First-principles study of the electronic structure and dynamical electronic excitations of strong spin-orbit metal Pb: bulk, surface and nanosized films

En la presente tesis se ha realizado el estudio de primeros principios (esto es, sinhacer uso de parámetros ajustables) de la estructura electrónica y la dinámica deexcitaciones electrónicas en plomo, tanto en volumen como en superficie y en formade películas de espesor nanométrico. Al presentar el plomo un número atómico alto(82), deben tenerse en cuenta los efectos relativistas. Con este fin, el doctorando haimplementado el acoplo espín-órbita en los códigos computacionales que hanrepresentado la principal herramienta de trabajo.En volumen, se han encontrado fuertes efectos relativistas asi como de lalocalización de los electrones, tanto en la respuesta dieléctrica (excitacioneselectrónicas colectivas) como en el tiempo de vida de electrones excitados. Lacomparación de nuestros resultados con medidas experimentales ha ayudado aprofundizar en dichos efectos.En el estudio de las películas a escala nanométrica se han hallado fuertes efectoscuánticos debido al confinamiento de los estados electrónicos. Dichos efectos semanifiestan tanto en el estado fundamental (en acuerdo con estudiosexperimentales), como en la respuesta dieléctrica a través de la aparición y dinámicade plasmones de diversas características. Los efectos relativistas, a pesar de no serimportantes en la estructura electrónica de las películas, son los responsables de ladesaparación del plasmón de baja energía en nuestros resultados.

Electronic spectroscopy of propofol, propofol homomers ad their hydratated clusters

538 p.

Processing Facilitation Strategies in OV and VO Languages: A Corpus Study

The present corpus study aimed to examine whether Basque (OV) resorts more often than Spanish (VO) to certain grammatical operations, in order to minimi ze the number of arguments to be processed before the verb. Ueno & Polinsky (2009) argue that VO/OV languages use certain grammatical resources with different frequencies in order to facilitate real-time processing. They observe that both OV and VO languages in their sample (Japanese, Turkish and Spanish) have a similar frequency of use of subject pro-drop; however, they find that OV languages (Japanese, Turkish) use more intransitive sentences than VO languages (English, Spanish), and conclude this is an OV-specific strategy to facilitate processing. We conducted a comparative corpus study of Spanish (VO) and Basque (OV). Results show (a) that the fre- quency of use of subject pro-drop is higher in Basque than in Spanish; and (b) Basque does not use more intransitive sentences than Spanish; both languages have a similar frequency of intransitive sentences. Based on these findings, we conclude that the frequency of use of grammatical resources to facilitate the processing does not depend on a single typological trait (VO/OV) but it is modulated by the concurrence of other grammatical feature.

Synthetic molecular machines for active self-assembly : prototype algorithms, designs, and experimental study

Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast–all while remaining functional.

This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of “active self-assembly” of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology’s numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules.

One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved.

One might think that because a system is Turing-complete, capable of computing “anything,” that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not “computations” in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface.

Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors “energetically incomplete” programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time.

As we will demonstrate and prove, a sufficiently expressive implementation of an “active” molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the the problem, so the system is not “energetically incomplete.” But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive.

Building on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly.

We show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self- assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics.

We developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this re- action over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction.

In addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molec- ular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.

Beyond Watson and Crick : programming the self-assembly and reconfiguration of DNA nanostructures based on stacking interactions

Life is the result of the execution of molecular programs: like how an embryo is fated to become a human or a whale, or how a person’s appearance is inherited from their parents, many biological phenomena are governed by genetic programs written in DNA molecules. At the core of such programs is the highly reliable base pairing interaction between nucleic acids. DNA nanotechnology exploits the programming power of DNA to build artificial nanostructures, molecular computers, and nanomachines. In particular, DNA origami—which is a simple yet versatile technique that allows one to create various nanoscale shapes and patterns—is at the heart of the technology. In this thesis, I describe the development of programmable self-assembly and reconfiguration of DNA origami nanostructures based on a unique strategy: rather than relying on Watson-Crick base pairing, we developed programmable bonds via the geometric arrangement of stacking interactions, which we termed stacking bonds. We further demonstrated that such bonds can be dynamically reconfigurable.

