A molecular dynamics study of swift heavy ion irradiation of amorphous silica: the role of thermal effects

Irradiation with swift heavy ions (SHI), roughly defined as those having atomic masses larger than 15 and energies exceeding 1 MeV/amu, may lead to significant modification of the irradiated material in a nanometric region around the (straight) ion trajectory (latent tracks). In the case of amorphous silica, SHI irradiation originates nano-tracks of higher density than the virgin material (densification). As a result, the refractive index is increased with respect to that of the surroundings. Moreover, track overlapping leads to continuous amorphous layers that present a significant contrast with respect to the pristine substrate. We have recently demonstrated that SHI irradiation produces a large number of point defects, easily detectable by a number of experimental techniques (work presented in the parallel conference ICDIM). The mechanisms of energy transfer from SHI to the target material have their origin in the high electronic excitation induced in the solid. A number of phenomenological approaches have been employed to describe these mechanisms: coulomb explosion, thermal spike, non-radiative exciton decay, bond weakening. However, a detailed microscopic description is missing due to the difficulty of modeling the time evolution of the electronic excitation. In this work we have employed molecular dynamics (MD) calculations to determine whether the irradiation effects are related to the thermal phenomena described by MD (in the ps domain) or to electronic phenomena (sub-ps domain), e.g., exciton localization. We have carried out simulations of up to 100 ps with large boxes (30x30x8 nm3) using a home-modified version of MDCASK that allows us to define a central hot cylinder (ion track) from which heat flows to the surrounding cold bath (unirradiated sample). We observed that once the cylinder has cooled down, the Si and O coordination numbers are 4 and 2, respectively, as in virgin silica. On the other hand, the density of the (cold) cylinder increases with respect to that of silica and, furthermore, the silica network ring size decreases. Both effects are in agreement with the observed densification. In conclusion, purely thermal effects do not explain the generation of point defects upon irradiation, but they do account for the silica densification.

Free-form optical systems for nonimaging applications : Sistemas ópticos anamórficos para aplicaciones anidólicas

