Experiences with OpenMP in tmLQCD

An overview is given of the lessons learned from the introduction of multi-threading using OpenMP in tmLQCD. In particular, programming style, performance measurements, cache misses, scaling, thread distribution for hybrid codes, race conditions, the overlapping of communication and computation and the measurement and reduction of certain overheads are discussed. Performance measurements and sampling profiles are given for different implementations of the hopping matrix computational kernel.

Excitonic Splitting, Delocalization, and Vibronic Quenching in the Benzonitrile Dimer

The excitonic S1/S2 state splitting and the localization/delocalization of the S1 and S2 electronic states are investigated in the benzonitrile dimer (BN)2 and its 13C and d5 isotopomers by mass-resolved two-color resonant two-photon ionization spectroscopy in a supersonic jet, complemented by calculations. The doubly hydrogen-bonded (BN-h5)2 and (BN-d5)2 dimers are C2h symmetric with equivalent BN moieties. Only the S0 → S2 electronic origin is observed, while the S0 → S1 excitonic component is electric-dipole forbidden. A single 12C/13C or 5-fold h5/d5 isotopic substitution reduce the dimer symmetry to Cs, so that the heteroisotopic dimers (BN)2-(h5 – h513C), (BN)2-(h5 – d5), and (BN)2-(h5 – h513C) exhibit both S0 → S1 and S0 → S2 origins. Isotope-dependent contributions Δiso to the excitonic splittings arise from the changes of the BN monomer zero-point vibrational energies; these range from Δiso(12C/13C) = 3.3 cm–1 to Δiso(h5/d5) = 155.6 cm–1. The analysis of the experimental S1/S2 splittings of six different isotopomeric dimers yields the S1/S2 exciton splitting Δexc = 2.1 ± 0.1 cm–1. Since Δiso(h5/d5) ≫ Δexc and Δiso(12C/13C) > Δexc, complete and near-complete exciton localization occurs upon 12C/13C and h5/d5 substitutions, respectively, as diagnosed by the relative S0 → S1 and S0 → S2 origin band intensities. The S1/S2 electronic energy gap of (BN)2 calculated by the spin-component scaled approximate second-order coupled-cluster (SCS-CC2) method is Δelcalc = 10 cm–1. This electronic splitting is reduced by the vibronic quenching factor Γ. The vibronically quenched exciton splitting Δelcalc·Γ = Δvibroncalc = 2.13 cm–1 is in excellent agreement with the observed splitting Δexc = 2.1 cm–1. The excitonic splittings can be converted to semiclassical exciton hopping times; the shortest hopping time is 8 ps for the homodimer (BN-h5)2, the longest is 600 ps for the (BN)2(h5 – d5) heterodimer.

High-peak-power pulse generation from a monolithic master oscillator power amplifier at 1.5 μm

We present an experimental study on the generation of high-peak-power short optical pulses from a fully integrated master-oscillator power-amplifier emitting at 1.5 μm. High-peak-power (2.7 W) optical pulses with short duration (100 ps) have been generated by gain switching the master oscillator under optimized driving conditions. The static and dynamic characteristics of the device have been studied as a function of the driving conditions. The ripples appearing in the power-current characteristics under cw conditions have been attributed to mode hopping between the master oscillator resonant mode and the Fabry-Perot modes of the entire device cavity. Although compound cavity effects have been evidenced to affect the static and dynamic performance of the device, we have demonstrated that trains of single-mode short optical pulses at gigahertz frequencies can be conveniently generated in these devices.

Electrical, photoelectrical and morphological properties of ZnO nanowire networks grown on SiO2 and on Si

ZnO nanofibre networks (NFNs) were grown by vapour transport method on Si-based substrates. One type of substrate was SiO2 thermally grown on Si and another consisted of a Si wafer onto which Si nanowires (NWs) had been grown having Au nanoparticles catalysts. The ZnO-NFN morphology was observed by scanning electron microscopy on samples grown at 600 °C and 720 °C substrate temperature, while an focused ion beam was used to study the ZnO NFN/Si NWs/Si and ZnO NFN/SiO2 interfaces. Photoluminescence, electrical conductance and photoconductance of ZnO-NFN was studied for the sample grown on SiO2. The photoluminescence spectra show strong peaks due to exciton recombination and lattice defects. The ZnO-NFN presents quasi-persistent photoconductivity effects and ohmic I-V characteristics which become nonlinear and hysteretic as the applied voltage is increased. The electrical conductance as a function of temperature can be described by a modified three dimensional variable hopping model with nanometer-ranged typical hopping distances.