The first part of this thesis describes the design and implementation of stacking bonds. Our work addresses the fundamental question of whether one can create diverse bond types out of a single kind of attractive interaction—a question first posed implicitly by Francis Crick while seeking a deeper understanding of the origin of life and primitive genetic code. For the creation of multiple specific bonds, we used two different approaches: binary coding and shape coding of geometric arrangement of stacking interaction units, which are called blunt ends. To construct a bond space for each approach, we performed a systematic search using a computer algorithm. We used orthogonal bonds to experimentally implement the connection of five distinct DNA origami nanostructures. We also programmed the bonds to control cis/trans configuration between asymmetric nanostructures.

The second part of this thesis describes the large-scale self-assembly of DNA origami into two-dimensional checkerboard-pattern crystals via surface diffusion. We developed a protocol where the diffusion of DNA origami occurs on a substrate and is dynamically controlled by changing the cationic condition of the system. We used stacking interactions to mediate connections between the origami, because of their potential for reconfiguring during the assembly process. Assembling DNA nanostructures directly on substrate surfaces can benefit nano/microfabrication processes by eliminating a pattern transfer step. At the same time, the use of DNA origami allows high complexity and unique addressability with six-nanometer resolution within each structural unit.

The third part of this thesis describes the use of stacking bonds as dynamically breakable bonds. To break the bonds, we used biological machinery called the ParMRC system extracted from bacteria. The system ensures that, when a cell divides, each daughter cell gets one copy of the cell’s DNA by actively pushing each copy to the opposite poles of the cell. We demonstrate dynamically expandable nanostructures, which makes stacking bonds a promising candidate for reconfigurable connectors for nanoscale machine parts.

Creating a German–Basque Electronic Dictionary for German Learners

Revista OJS

Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry.

In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive.

Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

In Chapters 3 and 4, we identify and overcome the crucial experimental challenges involved in using our general DNA-based technology for engineering dynamical behaviors in the test tube. In this process, we identify important design rules that inform our choice of molecular motifs and our algorithms for designing and verifying DNA sequences for our molecular implementation. We also develop flexible molecular strategies for "tuning" our reaction rates and stoichiometries in order to compensate for unavoidable non-idealities in the molecular implementation, such as imperfectly synthesized molecules and spurious "leak" pathways that compete with desired pathways.

We successfully implement three distinct autocatalytic reactions, which we then combine into a de novo chemical oscillator. Unlike biological networks, which use sophisticated evolved molecules (like proteins) to realize such behavior, our test tube realization is the first to demonstrate that Watson-Crick base pairing interactions alone suffice for oscillatory dynamics. Since our design pipeline is general and applicable to any CRN, our experimental demonstration of a de novo chemical oscillator could enable the systematic construction of CRNs with other dynamic behaviors.