La óptica anidólica es una rama de la óptica cuyo desarrollo comenzó a mediados de la década de 1960. Este relativamente nuevo campo de la óptica se centra en la transferencia eficiente de la luz, algo necesario en muchas aplicaciones, entre las que destacamos los concentradores solares y los sistemas de iluminación. Las soluciones de la óptica clásica a los problemas de la transferencia de energía de la luz sólo son adecuadas cuando los rayos de luz son paraxiales. La condición paraxial no se cumple en la mayoría de las aplicaciones para concentración e iluminación. Esta tesis contiene varios diseños free-form (aquellos que no presentan ninguna simetría, ni de rotación ni lineal) cuyas aplicaciones van destinadas a estos dos campos. El término nonimaging viene del hecho de que estos sistemas ópticos no necesitan formar una imagen del objeto, aunque no formar la imagen no es una condición necesaria. Otra palabra que se utiliza a veces en lugar de nonimaging es la palabra anidólico, viene del griego "an+eidolon" y tiene el mismo significado. La mayoría de los sistemas ópticos diseñados para aplicaciones anidólicas no presentan ninguna simetría, es decir, son free-form (anamórficos). Los sistemas ópticos free-form están siendo especialmente relevantes durante los últimos años gracias al desarrollo de las herramientas para su fabricación como máquinas de moldeo por inyección y el mecanizado multieje. Sin embargo, solo recientemente se han desarrollado técnicas de diseño anidólicas capaces de cumplir con estos grados de libertad. En aplicaciones de iluminación el método SMS3D permite diseñar dos superficies free-form para controlar las fuentes de luz extensas. En los casos en que se requiere una elevada asimetría de la fuente, el objeto o las restricciones volumétricos, las superficies free-form permiten obtener soluciones de mayor eficiencia, o disponer de menos elementos en comparación con las soluciones de simetría de rotación, dado que las superficies free-form tienen más grados de libertad y pueden realizar múltiples funciones debido a su naturaleza anamórfica. Los concentradores anidólicos son muy adecuados para la captación de energía solar, ya que el objetivo no es la reproducción de una imagen exacta del sol, sino sencillamente la captura de su energía. En este momento, el campo de la concentración fotovoltaica (CPV) tiende hacia sistemas de alta concentración con el fin de compensar el gasto de las células solares multi-unión (MJ) utilizadas como receptores, reduciendo su área. El interés en el uso de células MJ radica en su alta eficiencia de conversión. Para obtener sistemas competitivos en aplicaciones terrestres se recurre a sistemas fotovoltaicos de alta concentración (HCPV), con factores de concentración geométrica por encima de 500x. Estos sistemas se componen de dos (o más) elementos ópticos (espejos y/o lentes). En los sistemas presentados a lo largo de este trabajo se presentan ejemplos de concentradores HCPV con elementos reflexivos como etapa primaria, así como concentradores con elementos refractivos (lente de Fresnel). Con la necesidad de aumentar la eficiencia de los sistemas HCPV reales y con el fin de proporcionar la división más eficiente del espectro solar, células conteniendo cuatro o más uniones (con un potencial de alcanzar eficiencias de más del 45% a una concentración de cientos de soles) se exploran hoy en día. En esta tesis se presenta una de las posibles arquitecturas de división del espectro (spectrum-splitting en la literatura anglosajona) que utilizan células de concentración comercial. Otro campo de aplicación de la óptica nonimaging es la iluminación, donde es necesario proporcionar un patrón de distribución de la iluminación específico. La iluminación de estado sólido (SSL), basada en la electroluminiscencia de materiales semiconductores, está proporcionando fuentes de luz para aplicaciones de iluminación general. En la última década, los diodos emisores de luz (LED) de alto brillo han comenzado a reemplazar a las fuentes de luz convencionales debido a la superioridad en la calidad de la luz emitida, elevado tiempo de vida, compacidad y ahorro de energía. Los colimadores utilizados con LEDs deben cumplir con requisitos tales como tener una alta eficiencia, un alto control del haz de luz, una mezcla de color espacial y una gran compacidad. Presentamos un colimador de luz free-form con microestructuras capaz de conseguir buena colimación y buena mezcla de colores con una fuente de LED RGGB. Una buena mezcla de luz es importante no sólo para simplificar el diseño óptico de la luminaria sino también para evitar hacer binning de los chips. La mezcla de luz óptica puede reducir los costes al evitar la modulación por ancho de pulso y otras soluciones electrónicas patentadas para regulación y ajuste de color. Esta tesis consta de cuatro capítulos. Los capítulos que contienen la obra original de esta tesis son precedidos por un capítulo introductorio donde se presentan los conceptos y definiciones básicas de la óptica geométrica y en el cual se engloba la óptica nonimaging. Contiene principios de la óptica no formadora de imagen junto con la descripción de sus problemas y métodos de diseño. Asimismo se describe el método de Superficies Múltiples Simultáneas (SMS), que destaca por su versatilidad y capacidad de controlar varios haces de rayos. Adicionalmente también se describe la integración Köhler y sus aplicaciones en el campo de la energía fotovoltaica. La concentración fotovoltaica y la iluminación de estado sólido son introducidas junto con la revisión de su estado actual. El Segundo y Tercer Capítulo contienen diseños ópticos avanzados con aplicación en la concentración solar principalmente, mientras que el Cuarto Capítulo describe el colimador free-form con surcos que presenta buena mezcla de colores para aplicaciones de iluminación. El Segundo Capítulo describe dos concentradores ópticos HCPV diseñados con el método SMS en tres dimensiones (SMS3D) que llevan a cabo integración Köhler en dos direcciones con el fin de proporcionar una distribución de irradiancia uniforme libre de aberraciones cromáticas sobre la célula solar. Uno de los diseños es el concentrador XXR free-form diseñado con el método SMS3D, donde el espejo primario (X) y la lente secundaria (R) se dividen en cuatro sectores simétricos y llevan a cabo la integración Köhler (proporcionando cuatro unidades del array Köhler), mientras que el espejo intermedio (X) presenta simetría rotacional. Otro concentrador HCPV presentado es el Fresnel-RXI (FRXI) con una lente de Fresnel funcionando como elemento primario (POE) y una lente RXI como elemento óptico secundario (SOE), que presenta configuración 4-fold con el fin de realizar la integración Köhler. Las lentes RXI son dispositivos nonimaging conocidos, pero su aplicación como elemento secundario es novedosa. Los concentradores XXR y FRXI Köhler son ejemplos académicos de muy alta concentración (más de 2,000x, mientras que los sistemas