Design and Validation of an Optimized MB-OFDM Ultra Wideband Transceiver System

Esta tesis está incluida dentro del campo del campo de Multiband Orthogonal Frequency Division Multiplexing Ultra Wideband (MB-OFDM UWB), el cual ha adquirido una gran importancia en las comunicaciones inalámbricas de alta tasa de datos en la última década. UWB surgió con el objetivo de satisfacer la creciente demanda de conexiones inalámbricas en interiores y de uso doméstico, con bajo coste y alta velocidad. La disponibilidad de un ancho de banda grande, el potencial para alta velocidad de transmisión, baja complejidad y bajo consumo de energía, unido al bajo coste de implementación, representa una oportunidad única para que UWB se convierta en una solución ampliamente utilizada en aplicaciones de Wireless Personal Area Network (WPAN). UWB está definido como cualquier transmisión que ocupa un ancho de banda de más de 20% de su frecuencia central, o más de 500 MHz. En 2002, la Comisión Federal de Comunicaciones (FCC) definió que el rango de frecuencias de transmisión de UWB legal es de 3.1 a 10.6 GHz, con una energía de transmisión de -41.3 dBm/Hz. Bajo las directrices de FCC, el uso de la tecnología UWB puede aportar una enorme capacidad en las comunicaciones de corto alcance. Considerando las ecuaciones de capacidad de Shannon, incrementar la capacidad del canal requiere un incremento lineal en el ancho de banda, mientras que un aumento similar de la capacidad de canal requiere un aumento exponencial en la energía de transmisión. En los últimos años, s diferentes desarrollos del UWB han sido extensamente estudiados en diferentes áreas, entre los cuales, el protocolo de comunicaciones inalámbricas MB-OFDM UWB está considerado como la mejor elección y ha sido adoptado como estándar ISO/IEC para los WPANs. Combinando la modulación OFDM y la transmisión de datos utilizando las técnicas de salto de frecuencia, el sistema MB-OFDM UWB es capaz de soportar tasas de datos con que pueden variar de los 55 a los 480 Mbps, alcanzando una distancia máxima de hasta 10 metros. Se esperara que la tecnología MB-OFDM tenga un consumo energético muy bajo copando un are muy reducida en silicio, proporcionando soluciones de bajo coste que satisfagan las demandas del mercado. Para cumplir con todas estas expectativas, el desarrollo y la investigación del MBOFDM UWB deben enfrentarse a varios retos, como son la sincronización de alta sensibilidad, las restricciones de baja complejidad, las estrictas limitaciones energéticas, la escalabilidad y la flexibilidad. Tales retos requieren un procesamiento digital de la señal de última generación, capaz de desarrollar sistemas que puedan aprovechar por completo las ventajas del espectro UWB y proporcionar futuras aplicaciones inalámbricas en interiores. Esta tesis se centra en la completa optimización de un sistema de transceptor de banda base MB-OFDM UWB digital, cuyo objetivo es investigar y diseñar un subsistema de comunicación inalámbrica para la aplicación de las Redes de Sensores Inalámbricas Visuales. La complejidad inherente de los procesadores FFT/IFFT y el sistema de sincronización así como la alta frecuencia de operación para todos los elementos de procesamiento, se convierten en el cuello de la botella para el diseño y la implementación del sistema de UWB digital en base de banda basado en MB-OFDM de baja energía. El objetivo del transceptor propuesto es conseguir baja energía y baja complejidad bajo la premisa de un alto rendimiento. Las optimizaciones están realizadas tanto a nivel algorítmico como a nivel arquitectural para todos los elementos del sistema. Una arquitectura hardware eficiente en consumo se propone en primer lugar para aquellos módulos correspondientes a núcleos de computación. Para el procesado de la Transformada Rápida de Fourier (FFT/IFFT), se propone un algoritmo mixed-radix, basado en una arquitectura con pipeline y se ha desarrollado un módulo de Decodificador de Viterbi (VD) equilibrado en coste-velocidad con el objetivo de reducir el consumo energético e incrementar la velocidad de procesamiento. También se ha implementado un correlador signo-bit simple basado en la sincronización del tiempo de símbolo es presentado. Este correlador es usado para detectar y sincronizar los paquetes de OFDM de forma robusta y precisa. Para el desarrollo de los subsitemas de procesamiento y realizar la integración del sistema completo se han empleado tecnologías de última generación. El dispositivo utilizado para el sistema propuesto es una FPGA Virtex 5 XC5VLX110T del fabricante Xilinx. La validación el propuesta para el sistema transceptor se ha implementado en dicha placa de FPGA. En este trabajo se presenta un algoritmo, y una arquitectura, diseñado con filosofía de co-diseño hardware/software para el desarrollo de sistemas de FPGA complejos. El objetivo principal de la estrategia propuesta es de encontrar una metodología eficiente para el diseño de un sistema de FPGA configurable optimizado con el empleo del mínimo esfuerzo posible en el sistema de procedimiento de verificación, por tanto acelerar el periodo de desarrollo del sistema. La metodología de co-diseño presentada tiene la ventaja de ser fácil de usar, contiene todos los pasos desde la propuesta del algoritmo hasta la verificación del hardware, y puede ser ampliamente extendida para casi todos los tipos de desarrollos de FPGAs. En este trabajo se ha desarrollado sólo el sistema de transceptor digital de banda base por lo que la comprobación de señales transmitidas a través del canal inalámbrico en los entornos reales de comunicación sigue requiriendo componentes RF y un front-end analógico. No obstante, utilizando la metodología de co-simulación hardware/software citada anteriormente, es posible comunicar el sistema de transmisor y el receptor digital utilizando los modelos de canales propuestos por IEEE 802.15.3a, implementados en MATLAB. Por tanto, simplemente ajustando las características de cada modelo de canal, por ejemplo, un incremento del retraso y de la frecuencia central, podemos estimar el comportamiento del sistema propuesto en diferentes escenarios y entornos. Las mayores contribuciones de esta tesis son: • Se ha propuesto un nuevo algoritmo 128-puntos base mixto FFT usando la arquitectura pipeline multi-ruta. Los complejos multiplicadores para