THE AINU LANGUAGES: TRADITIONAL RECONSTRUCTION, EURASIAN AREAL LINGUISTICS, AND DIACHRONIC (HOLISTIC) TYPOLOGY

El objetivo principal de esta tesis doctoral es, en primer lugar, ofrecer una reconstrucción alternativa del protoainu para, en segundo lugar, aplicar conceptos de tipología diacrónicaholística con el fin de discernir algún patrón evolutivo que ayude a responder a la pregunta:¿por qué la lengua ainu es como es en su contexto geolingüístico (lengua AOV con prefijos),cuando en la región euroasiática lo normal es encontrar el perfil 'lengua AOV con sufijos'? En suma, se trata de explorar las posibilidades que ofrece la tipología diacrónica holística,combinada con métodos más tradicionales, en la investigación de las etapas prehistóricas delenguas aisladas, es decir, sin parientes conocidos, como el ainu, el vasco, el zuñi o elburushaski. Este trabajo se divide en tres grandes bloques con un total de ocho capítulos, unapéndice con las nuevas reconstrucciones protoainúes y la bibliografía.El primer bloque se abre con el capítulo 1, donde se hace una breve presentación delas lenguas ainus y su filología. El capítulo 2 está dedicado a la reconstrucción de la fonologíaprotoainu. La reconstrucción pionera pertenece a A. Vovin (1992), que de hecho sirve comobase sobre la que ampliar, corregir o modificar nuevos elementos. En el capítulo 3 se describela morfología histórica de las lenguas ainus. En el capítulo 4 se investiga esta opción dentrode un marco más amplio que tiene como objetivo analizar los patrones elementales deformación de palabras. El capítulo 5, con el que se inicia el segundo bloque, da cabida a lapresentación de una hipótesis tipológica diacrónica, a cargo de P. Donegan y D. Stampe, conla que especialistas en lenguas munda y mon-khmer han sido capaces de alcanzar unreconstrucción del protoaustroasiático según la cual el tipo aglutinante de las lenguas mundasería secundario, frente al original monosilábico de las lenguas mon-khmer. En el capítulo 6se retoma la perspectiva tradicional de la lingüística geográfica, pero no se olvidan algunas delas consideraciones tipológicas apuntadas en el capítulo anterior (el hecho de que la hipótesisde Donegan y Stampe no funcione con el ainu no significa que la tipología diacrónica nopueda ser todavía de utilidad). En el capítulo 7 se presentan algunas incongruencias queresultan tras combinar las supuestas evidencias arqueológicas con el escenario lingüísticodescrito en capítulos anteriores. Las conclusiones generales se presentan en el capítulo 8. Elapéndice es una tabla comparativa con las dos reconstrucciones disponibles a fecha de hoypara la lengua protoainu, es decir, las propuestas por A. Vovin en su estudio seminal de 1992y en el capítulo 3 de la presente tesis. Dicha tabla incluye 686 reconstrucciones (puedehacerse una sencilla referencia cruzada con Vovin, puesto que ambas están ordenadasalfabéticamente).

Optimisation of the first principle code Octopus for massive parallel architectures: application to light harvesting complexes

150 p.

Proficiency, Attitude and Conventions in Minority Languages

In this paper we study a simple mathematical model of a bilingual community in which all agents are f luent in the majority language but only a fraction of the population has some degree of pro ficiency in the minority language. We investigate how different distributions of pro ficiency, combined with the speaker´attitudes towards or against the minority language, may infl uence its use in pair conversations.

Efficient electronic implementations of adaptive systems for ambient intelligence environments

183 p.

Electronic properties of graphene grain boundaries

Grain boundaries and defect lines in graphene are intensively studied for their novel electronic and magnetic properties. However, there is not a complete comprehension of the appearance of localized states along these defects. Graphene grain boundaries are herein seen as the outcome of matching two semi-infinite graphene sheets with different edges. We classify the energy spectra of grain boundaries into three different types, directly related to the combination of the four basic classes of spectra of graphene edges. From the specific geometry of the grains, we are able to obtain the band structure and the number of localized states close to the Fermi energy. This provides a new understanding of states localized at grain boundaries, showing that they are derived from the edge states of graphene. Such knowledge is crucial for the ultimate tailoring of electronic and optoelectronic applications.

Defect and structural imperfection effects on the electronic properties of BiTeI surfaces

The surface electronic structure of the narrow-gap seminconductor BiTeI exhibits a large Rashba-splitting which strongly depends on the surface termination. Here we report on a detailed investigation of the surface morphology and electronic properties of cleaved BiTeI single crystals by scanning tunneling microscopy, photoelectron spectroscopy (ARPES, XPS), electron diffraction (SPA-LEED) and density functional theory calculations. Our measurements confirm a previously reported coexistence of Te- and I-terminated surface areas

Desarrollo e implementación de un relay de mensajería para la aplicación Kde-Connect.

[EN]Nowadays, with the unstoppable raise of different types of electronic devices (mobile phones, tablets, computers…), it has become a necessity to share all the information and functionalities they have. In order to achieve that, back in the 2013, KDE community developed an application called KDE-Connect. This application has been really useful since then, but it’s limited as it can only operate with devices in the same network. Therefore, in the following pages, this project will explain and develop the best solution to extend its functionalities so any pair of devices can share information in an anonymous, private and easy way, at any geographic location.