramenta de posicionamento de nós roteadores intermediários, chamado POSIMNET (Positioning Immune Network Rede Imunológica de Posicionamento), que auxilia o projetista da rede de automação industrial a encontrar a melhor configuração da rede sem fio. O POSIMNET é baseado nas redes imunológicas artificiais, que propõe criar n caminhos quaisquer ou disjuntos para as informações enviadas pelos nós sensores chegarem ao gateway, através da supressão, clonagem e reconfiguração de nós roteadores intermediários. Além disso, o algoritmo também é capaz de atender os critérios de baixo grau de falha e baixo número de retransmissão pelos roteadores. Esses critérios podem ser habilitados individualmente ou combinados com pesos iguais ou diferentes para cada um, a critério do usuário. A ferramenta POSIMNET é formada por dois módulos: (i) Rede Imunológica agrega elementos de dois modelos de redes imunológicas (SSAIS e AiNet); (ii) Campos Potenciais - posiciona os nós roteadores pelos campos potenciais, onde os sensores críticos os atraem enquanto que os obstáculos e outros roteadores os repelem.