cada etapa de procesamiento son diseñados usando la arquitectura modificada shiftadd. Los sistemas word length y twiddle word length son comparados y seleccionados basándose en la señal para cuantización del SQNR y el análisis de energías. • El desempeño del procesador IFFT es analizado bajo diferentes situaciones aritméticas de bloques de punto flotante (BFP) para el control de desbordamiento, por tanto, para encontrar la arquitectura perfecta del algoritmo IFFT basado en el procesador FFT propuesto. • Para el sistema de receptor MB-OFDM UWB se ha empleado una sincronización del tiempo innovadora, de baja complejidad y esquema de compensación, que consiste en funciones de Detector de Paquetes (PD) y Estimación del Offset del tiempo. Simplificando el cross-correlation y maximizar las funciones probables solo a sign-bit, la complejidad computacional se ve reducida significativamente. • Se ha propuesto un sistema de decodificadores Viterbi de 64 estados de decisión-débil usando velocidad base-4 de arquitectura suma-comparaselecciona. El algoritmo Two-pointer Even también es introducido en la unidad de rastreador de origen con el objetivo de conseguir la eficiencia en el hardware. • Se han integrado varias tecnologías de última generación en el completo sistema transceptor basebanda , con el objetivo de implementar un sistema de comunicación UWB altamente optimizado. • Un diseño de flujo mejorado es propuesto para el complejo sistema de implementación, el cual puede ser usado para diseños de Cadena de puertas de campo programable general (FPGA). El diseño mencionado no sólo reduce dramáticamente el tiempo para la verificación funcional, sino también provee un análisis automático como los errores del retraso del output para el sistema de hardware implementado. • Un ambiente de comunicación virtual es establecido para la validación del propuesto sistema de transceptores MB-OFDM. Este método es provisto para facilitar el uso y la conveniencia de analizar el sistema digital de basebanda sin parte frontera analógica bajo diferentes ambientes de comunicación. Esta tesis doctoral está organizada en seis capítulos. En el primer capítulo se encuentra una breve introducción al campo del UWB, tanto relacionado con el proyecto como la motivación del desarrollo del sistema de MB-OFDM. En el capítulo 2, se presenta la información general y los requisitos del protocolo de comunicación inalámbrica MBOFDM UWB. En el capítulo 3 se habla de la arquitectura del sistema de transceptor digital MB-OFDM de banda base . El diseño del algoritmo propuesto y la arquitectura para cada elemento del procesamiento está detallado en este capítulo. Los retos de diseño del sistema que involucra un compromiso de discusión entre la complejidad de diseño, el consumo de energía, el coste de hardware, el desempeño del sistema, y otros aspectos. En el capítulo 4, se ha descrito la co-diseñada metodología de hardware/software. Cada parte del flujo del diseño será detallado con algunos ejemplos que se ha hecho durante el desarrollo del sistema. Aprovechando esta estrategia de diseño, el procedimiento de comunicación virtual es llevado a cabo para probar y analizar la arquitectura del transceptor propuesto. Los resultados experimentales de la co-simulación y el informe sintético de la implementación del sistema FPGA son reflejados en el capítulo 5. Finalmente, en el capítulo 6 se incluye las conclusiones y los futuros proyectos, y también los resultados derivados de este proyecto de doctorado. ABSTRACT In recent years, the Wireless Visual Sensor Network (WVSN) has drawn great interest in wireless communication research area. They enable a wealth of new applications such as building security control, image sensing, and target localization. However, nowadays wireless communication protocols (ZigBee, Wi-Fi, and Bluetooth for example) cannot fully satisfy the demands of high data rate, low power consumption, short range, and high robustness requirements. New communication protocol is highly desired for such kind of applications. The Ultra Wideband (UWB) wireless communication protocol, which has increased in importance for high data rate wireless communication field, are emerging as an important topic for WVSN research. UWB has emerged as a technology that offers great promise to satisfy the growing demand for low-cost, high-speed digital wireless indoor and home networks. The large bandwidth available, the potential for high data rate transmission, and the potential for low complexity and low power consumption, along with low implementation cost, all present a unique opportunity for UWB to become a widely adopted radio solution for future Wireless Personal Area Network (WPAN) applications. UWB is defined as any transmission that occupies a bandwidth of more than 20% of its center frequency, or more than 500 MHz. In 2002, the Federal Communications Commission (FCC) has mandated that UWB radio transmission can legally operate in the range from 3.1 to 10.6 GHz at a transmitter power of －41.3 dBm/Hz. Under the FCC guidelines, the use of UWB technology can provide enormous capacity over short communication ranges. Considering Shannon’s capacity equations, increasing the channel capacity requires linear increasing in bandwidth, whereas similar channel capacity increases would require exponential increases in transmission power. In recent years, several different UWB developments has been widely studied in different area, among which, the MB-OFDM UWB wireless communication protocol is considered to be the leading choice and has recently been adopted in the ISO/IEC standard for WPANs. By combing the OFDM modulation and data transmission using frequency hopping techniques, the MB-OFDM UWB system is able to support various data rates, ranging from 55 to 480 Mbps, over distances up to 10 meters. The MB-OFDM technology is expected to consume very little power and silicon area, as well as provide low-cost solutions that can satisfy consumer market demands. To fulfill these expectations, MB-OFDM UWB research and development have to cope with several challenges, which consist of high-sensitivity synchronization, low- complexity constraints, strict power limitations, scalability, and flexibility. Such challenges require state-of-the-art digital signal processing expertise to develop systems that could fully