convencionales hoy en día no suelen llegar a 1,000x) preparados para las células solares N-unión (con N>3), que probablemente requerirán una mayor concentración y alta uniformidad espectral de irradiancia con el fin de obtener sistemas CPV terrestres eficientes y rentables. Ambos concentradores están diseñados maximizando funciones de mérito como la eficiencia óptica, el producto concentración-aceptancia (CAP) y la uniformidad de irradiancia sobre la célula libre de la aberración cromática (integración Köhler). El Tercer Capítulo presenta una arquitectura para la división del espectro solar basada en un módulo HCPV con alta concentración (500x) y ángulo de aceptancia alto (>1º) que tiene por objeto reducir ambas fuentes de pérdidas de las células triple unión (3J) comerciales: el uso eficiente del espectro solar y la luz reflejada de los contactos metálicos y de la superficie de semiconductor. El módulo para la división del espectro utiliza el espectro solar más eficiente debido a la combinación de una alta eficiencia de una célula de concentración 3J (GaInP/GaInAs/Ge) y una de contacto posterior (BPC) de concentración de silicio (Si), así como la técnica de confinamiento externo para la recuperación de la luz reflejada por la célula 3J con el fin de ser reabsorbida por la célula. En la arquitectura propuesta, la célula 3J opera con su ganancia de corriente optimizada (concentración geométrica de 500x), mientras que la célula de silicio trabaja cerca de su óptimo también (135x). El módulo de spectrum-splitting consta de una lente de Fresnel plana como POE y un concentrador RXI free-form como SOE con un filtro paso-banda integrado en él. Tanto POE como SOE realizan la integración Köhler para producir homogeneización de luz sobre la célula. El filtro paso banda envía los fotones IR en la banda 900-1,150nm a la célula de silicio. Hay varios aspectos prácticos de la arquitectura del módulo presentado que ayudan a reducir la complejidad de los sistemas spectrum-splitting (el filtro y el secundario forman una sola pieza sólida, ambas células son coplanarias simplificándose el cableado y la disipación de calor, etc.). Prototipos prueba-de-concepto han sido ensamblados y probados a fin de demostrar la fabricabilidad del filtro y su rendimiento cuando se combina con la técnica de reciclaje de luz externa. Los resultados obtenidos se ajustan bastante bien a los modelos y a las simulaciones e invitan al desarrollo de una versión más compleja de este prototipo en el futuro. Dos colimadores sólidos con surcos free-form se presentan en el Cuarto Capítulo. Ambos diseños ópticos están diseñados originalmente usando el método SMS3D. La segunda superficie ópticamente activa está diseñada a posteriori como una superficie con surcos. El diseño inicial de dos espejos (XX) está diseñado como prueba de concepto. En segundo lugar, el diseño RXI free-form es comparable con los colimadores RXI existentes. Se trata de un diseño muy compacto y eficiente que proporciona una muy buena mezcla de colores cuando funciona con LEDs RGB fuera del eje óptico como en los RGB LEDs convencionales. Estos dos diseños son dispositivos free-form diseñados con la intención de mejorar las propiedades de mezcla de colores de los dispositivos no aplanáticos RXI con simetría de revolución y la eficiencia de los aplanáticos, logrando una buena colimación y una buena mezcla de colores. La capacidad de mezcla de colores del dispositivo no-aplanático mejora añadiendo características de un aplanático a su homólogo simétrico sin pérdida de eficiencia. En el caso del diseño basado en RXI, su gran ventaja consiste en su menor coste de fabricación ya que el proceso de metalización puede evitarse. Aunque algunos de los componentes presentan formas muy complejas, los costes de fabricación son relativamente insensibles a la complejidad del molde, especialmente en el caso de la producción en masa (tales como inyección de plástico), ya que el coste del molde se reparte entre todas las piezas fabricadas. Por último, las últimas dos secciones son las conclusiones y futuras líneas de investigación. ABSTRACT Nonimaging optics is a branch of optics whose development began in the mid-1960s. This rather new field of optics focuses on the efficient light transfer necessary in many applications, among which we highlight solar concentrators and illumination systems. The classical optics solutions to the problems of light energy transfer are only appropriate when the light rays are paraxial. The paraxial condition is not met in most applications for the concentration and illumination. This thesis explores several free-form designs (with neither rotational nor linear symmetry) whose applications are intended to cover the above mentioned areas and more. The term nonimaging comes from the fact that these optical systems do not need to form an image of the object, although it is not a necessary condition not to form an image. Another word sometimes used instead of nonimaging is anidolic, and it comes from the Greek “an+eidolon” and has the same meaning. Most of the optical systems designed for nonimaging applications are without any symmetry, i.e. free-form. Free-form optical systems become especially relevant lately with the evolution of free-form tooling (injection molding machines, multi-axis machining techniques, etc.). Nevertheless, only recently there are nonimaging design techniques that are able to meet these degrees of freedom. In illumination applications, the SMS3D method allows designing two free-form surfaces to control very well extended sources. In cases when source, target or volumetric constrains have very asymmetric requirements free-form surfaces are offering solutions with higher efficiency or with fewer elements in comparison with rotationally symmetric solutions, as free-forms have more degrees of freedom and they can perform multiple functions due to their free-form nature. Anidolic concentrators are well suited for the collection of solar energy, because the goal is not the reproduction of an exact image of the sun, but instead the collection of its energy. At this time, Concentration Photovoltaics (CPV) field is turning to high concentration systems in order to compensate the expense of multi-junction (MJ) solar cells used as receivers by reducing its area. Interest in the use of MJ cells lies in their very high conversion efficiency. High Concentration Photovoltaic systems (HCPV) with geometric concentration of more than 500x are required in order to have competitive systems in terrestrial applications. These systems comprise two (or more) optical elements, mirrors and/or lenses. Systems presented in this thesis encompass both main types of HCPV architectures: concentrators with primary reflective element and concentrators with primary refractive element (Fresnel lens). Demand for the efficiency increase of the actual HCPV systems as well as feasible more efficient partitioning of the solar spectrum, leads to exploration of four or