take advantages of the UWB spectrum and support future indoor wireless applications. This thesis focuses on fully optimization for the MB-OFDM UWB digital baseband transceiver system, aiming at researching and designing a wireless communication subsystem for the Wireless Visual Sensor Networks (WVSNs) application. The inherent high complexity of the FFT/IFFT processor and synchronization system, and high operation frequency for all processing elements, becomes the bottleneck for low power MB-OFDM based UWB digital baseband system hardware design and implementation. The proposed transceiver system targets low power and low complexity under the premise of high performance. Optimizations are made at both algorithm and architecture level for each element of the transceiver system. The low-power hardwareefficient structures are firstly proposed for those core computation modules, i.e., the mixed-radix algorithm based pipelined architecture is proposed for the Fast Fourier Transform (FFT/IFFT) processor, and the cost-speed balanced Viterbi Decoder (VD) module is developed, in the aim of lowering the power consumption and increasing the processing speed. In addition, a low complexity sign-bit correlation based symbol timing synchronization scheme is presented so as to detect and synchronize the OFDM packets robustly and accurately. Moreover, several state-of-the-art technologies are used for developing other processing subsystems and an entire MB-OFDM digital baseband transceiver system is integrated. The target device for the proposed transceiver system is Xilinx Virtex 5 XC5VLX110T FPGA board. In order to validate the proposed transceiver system in the FPGA board, a unified algorithm-architecture-circuit hardware/software co-design environment for complex FPGA system development is presented in this work. The main objective of the proposed strategy is to find an efficient methodology for designing a configurable optimized FPGA system by using as few efforts as possible in system verification procedure, so as to speed up the system development period. The presented co-design methodology has the advantages of easy to use, covering all steps from algorithm proposal to hardware verification, and widely spread for almost all kinds of FPGA developments. Because only the digital baseband transceiver system is developed in this thesis, the validation of transmitting signals through wireless channel in real communication environments still requires the analog front-end and RF components. However, by using the aforementioned hardware/software co-simulation methodology, the transmitter and receiver digital baseband systems get the opportunity to communicate with each other through the channel models, which are proposed from the IEEE 802.15.3a research group, established in MATLAB. Thus, by simply adjust the characteristics of each channel model, e.g. mean excess delay and center frequency, we can estimate the transmission performance of the proposed transceiver system through different communication situations. The main contributions of this thesis are: • A novel mixed radix 128-point FFT algorithm by using multipath pipelined architecture is proposed. The complex multipliers for each processing stage are designed by using modified shift-add architectures. The system wordlength and twiddle word-length are compared and selected based on Signal to Quantization Noise Ratio (SQNR) and power analysis. • IFFT processor performance is analyzed under different Block Floating Point (BFP) arithmetic situations for overflow control, so as to find out the perfect architecture of IFFT algorithm based on the proposed FFT processor. • An innovative low complex timing synchronization and compensation scheme, which consists of Packet Detector (PD) and Timing Offset Estimation (TOE) functions, for MB-OFDM UWB receiver system is employed. By simplifying the cross-correlation and maximum likelihood functions to signbit only, the computational complexity is significantly reduced. • A 64 state soft-decision Viterbi Decoder system by using high speed radix-4 Add-Compare-Select architecture is proposed. Two-pointer Even algorithm is also introduced into the Trace Back unit in the aim of hardware-efficiency. • Several state-of-the-art technologies are integrated into the complete baseband transceiver system, in the aim of implementing a highly-optimized UWB communication system. • An improved design flow is proposed for complex system implementation which can be used for general Field-Programmable Gate Array (FPGA) designs. The design method not only dramatically reduces the time for functional verification, but also provides automatic analysis such as errors and output delays for the implemented hardware systems. • A virtual communication environment is established for validating the proposed MB-OFDM transceiver system. This methodology is proved to be easy for usage and convenient for analyzing the digital baseband system without analog frontend under different communication environments. This PhD thesis is organized in six chapters. In the chapter 1 a brief introduction to the UWB field, as well as the related work, is done, along with the motivation of MBOFDM system development. In the chapter 2, the general information and requirement of MB-OFDM UWB wireless communication protocol is presented. In the chapter 3, the architecture of the MB-OFDM digital baseband transceiver system is presented. The design of the proposed algorithm and architecture for each processing element is detailed in this chapter. Design challenges of such system involve trade-off discussions among design complexity, power consumption, hardware cost, system performance, and some other aspects. All these factors are analyzed and discussed. In the chapter 4, the hardware/software co-design methodology is proposed. Each step of this design flow will be detailed by taking some examples that we met during system development. Then, taking advantages of this design strategy, the Virtual Communication procedure is carried out so as to test and analyze the proposed transceiver architecture. Experimental results from the co-simulation and synthesis report of the implemented FPGA system are given in the chapter 5. The chapter 6 includes conclusions and future work, as well as the results derived from this PhD work.

Nuevo algoritmo de compresión multimedia: codificación por saltos logaritmicos

Quizás el Código Morse, inventado en 1838 para su uso en la telegrafía, es uno de los primeros ejemplos de la utilización práctica de la compresión de datos [1], donde las letras más comunes del alfabeto son codificadas con códigos más cortos que las demás. A partir de 1940 y tras el desarrollo de la teoría de la información y la creación de los primeros ordenadores, la compresión de la información ha sido un reto constante y fundamental entre los campos de trabajo de investigadores de todo tipo. Cuanto mayor es nuestra comprensión sobre el significado de la información, mayor es nuestro éxito comprimiéndola. En el caso de la información multimedia, su naturaleza permite la compresión con pérdidas, alcanzando así cotas de compresión imposibles para los algoritmos sin pérdidas. Estos “recientes” algoritmos con pérdidas han estado mayoritariamente basados en transformación de la información al dominio de la frecuencia y en la eliminación de parte de la información en dicho dominio. Transformar al dominio de la frecuencia posee ventajas pero también involucra unos costes computacionales inevitables. Esta tesis presenta un nuevo algoritmo de compresión multimedia llamado “LHE” (Logarithmical Hopping Encoding) que no requiere transformación al dominio de la frecuencia, sino que trabaja en el dominio del espacio. Esto lo convierte en un algoritmo lineal de reducida complejidad computacional. Los resultados del algoritmo son prometedores, superando al estándar JPEG en calidad y velocidad. Para ello el algoritmo utiliza como base la respuesta fisiológica del ojo humano ante el estímulo luminoso. El ojo, al igual que el resto de los sentidos, responde al logaritmo de la señal de acuerdo a la ley de Weber. El algoritmo se compone de varias etapas. Una de ellas es la medición de la “Relevancia Perceptual”, una nueva métrica que nos va a permitir medir la relevancia que tiene la información en la mente del sujeto y en base a la misma, degradar en mayor o menor medida su contenido, a través de lo que he llamado “sub-muestreado elástico”. La etapa de sub-muestreado elástico constituye una nueva técnica sin precedentes en el tratamiento digital de imágenes. Permite tomar más o menos muestras en diferentes áreas de una imagen en función de su relevancia perceptual. En esta tesis se dan los primeros pasos para la elaboración de lo que puede llegar a ser un nuevo formato estándar de compresión multimedia (imagen, video y audio) libre de patentes y de alto rendimiento tanto en velocidad como en calidad. ABSTRACT The Morse code, invented in 1838 for use in telegraphy, is one of the first examples of the practical use of data compression [1], where the most common letters of the alphabet are coded shorter than the rest of codes. From 1940 and after the development of the theory of information and the creation of the first computers, compression of information has been a constant and fundamental challenge among any type of researchers. The greater our understanding of the meaning of information, the greater our success at compressing. In the case of multimedia information, its nature allows lossy compression, reaching impossible compression rates compared with lossless algorithms. These "recent" lossy algorithms have been mainly based on information transformation to frequency domain and elimination of some of the information in that domain. Transforming the frequency domain has advantages but also involves inevitable computational costs. This thesis introduces a new multimedia compression algorithm called "LHE" (logarithmical Hopping Encoding) that does not require transformation to frequency domain, but works in the space domain. This feature makes LHE a linear algorithm of reduced computational complexity. The results of the algorithm are promising, outperforming the JPEG standard in quality and speed. The basis of the algorithm is the physiological response of the human eye to the light stimulus. The eye, like other senses, responds to the logarithm of the signal according with Weber law. The algorithm consists of several stages. One is the measurement of "perceptual relevance," a new metric that will allow us to measure the relevance of information in the subject's mind and based on it; degrade accordingly their contents, through what I have called "elastic downsampling". Elastic downsampling stage is an unprecedented new technique in digital image processing. It lets take more or less samples in different areas of an image based on their perceptual relevance. This thesis introduces the first steps for the development of what may become a new standard multimedia compression format (image, video and audio) free of patents and high performance in both speed and quality.