more junction solar cells or submodules. They have a potential of reaching over 45% efficiency at concentration of hundreds of suns. One possible architectures of spectrum splitting module using commercial concentration cells is presented in this thesis. Another field of application of nonimaging optics is illumination, where a specific illuminance distribution pattern is required. The Solid State Lighting (SSL) based on semiconductor electroluminescence provides light sources for general illumination applications. In the last decade high-brightness Light Emitting Diodes (LEDs) started replacing conventional light sources due to their superior output light quality, unsurpassed lifetime, compactness and energy savings. Collimators used with LEDs have to meet requirements like high efficiency, high beam control, color and position mixing, as well as a high compactness. We present a free-form collimator with microstructures that performs good collimation and good color mixing with RGGB LED source. Good light mixing is important not only for simplifying luminaire optical design but also for avoiding die binning. Optical light mixing may reduce costs by avoiding pulse-width modulation and other patented electronic solutions for dimming and color tuning. This thesis comprises four chapters. Chapters containing the original work of this thesis are preceded by the introductory chapter that addresses basic concepts and definitions of geometrical optics on which nonimaging is developed. It contains fundamentals of nonimaging optics together with the description of its design problems, principles and methods, and with the Simultaneous Multiple Surface (SMS) method standing out for its versatility and ability to control several bundles of rays. Köhler integration and its applications in the field of photovoltaics are described as well. CPV and SSL fields are introduced together with the review on their background and their current status. Chapter 2 and Chapter 3 contain advanced optical designs with primarily application in solar concentration; meanwhile Chapter 4 portrays the free-form V-groove collimator with good color mixing property for illumination application. Chapter 2 describes two HCPV optical concentrators designed with the SMS method in three dimensions (SMS3D). Both concentrators represent Köhler integrator arrays that provide uniform irradiance distribution free from chromatic aberrations on the solar cell. One of the systems is the XXR free-form concentrator designed with the SMS3D method. The primary mirror (X) of this concentrator and secondary lens (R) are divided in four symmetric sectors (folds) that perform Köhler integration; meanwhile the intermediate mirror (X) is rotationally symmetric. Second HCPV concentrator is the Fresnel-RXI (FRXI) with flat Fresnel lens as the Primary Optical Element (POE) and an RXI lens as the Secondary Optical Element (SOE). This architecture manifests 4-fold configuration for performing Köhler integration (4 array units), as well. The RXI lenses are well-known nonimaging devices, but their application as SOE is novel. Both XXR and FRXI Köhler HCPV concentrators are academic examples of very high concentration (more than 2,000x meanwhile conventional systems nowadays have up to 1,000x) prepared for the near future N-junction (N>3) solar cells. In order to have efficient and cost-effective terrestrial CPV systems, those cells will probably require higher concentrations and high spectral irradiance uniformity. Both concentrators are designed by maximizing merit functions: the optical efficiency, concentration-acceptance angle (CAP) and cell-irradiance uniformity free from chromatic aberrations (Köhler integration). Chapter 3 presents the spectrum splitting architecture based on a HCPV module with high concentration (500x) and high acceptance angle (>1º). This module aims to reduce both sources of losses of the actual commercial triple-junction (3J) solar cells with more efficient use of the solar spectrum and with recovering the light reflected from the 3J cells’ grid lines and semiconductor surface. The solar spectrum is used more efficiently due to the combination of a high efficiency 3J concentration cell (GaInP/GaInAs/Ge) and external Back-Point-Contact (BPC) concentration silicon (Si) cell. By employing external confinement techniques, the 3J cell’s reflections are recovered in order to be re-absorbed by the cell. In the proposed concentrator architecture, the 3J cell operates at its optimized current gain (at geometrical concentration of 500x), while the Si cell works near its optimum, as well (135x). The spectrum splitting module consists of a flat Fresnel lens (as the POE), and a free-form RXI-type concentrator with a band-pass filter embedded in it (as the SOE), both POE and SOE performing Köhler integration to produce light homogenization. The band-pass filter sends the IR photons in the 900-1,150nm band to the Si cell. There are several practical aspects of presented module architecture that help reducing the added complexity of the beam splitting systems: the filter and secondary are forming a single solid piece, both cells are coplanar so the heat management and wiring is simplified, etc. Two proof-of-concept prototypes are assembled and tested in order to prove filter manufacturability and performance, as well as the potential of external light recycling technique. Obtained measurement results agree quite well with models and simulations, and show an opened path to manufacturing of the Fresnel RXI-type secondary concentrator with spectrum splitting strategy. Two free-form solid V-groove collimators are presented in Chapter 4. Both free-form collimators are originally designed with the SMS3D method. The second mirrored optically active surface is converted in a grooved surface a posteriori. Initial two mirror (XX) design is presented as a proof-of-concept. Second, RXI free-form design is comparable with existing RXI collimators as it is a highly compact and a highly efficient design. It performs very good color mixing of the RGGB LED sources placed off-axis like in conventional RGB LEDs. Collimators described here improve color mixing property of the prior art rotationally symmetric no-aplanatic RXI devices, and the efficiency of the aplanatic ones, accomplishing both good collimation and good color mixing. Free-form V-groove collimators enhance the no-aplanatic device's blending capabilities by adding aplanatic features to its symmetric counterpart with no loss in efficiency. Big advantage of the RXI design is its potentially lower manufacturing cost, since the process of metallization may be avoided. Although some components are very complicated for shaping, the manufacturing costs are relatively insensitive to the complexity of the mold especially in the case of mass production (such as plastic injection), as the cost of the mold is spread in many parts. Finally, last two sections are conclusions and future lines of investigation.