Charge transfer and transport in DNA

We explore charge migration in DNA, advancing two distinct mechanisms of charge separation in a donor (d)–bridge ({Bj})–acceptor (a) system, where {Bj} = B1,B2, … , BN are the N-specific adjacent bases of B-DNA: (i) two-center unistep superexchange induced charge transfer, d*{Bj}a → d∓{Bj}a±, and (ii) multistep charge transport involves charge injection from d* (or d+) to {Bj}, charge hopping within {Bj}, and charge trapping by a. For off-resonance coupling, mechanism i prevails with the charge separation rate and yield exhibiting an exponential dependence ∝ exp(−βR) on the d-a distance (R). Resonance coupling results in mechanism ii with the charge separation lifetime τ ∝ Nη and yield Y ≃ (1 + δ̄ Nη)−1 exhibiting a weak (algebraic) N and distance dependence. The power parameter η is determined by charge hopping random walk. Energetic control of the charge migration mechanism is exerted by the energetics of the ion pair state d∓B1±B2 … BNa relative to the electronically excited donor doorway state d*B1B2 … BNa. The realization of charge separation via superexchange or hopping is determined by the base sequence within the bridge. Our energetic–dynamic relations, in conjunction with the energetic data for d*/d− and for B/B+, determine the realization of the two distinct mechanisms in different hole donor systems, establishing the conditions for “chemistry at a distance” after charge transport in DNA. The energetic control of the charge migration mechanisms attained by the sequence specificity of the bridge is universal for large molecular-scale systems, for proteins, and for DNA.

EphA4 (Sek1) receptor tyrosine kinase is required for the development of the corticospinal tract

Members of the Eph family of tyrosine kinase receptors have been implicated in the regulation of developmental processes and, in particular, axon guidance in the developing nervous system. The function of the EphA4 (Sek1) receptor was explored through creation of a null mutant mouse. Mice with a null mutation in the EphA4 gene are viable and fertile but have a gross motor dysfunction, which is evidenced by a loss of coordination of limb movement and a resultant hopping, kangaroo-like gait. Consistent with the observed phenotype, anatomical studies and anterograde tracing experiments reveal major disruptions of the corticospinal tract within the medulla and spinal cord in the null mutant animals. These results demonstrate a critical role for EphA4 in establishing the corticospinal projection.

Peptide nucleic acid–DNA duplexes: Long range hole migration from an internally linked anthraquinone

The discovery that peptide nucleic acids (PNA) mimic DNA and RNA by forming complementary duplex structures following Watson–Crick base pairing rules opens fields in biochemistry, diagnostics, and medicine for exploration. Progress requires the development of modified PNA duplexes having unique and well defined properties. We find that anthraquinone groups bound to internal positions of a PNA oligomer intercalate in the PNA–DNA hybrid. Their irradiation with near-UV light leads to electron transfer and oxidative damage at remote GG doublets on the complementary DNA strand. This behavior mimics that observed in related DNA duplexes and provides the first evidence for long range electron (hole) transport in PNA–DNA hybrid. Analysis of the mechanism for electron transport supports hole hopping.

Dynamical principles in biological processes: A model of charge migration in proteins and DNA

The generalized master equations (GMEs) that contain multiple time scales have been derived quantum mechanically. The GME method has then been applied to a model of charge migration in proteins that invokes the hole hopping between local amino acid sites driven by the torsional motions of the floppy backbones. This model is then applied to analyze the experimental results for sequence-dependent long-range hole transport in DNA reported by Meggers et al. [Meggers, E., Michel-Beyerle, M. E., & Giese, B. (1998) J. Am. Chem. Soc. 120, 12950–12955]. The model has also been applied to analyze the experimental results of femtosecond dynamics of DNA-mediated electron transfer reported by Zewail and co-workers [Wan, C., Fiebig, T., Kelley, S. O., Treadway, C. R., Barton, J. K. & Zewail, A. H. (1999) Proc. Natl. Acad. Sci. USA 96, 6014–6019]. The initial events in the dynamics of protein folding have begun to attract attention. The GME obtained in this paper will be applicable to this problem.

Electrical investigation of p-type 4H-SiC heavily doped by ion implantation

In the last decades, an increasing interest in the research field of wide bandgap semiconductors was observed, mostly due to the progressive approaching of silicon-based devices to their theoretical limits. 4H-SiC is an example among these, and is a mature compound for applications. The main advantages offered 4H-SiC in comparison with silicon are an higher breakdown field, an higher thermal conductivity, a higher operating temperature, very high hardness and melting point, biocompatibility, but also low switching losses in high frequencies applications and lower on-resistances in unipolar devices. Then, 4H-SiC power devices offer great performance improvement; moreover, they can work in hostile environments where silicon power devices cannot function. Ion implantation technology is a key process in the fabrication of almost all kinds of SiC devices, owing to the advantage of a spatially selective doping. This work is dedicated to the electrical investigation of several differently-processed 4H-SiC ion- implanted samples, mainly through Hall effect and space charge spectroscopy experiments. It was also developed the automatic control (Labview) of several experiments. In the work, the effectiveness of high temperature post-implant thermal treatments (up to 2000°C) were studied and compared considering: (i) different methods, (ii) different temperatures and (iii) different duration of the annealing process. Preliminary p + /n and Schottky junctions were also investigated as simple test devices. 1) Heavy doping by ion implantation of single off-axis 4H-SiC layers The electrical investigation is one of the most important characterization of ion-implanted samples, which must be submitted to mandatory post-implant thermal treatment in order to both (i) recover the lattice after ion bombardment, and (ii) address the implanted impurities into lattice sites so that they can effectively act as dopants. Electrical investigation can give fundamental information on the efficiency of the electrical impurity activation. To understand the results of the research it should be noted that: (a) To realize good ohmic contacts it is necessary to obtain spatially defined highly doped regions, which must have conductivity as low as possible. (b) It has been shown that the electrical activation efficiency and the electrical conductivity increase with the annealing temperature increasing. (c) To maximize the layer conductivity, temperatures around 1700°C are generally used and implantation density high till to 10 21 cm -3 . In this work, an original approach, different from (c), is explored by the using very high annealing temperature, around 2000°C, on samples of Al + -implant concentration of the order of 10 20 cm -3 . Several Al + -implanted 4H-SiC samples, resulting of p-type conductivity, were investigated, with a nominal density varying in the range of about 1-5∙10 20 cm -3 and subjected to two different high temperature thermal treatments. One annealing method uses a radiofrequency heated furnace till to 1950°C (Conventional Annealing, CA), the other exploits a microwave field, providing a fast heating rate up to 2000°C (Micro-Wave Annealing, MWA). In this contest, mainly ion implanted p-type samples were investigated, both off-axis and on-axis <0001> semi-insulating 4H-SiC. Concerning p-type off-axis samples, a high electrical activation of implanted Al (50-70%) and a compensation ratio below 10% were estimated. In the work, the main sample processing parameters have been varied, as the implant temperature, CA annealing duration, and heating/cooling rates, and the best values assessed. MWA method leads to higher hole density and lower mobility than CA in equivalent ion implanted layers, resulting in lower resistivity, probably related to the 50°C higher annealing temperature. An optimal duration of the CA treatment was estimated in about 12-13 minutes. A RT resistivity on the lowest reported in literature for this kind of samples, has been obtained. 2) Low resistivity data: variable range hopping Notwithstanding the heavy p-type doping levels, the carrier density remained less than the critical one required for a semiconductor to metal transition. However, the high carrier densities obtained was enough to trigger a low temperature impurity band (IB) conduction. In the heaviest doped samples, such a conduction mechanism persists till to RT, without significantly prejudice the mobility values. This feature can have an interesting technological fall, because it guarantee a nearly temperature- independent carrier density, it being not affected by freeze-out effects. The usual transport mechanism occurring in the IB conduction is the nearest neighbor hopping: such a regime is effectively consistent with the resistivity temperature behavior of the lowest doped samples. In the heavier doped samples, however, a trend of the resistivity data compatible with a variable range hopping (VRH) conduction has been pointed out, here highlighted for the first time in p-type 4H-SiC. Even more: in the heaviest doped samples, and in particular, in those annealed by MWA, the temperature dependence of the resistivity data is consistent with a reduced dimensionality (2D) of the VRH conduction. In these samples, TEM investigation pointed out faulted dislocation loops in the basal plane, whose average spacing along the c-axis is comparable with the optimal length of the hops in the VRH transport. This result suggested the assignment of such a peculiar behavior to a kind of spatial confinement into a plane of the carrier hops. 3) Test device the p + -n junction In the last part of the work, the electrical properties of 4H-SiC diodes were also studied. In this case, a heavy Al + ion implantation was realized on n-type epilayers, according to the technological process applied for final devices. Good rectification properties was shown from these preliminary devices in their current-voltage characteristics. Admittance spectroscopy and deep level transient spectroscopy measurements showed the presence of electrically active defects other than the dopants ones, induced in the active region of the diodes by ion implantation. A critical comparison with the literature of these defects was performed. Preliminary to such an investigation, it was assessed the experimental set up for the admittance spectroscopy and current-voltage investigation and the automatic control of these measurements.