Time domain passivity control for delayed teleoperation

La telepesencia combina diferentes modalidades sensoriales, incluyendo, entre otras, la visual y la del tacto, para producir una sensación de presencia remota en el operador. Un elemento clave en la implementación de sistemas de telepresencia para permitir una telemanipulación del entorno remoto es el retorno de fuerza. Durante una telemanipulación, la energía mecánica es transferida entre el operador humano y el entorno remoto. En general, la energía es una propiedad de los objetos físicos, fundamental en su mutual interacción. En esta interacción, la energía se puede transmitir entre los objetos, puede cambiar de forma pero no puede crearse ni destruirse. En esta tesis, se aplica este principio fundamental para derivar un nuevo método de control bilateral que permite el diseño de sistemas de teleoperación estables para cualquier arquitectura concebible. El razonamiento parte del hecho de que la energía mecánica insertada por el operador humano en el sistema debe transferirse hacia el entorno remoto y viceversa. Tal como se verá, el uso de la energía como variable de control permite un tratamiento más general del sistema que el control convencional basado en variables específicas del sistema. Mediante el concepto de Red de Potencia de Retardo Temporal (RPRT), el problema de definir los flujos de energía en un sistema de teleoperación es solucionado con independencia de la arquitectura de comunicación. Como se verá, los retardos temporales son la principal causa de generación de energía virtual. Este hecho se observa con retardos a partir de 1 milisegundo. Esta energía virtual es añadida al sistema de forma intrínseca y representa la causa principal de inestabilidad. Se demuestra que las RPRTs son transportadoras de la energía deseada intercambiada entre maestro y esclavo pero a la vez generadoras de energía virtual debido al retardo temporal. Una vez estas redes son identificadas, el método de Control de Pasividad en el Dominio Temporal para RPRTs se propone como mecanismo de control para asegurar la pasividad del sistema, y as__ la estabilidad. El método se basa en el simple hecho de que esta energía virtual debido al retardo debe transformarse en disipación. As__ el sistema se aproxima al sistema deseado, donde solo la energía insertada desde un extremo es transferida hacia el otro. El sistema resultante presenta dos cualidades: por un lado la estabilidad del sistema queda garantizada con independencia de la arquitectura del sistema y del canal de comunicación; por el otro, el rendimiento es maximizado en términos de fidelidad de transmisión energética. Los métodos propuestos se sustentan con sistemas experimentales con diferentes arquitecturas de control y retardos entre 2 y 900 ms. La tesis concluye con un experimento que incluye una comunicación espacial basada en el satélite geoestacionario ASTRA. ABSTRACT Telepresence combines different sensorial modalities, including vision and touch, to produce a feeling of being present in a remote location. The key element to successfully implement a telepresence system and thus to allow telemanipulation of a remote environment is force feedback. In a telemanipulation, mechanical energy must convey from the human operator to the manipulated object found in the remote environment. In general, energy is a property of all physical objects, fundamental to their mutual interactions in which the energy can be transferred among the objects and can change form but cannot be created or destroyed. In this thesis, we exploit this fundamental principle to derive a novel bilateral control mechanism that allows designing stable teleoperation systems with any conceivable communication architecture. The rationale starts from the fact that the mechanical energy injected by a human operator into the system must be conveyed to the remote environment and Vice Versa. As will be seen, setting energy as the control variable allows a more general treatment of the controlled system in contrast to the more conventional control of specific systems variables. Through the Time Delay Power Network (TDPN) concept, the issue of defining the energy flows involved in a teleoperation system is solved with independence of the communication architecture. In particular, communication time delays are found to be a source of virtual energy. This fact is observed with delays starting from 1 millisecond. Since this energy is added, the resulting teleoperation system can be non-passive and thus become unstable. The Time Delay Power Networks are found to be carriers of the desired exchanged energy but also generators of virtual energy due to the time delay. Once these networks are identified, the Time Domain Passivity Control approach for TDPNs is proposed as a control mechanism to ensure system passivity and therefore, system stability. The proposed method is based on the simple fact that this intrinsically added energy due to the communication must be transformed into dissipation. Then the system becomes closer to the ambitioned one, where only the energy injected from one end of the system is conveyed to the other one. The resulting system presents two benefits: On one hand, system stability is guaranteed through passivity independently from the chosen control architecture and communication channel; on the other, performance is maximized in terms of energy transfer faithfulness. The proposed methods are sustained with a set of experimental implementations using different control architectures and communication delays ranging from 2 to 900 milliseconds. An experiment that includes a communication Space link based on the geostationary satellite ASTRA concludes this thesis.

The structure and organization within the membrane of the helices composing the pore-forming domain of Bacillus thuringiensis δ-endotoxin are consistent with an “umbrella-like” structure of the pore

The aim of this study was to elucidate the mechanism of membrane insertion and the structural organization of pores formed by Bacillus thuringiensis δ-endotoxin. We determined the relative affinities for membranes of peptides corresponding to the seven helices that compose the toxin pore-forming domain, their modes of membrane interaction, their structures within membranes, and their orientations relative to the membrane normal. In addition, we used resonance energy transfer measurements of all possible combinatorial pairs of membrane-bound helices to map the network of interactions between helices in their membrane-bound state. The interaction of the helices with the bilayer membrane was also probed by a Monte Carlo simulation protocol to determine lowest-energy orientations. Our results are consistent with a situation in which helices α4 and α5 insert into the membrane as a helical hairpin in an antiparallel manner, while the other helices lie on the membrane surface like the ribs of an umbrella (the “umbrella model”). Our results also support the suggestion that α7 may serve as a binding sensor to initiate the structural rearrangement of the pore-forming domain.

Optical detection of cytochrome P450 by sensitizer-linked substrates

The ability to detect, characterize, and manipulate specific biomolecules in complex media is critical for understanding metabolic processes. Particularly important targets are oxygenases (cytochromes P450) involved in drug metabolism and many disease states, including liver and kidney dysfunction, neurological disorders, and cancer. We have found that Ru photosensitizers linked to P450 substrates specifically recognize submicromolar cytochrome P450cam in the presence of other heme proteins. In the P450:Ru-substrate conjugates, energy transfer to the heme dramatically accelerates the Ru-luminescence decay. The crystal structure of a P450cam:Ru-adamantyl complex reveals access to the active center via a channel whose depth (Ru-Fe distance is 21 Å) is virtually the same as that extracted from an analysis of the energy-transfer kinetics. Suitably constructed libraries of sensitizer-linked substrates could be employed to probe the steric and electronic properties of buried active sites.

Inverse radiation dose-rate effects on somatic and germ-line mutations and DNA damage rates

The mutagenic effect of low linear energy transfer ionizing radiation is reduced for a given dose as the dose rate (DR) is reduced to a low level, a phenomenon known as the direct DR effect. Our reanalysis of published data shows that for both somatic and germ-line mutations there is an opposite, inverse DR effect, with reduction from low to very low DR, the overall dependence of induced mutations being parabolically related to DR, with a minimum in the range of 0.1 to 1.0 cGy/min (rule 1). This general pattern can be attributed to an optimal induction of error-free DNA repair in a DR region of minimal mutability (MMDR region). The diminished activation of repair at very low DRs may reflect a low ratio of induced (“signal”) to spontaneous background DNA damage (“noise”). Because two common DNA lesions, 8-oxoguanine and thymine glycol, were already known to activate repair in irradiated mammalian cells, we estimated how their rates of production are altered upon radiation exposure in the MMDR region. For these and other abundant lesions (abasic sites and single-strand breaks), the DNA damage rate increment in the MMDR region is in the range of 10% to 100% (rule 2). These estimates suggest a genetically programmed optimatization of response to radiation in the MMDR region.

Effects of unique ion chemistry on thin-film growth by plasma–surface interactions

Plasma processing is a standard industrial method for the modification of material surfaces and the deposition of thin films. Polyatomic ions and neutrals larger than a triatomic play a critical role in plasma-induced surface chemistry, especially in the deposition of polymeric films from fluorocarbon plasmas. In this paper, low energy CF3+ and C3F5+ ions are used to modify a polystyrene surface. Experimental and computational studies are combined to quantify the effect of the unique chemistry and structure of the incident ions on the result of ion-polymer collisions. C3F5+ ions are more effective at growing films than CF3+, both at similar energy/atom of ≈6 eV/atom and similar total kinetic energies of 25 and 50 eV. The composition of the films grown experimentally also varies with both the structure and kinetic energy of the incident ion. Both C3F5+ and CF3+ should be thought of as covalently bound polyatomic precursors or fragments that can react and become incorporated within the polystyrene surface, rather than merely donating F atoms. The size and structure of the ions affect polymer film formation via differing chemical structure, reactivity, sticking probabilities, and energy transfer to the surface. The different reactivity of these two ions with the polymer surface supports the argument that larger species contribute to the deposition of polymeric films from fluorocarbon plasmas. These results indicate that complete understanding and accurate computer modeling of plasma–surface modification requires accurate measurement of the identities, number densities, and kinetic energies of higher mass ions and energetic neutrals.