Desenvolvimento de microssensores eletroquímicos e aplicações no estudo de processos dinâmicos interfaciais utilizando microscopia eletroquímica de varredura

O trabalho descrito nesta tese mostra de forma detalhada a fabricação e caracterização de diferentes microssensores eletroquímicos os quais têm sido recentemente utilizados como sondas em grupo de técnicas conhecida como Scanning Electrochemical Probe Microscopy (SEPM). Desta forma, a caracterização de superfícies pode ser feita explorando diferentes fenômenos interfaciais relevantes à Ciência. Neste sentido, as interfaces de materiais cristalinos como hidroxiapatita (materiais dentários) e calcita foram o foco de estudo neste trabalho. Assim, diferentes técnicas SEPM foram exploradas no sentido de se obter informações relevantes relacionadas aos processos dentários, como a erosão ácida e hipersensibilidade. Inicialmente, microeletrodos de platina foram desenvolvidos empregando uma metodologia convencional na qual são utilizados microfibras encapsuladas em capilares de vidro. Scanning Electrochemical Microscopy (SECM) no modo amperométrico foi utilizada para obtenção de informações com relação às alterações de topografia do esmalte dentário causadas pelo contato com substâncias ácidas. Adicionalmente, SECM foi empregada no estudo do transporte de espécies eletroativas em amostras de dentina e investigações relacionadas ao bloqueio dos túbulos empregando-se cremes dentais comerciais foram realizadas. A permeação de peróxido de hidrogênio pela dentina também foi estudada. Os resultados de SECM foram comparados com imagens SEM obtidas nas mesmas condições experimentais. Microeletrodos de membrana ionófora íon-seletiva (Ion Selective Microelectrodes-ISMEs) sensíveis a íons cálcio também foram desenvolvidos e caracterizados, com subsequente aplicação em SECM no modo potenciométrico. A dissolução ácida de esmalte bovino (erosão dentária) foi investigada em diferentes valores de pH (2,5; 4,5; 6,8). Além disso, o transporte de íons cálcio através de membranas porosas sintéticas foi avaliado a uma distância tip/substrato de 300µm. Alterações no fluxo de íons cálcio foram correlacionadas em experimentos realizados na presença e ausência de campos magnéticos gerados por nanopartículas de magnetita incorporadas à membrana porosa. Microcristais de calcita facilmente sintetizados pelo método de precipitação foram utilizados como superfície modelo para investigações interfaciais, cujos resultados podem ser correlacionados aos materiais dentários. Desta forma, nanopipetas de vidro preenchidas com eletrólito suporte foram fabricadas e utilizadas como sonda em Scanning Ion Conductance Microscopy (SICM). O mapeamento topográfico de alta resolução espacial da superfície de um microcristal de calcita foi obtido utilizando o modo de varredura hopping mode. Adicionalmente, sondas multifuncionais ISME-SICM também foram desenvolvidas e caracterizadas para investigações simultâneas com relação às alterações topográficas e quantificação de íons cálcio sobre a superfície de um microcristal de calcita. A adição de reagentes ácidos no canal SICM promoveu a dissolução da superfície do microcristal, sendo obtidos dados cinéticos de dissolução. Investigações em meio neutro também foram realizadas utilizando a sonda ISME-SICM. Os resultados experimentais obtidos também foram comparados com aqueles oriundos de simulação computacional.

Effects of the environment on the electric conductivity of double-stranded DNA molecules

We present a theoretical analysis of the effects of the environment on charge transport in double-stranded synthetic poly(G)-poly(C) DNA molecules attached to two ideal leads. Coupling of the DNA to the environment results in two effects: (i) localization of carrier functions due to static disorder and (ii) phonon-induced scattering of the carriers between the localized states, resulting in hopping conductivity. A nonlinear Pauli master equation for populations of localized states is used to describe the hopping transport and calculate the electric current as a function of the applied bias. We demonstrate that, although the electronic gap in the density of states shrinks as the disorder increases, the voltage gap in the I-V characteristics becomes wider. A simple physical explanation of this effect is provided.

Spin-orbit interaction in curved graphene ribbons

We study the electronic properties of electrons in flat and curved zigzag graphene nanoribbons using a tight-binding model within the Slater Koster approximation, including spin-orbit interaction. We find that a constant curvature across the ribbon dramatically enhances the action of the spin-orbit term, strongly influencing the spin orientation of the edge states: Whereas spins are normal to the surface in the case of flat ribbons, this is no longer the case for curved ribbons. This effect is very pronounced, the spins deviating from the normal to the ribbon, even for very small curvature and a realistic spin orbit coupling of carbon. We find that curvature results also in an effective second neighbor hopping that modifies the electronic properties of zigzag graphene ribbons. We discuss the implications of our findings in the spin Hall phase of curved graphene ribbons.

Interplay between sublattice and spin symmetry breaking in graphene

We study the effect of sublattice symmetry breaking on the electronic, magnetic, and transport properties of two-dimensional graphene as well as zigzag terminated one- and zero-dimensional graphene nanostructures. The systems are described with the Hubbard model within the collinear mean field approximation. We prove that for the noninteracting bipartite lattice with an unequal number of atoms in each sublattice, in-gap states still exist in the presence of a staggered on-site potential ±Δ/2. We compute the phase diagram of both 2D and 1D graphene with zigzag edges, at half filling, defined by the normalized interaction strength U/t and Δ/t, where t is the first neighbor hopping. In the case of 2D we find that the system is always insulating, and we find the Uc(Δ) curve above which the system goes antiferromagnetic. In 1D we find that the system undergoes a phase transition from nonmagnetic insulator for U