Clustered DNA damages induced in isolated DNA and in human cells by low doses of ionizing radiation

Clustered DNA damages—two or more closely spaced damages (strand breaks, abasic sites, or oxidized bases) on opposing strands—are suspects as critical lesions producing lethal and mutagenic effects of ionizing radiation. However, as a result of the lack of methods for measuring damage clusters induced by ionizing radiation in genomic DNA, neither the frequencies of their production by physiological doses of radiation, nor their repairability, nor their biological effects are known. On the basis of methods that we developed for quantitating damages in large DNAs, we have devised and validated a way of measuring ionizing radiation-induced clustered lesions in genomic DNA, including DNA from human cells. DNA is treated with an endonuclease that induces a single-strand cleavage at an oxidized base or abasic site. If there are two closely spaced damages on opposing strands, such cleavage will reduce the size of the DNA on a nondenaturing gel. We show that ionizing radiation does induce clustered DNA damages containing abasic sites, oxidized purines, or oxidized pyrimidines. Further, the frequency of each of these cluster classes is comparable to that of frank double-strand breaks; among all complex damages induced by ionizing radiation, double-strand breaks are only about 20%, with other clustered damage constituting some 80%. We also show that even low doses (0.1–1 Gy) of high linear energy transfer ionizing radiation induce clustered damages in human cells.

Role of metallothionein in nitric oxide signaling as revealed by a green fluorescent fusion protein

Although the function of metallothionein (MT), a 6- to 7-kDa cysteine-rich metal binding protein, remains unclear, it has been suggested from in vitro studies that MT is an important component of intracellular redox signaling, including being a target for nitric oxide (NO). To directly study the interaction between MT and NO in live cells, we generated a fusion protein consisting of MT sandwiched between two mutant green fluorescent proteins (GFPs). In vitro studies with this chimera (FRET-MT) demonstrate that fluorescent resonance energy transfer (FRET) can be used to follow conformational changes indicative of metal release from MT. Imaging experiments with live endothelial cells show that agents that increase cytoplasmic Ca2+ act via endogenously generated NO to rapidly and persistently release metal from MT. A role for this interaction in intact tissue is supported by the finding that the myogenic reflex of mesenteric arteries is absent in MT knockout mice (MT−/−) unless endogenous NO synthesis is blocked. These results are the first application of intramolecular green fluorescent protein (GFP)-based FRET in a native protein and demonstrate the utility of FRET-MT as an intracellular surrogate indicator of NO production. In addition, an important role of metal thiolate clusters of MT in NO signaling in vascular tissue is revealed.

Femtosecond dynamics of the forbidden carotenoid S1 state in light-harvesting complexes of purple bacteria observed after two-photon excitation

Time-resolved excited-state absorption intensities after direct two-photon excitation of the carotenoid S1 state are reported for light-harvesting complexes of purple bacteria. Direct excitation of the carotenoid S1 state enables the measurement of subsequent dynamics on a fs time scale without interference from higher excited states, such as the optically allowed S2 state or the recently discovered dark state situated between S1 and S2. The lifetimes of the carotenoid S1 states in the B800-B850 complex and B800-B820 complex of Rhodopseudomonas acidophila are 7 ± 0.5 ps and 6 ± 0.5 ps, respectively, and in the light-harvesting complex 2 of Rhodobacter sphaeroides ≈1.9 ± 0.5 ps. These results explain the differences in the carotenoid to bacteriochlorophyll energy transfer efficiency after S2 excitation. In Rps. acidophila the carotenoid S1 to bacteriochlorophyll energy transfer is found to be quite inefficient (φET1 <28%) whereas in Rb. sphaeroides this energy transfer is very efficient (φET1 ≈80%). The results are rationalized by calculations of the ensemble averaged time constants. We find that the Car S1 → B800 electronic energy transfer (EET) pathway (≈85%) dominates over Car S1 → B850 EET (≈15%) in Rb. sphaeroides, whereas in Rps. acidophila the Car S1 → B850 EET (≈60%) is more efficient than the Car S1 → B800 EET (≈40%). The individual electronic couplings for the Car S1 → BChl energy transfer are estimated to be approximately 5–26 cm−1. A major contribution to the difference between the energy transfer efficiencies can be explained by different Car S1 energy gaps in the two species.

Chlorophyll and carotenoid binding in a simple red algal light-harvesting complex crosses phylogenetic lines

The membrane proteins of peripheral light-harvesting complexes (LHCs) bind chlorophylls and carotenoids and transfer energy to the reaction centers for photosynthesis. LHCs of chlorophytes, chromophytes, dinophytes, and rhodophytes are similar in that they have three transmembrane regions and several highly conserved Chl-binding residues. All LHCs bind Chl a, but in specific taxa certain characteristic pigments accompany Chl a: Chl b and lutein in chlorophytes, Chl c and fucoxanthin in chromophytes, Chl c and peridinin in dinophytes, and zeaxanthin in rhodophytes. The specificity of pigment binding was examined by in vitro reconstitution of various pigments with a simple light-harvesting protein (LHCaR1), from a red alga (Porphyridium cruentum), that normally has eight Chl a and four zeaxanthin molecules. The pigments typical of a chlorophyte (Spinacea oleracea), a chromophyte (Thallasiosira fluviatilis), and a dinophyte (Prorocentrum micans) were found to functionally bind to this protein as evidenced by their participation in energy transfer to Chl a, the terminal pigment. This is a demonstration of a functional relatedness of rhodophyte and higher plant LHCs. The results suggest that eight Chl-binding sites per polypeptide are an ancestral trait, and that the flexibility to bind various Chl and carotenoid pigments may have been retained throughout the evolution of LHCs.

Logic gates using high Rydberg states

Connected logic gates can be operated on the levels of one molecule by making use of the special properties of high Rydberg states. Explicit experimental results for the NO molecule are provided as an example. A number of other options, including that of several gates concatenated so as to operate as a full adder, are discussed. Specific properties of high Rydberg states that are used are: their autoionization is delayed so that they can be distinguished from direct multiphoton ionization, during their long life such states also can decay by energy transfer to the molecular core in a way that can be controlled by the judicious application of very weak external electrical fields, and the Rydberg states can be detected by the application of an ionizing electrical field. The combination of two (or three) color photons with and without external weak fields allows the construction of quite elaborate logic circuit diagrams and shows that taking advantage of the different intramolecular dynamics of levels that differ by their excitation enables the compounding of logic operations on one molecular frame.

The Regulation of Photosynthetic Electron Transport during Nutrient Deprivation in Chlamydomonas reinhardtii1

The light-saturated rate of photosynthetic O2 evolution in Chlamydomonas reinhardtii declined by approximately 75% on a per-cell basis after 4 d of P starvation or 1 d of S starvation. Quantitation of the partial reactions of photosynthetic electron transport demonstrated that the light-saturated rate of photosystem (PS) I activity was unaffected by P or S limitation, whereas light-saturated PSII activity was reduced by more than 50%. This decline in PSII activity correlated with a decline in both the maximal quantum efficiency of PSII and the accumulation of the secondary quinone electron acceptor of PSII nonreducing centers (PSII centers capable of performing a charge separation but unable to reduce the plastoquinone pool). In addition to a decline in the light-saturated rate of O2 evolution, there was reduced efficiency of excitation energy transfer to the reaction centers of PSII (because of dissipation of absorbed light energy as heat and because of a transition to state 2). These findings establish a common suite of alterations in photosynthetic electron transport that results in decreased linear electron flow when C. reinhardtii is limited for either P or S. It was interesting that the decline in the maximum quantum efficiency of PSII and the accumulation of the secondary quinone electron acceptor of PSII nonreducing centers were regulated specifically during S-limited growth by the SacI gene product, which was previously shown to be critical for the acclimation of C. reinhardtii to S limitation (J.P. Davies, F.H. Yildiz, and A.R. Grossman [1996] EMBO J 15: 2150–2159).

Excited-state dynamics in photosystem II: Insights from the x-ray crystal structure

The heart of oxygenic photosynthesis is photosystem II (PSII), a multisubunit protein complex that uses solar energy to drive the splitting of water and production of molecular oxygen. The effectiveness of the photochemical reaction center of PSII depends on the efficient transfer of excitation energy from the surrounding antenna chlorophylls. A kinetic model for PSII, based on the x-ray crystal structure coordinates of 37 antenna and reaction center pigment molecules, allows us to map the major energy transfer routes from the antenna chlorophylls to the reaction center chromophores. The model shows that energy transfer to the reaction center is slow compared with the rate of primary electron transport and depends on a few bridging chlorophyll molecules. This unexpected energetic isolation of the reaction center in PSII is similar to that found in the bacterial photosystem, conflicts with the established view of the photophysics of PSII, and may be a functional requirement for primary photochemistry in photosynthesis. In addition, the model predicts a value for the intrinsic photochemical rate constant that is 4 times that found in bacterial reaction centers.

Mechanism of oligonucleotide release from cationic liposomes.

We propose a mechanism for oligonucleotide (ODN) release from cationic lipid complexes in cells that accounts for various observations on cationic lipid-nucleic acid-cell interactions. Fluorescent confocal microscopy of cells treated with rhodamine-labeled cationic liposome/ fluorescein-labeled ODN (F-ODN) complexes show the F-ODN separates from the lipid after internalization and enters the nucleus leaving the fluorescent lipid in cytoplasmic structures. ODN displacement from the complex was studied by fluorescent resonance energy transfer. Anionic liposome compositions (e.g., phosphatidylserine) that mimic the cytoplasmic facing monolayer of the cell membrane released ODN from the complex at about a 1:1 (-/+) charge ratio. Release was independent of ionic strength and pH. Physical separation of the F-ODN from monovalent and multivalent cationic lipids was confirmed by gel electrophoresis. Fluid but not solid phase anionic liposomes are required, whereas the physical state of the cationic lipids does not effect the release. Water soluble molecules with a high negative linear charge density, dextran sulfate, or heparin also release ODN. However, ATP, spermidine, spermine, tRNA, DNA, polyglutamic acid, polylysine, bovine serum albumin, or histone did not release ODN, even at 100-fold charge excess (-/+). Based upon these results, we propose that the complex, after internalization by endocytosis, induces flip-flop of anionic lipids from the cytoplasmic facing monolayer. Anionic lipids laterally diffuse into the complex and form a charged neutralized ion-pair with the cationic lipids. This leads to displacement of the ODN from the cationic lipid and its release into the cytoplasm.