Photon Management Structures for Absorption Enhancement in Intermediate Band Solar Cells and Crystalline Silicon Solar Cells

El objetivo de la tesis es investigar los beneficios que el atrapamiento de la luz mediante fenómenos difractivos puede suponer para las células solares de silicio cristalino y las de banda intermedia. Ambos tipos de células adolecen de una insuficiente absorción de fotones en alguna región del espectro solar. Las células solares de banda intermedia son teóricamente capaces de alcanzar eficiencias mucho mayores que los dispositivos convencionales (con una sola banda energética prohibida), pero los prototipos actuales se resienten de una absorción muy débil de los fotones con energías menores que la banda prohibida. Del mismo modo, las células solares de silicio cristalino absorben débilmente en el infrarrojo cercano debido al carácter indirecto de su banda prohibida. Se ha prestado mucha atención a este problema durante las últimas décadas, de modo que todas las células solares de silicio cristalino comerciales incorporan alguna forma de atrapamiento de luz. Por razones de economía, en la industria se persigue el uso de obleas cada vez más delgadas, con lo que el atrapamiento de la luz adquiere más importancia. Por tanto aumenta el interés en las estructuras difractivas, ya que podrían suponer una mejora sobre el estado del arte. Se comienza desarrollando un método de cálculo con el que simular células solares equipadas con redes de difracción. En este método, la red de difracción se analiza en el ámbito de la óptica física, mediante análisis riguroso con ondas acopladas (rigorous coupled wave analysis), y el sustrato de la célula solar, ópticamente grueso, se analiza en los términos de la óptica geométrica. El método se ha implementado en ordenador y se ha visto que es eficiente y da resultados en buen acuerdo con métodos diferentes descritos por otros autores. Utilizando el formalismo matricial así derivado, se calcula el límite teórico superior para el aumento de la absorción en células solares mediante el uso de redes de difracción. Este límite se compara con el llamado límite lambertiano del atrapamiento de la luz y con el límite absoluto en sustratos gruesos. Se encuentra que las redes biperiódicas (con geometría hexagonal o rectangular) pueden producir un atrapamiento mucho mejor que las redes uniperiódicas. El límite superior depende mucho del periodo de la red. Para periodos grandes, las redes son en teoría capaces de alcanzar el máximo atrapamiento, pero sólo si las eficiencias de difracción tienen una forma peculiar que parece inalcanzable con las herramientas actuales de diseño. Para periodos similares a la longitud de onda de la luz incidente, las redes de difracción pueden proporcionar atrapamiento por debajo del máximo teórico pero por encima del límite Lambertiano, sin imponer requisitos irrealizables a la forma de las eficiencias de difracción y en un margen de longitudes de onda razonablemente amplio. El método de cálculo desarrollado se usa también para diseñar y optimizar redes de difracción para el atrapamiento de la luz en células solares. La red propuesta consiste en un red hexagonal de pozos cilíndricos excavados en la cara posterior del sustrato absorbente de la célula solar. La red se encapsula en una capa dieléctrica y se cubre con un espejo posterior. Se simula esta estructura para una célula solar de silicio y para una de banda intermedia y puntos cuánticos. Numéricamente, se determinan los valores óptimos del periodo de la red y de la profundidad y las dimensiones laterales de los pozos para ambos tipos de células. Los valores se explican utilizando conceptos físicos sencillos, lo que nos permite extraer conclusiones generales que se pueden aplicar a células de otras tecnologías. Las texturas con redes de difracción se fabrican en sustratos de silicio cristalino mediante litografía por nanoimpresión y ataque con iones reactivos. De los cálculos precedentes, se conoce el periodo óptimo de la red que se toma como una constante de diseño. Los sustratos se procesan para obtener estructuras precursoras de células solares sobre las que se realizan medidas ópticas. Las medidas de reflexión en función de la longitud de onda confirman que las redes cuadradas biperiódicas consiguen mejor atrapamiento que las uniperiódicas. Las estructuras fabricadas se simulan con la herramienta de cálculo descrita en los párrafos precedentes y se obtiene un buen acuerdo entre la medida y los resultados de la simulación. Ésta revela que una fracción significativa de los fotones incidentes son absorbidos en el reflector posterior de aluminio, y por tanto desaprovechados, y que este efecto empeora por la rugosidad del espejo. Se desarrolla un método alternativo para crear la capa dieléctrica que consigue que el reflector se deposite sobre una superficie plana, encontrándose que en las muestras preparadas de esta manera la absorción parásita en el espejo es menor. La siguiente tarea descrita en la tesis es el estudio de la absorción de fotones en puntos cuánticos semiconductores. Con la aproximación de masa efectiva, se calculan los niveles de energía de los estados confinados en puntos cuánticos de InAs/GaAs. Se emplea un método de una y de cuatro bandas para el cálculo de la función de onda de electrones y huecos, respectivamente; en el último caso se utiliza un hamiltoniano empírico. La regla de oro de Fermi permite obtener la intensidad de las transiciones ópticas entre los estados confinados. Se investiga el efecto de las dimensiones del punto cuántico en los niveles de energía y la intensidad de las transiciones y se obtiene que, al disminuir la anchura del punto cuántico respecto a su valor en los prototipos actuales, se puede conseguir una transición más intensa entre el nivel intermedio fundamental y la banda de conducción. Tomando como datos de partida los niveles de energía y las intensidades de las transiciones calculados como se ha explicado, se desarrolla un modelo de equilibrio o balance detallado realista para células solares de puntos cuánticos. Con el modelo se calculan las diferentes corrientes debidas a transiciones ópticas entre los numerosos niveles intermedios y las bandas de conducción y de valencia bajo ciertas condiciones. Se distingue de modelos de equilibrio detallado previos, usados para calcular límites de eficiencia, en que se adoptan suposiciones realistas sobre la absorción de fotones para cada transición. Con este modelo se reproducen datos publicados de eficiencias cuánticas experimentales a diferentes temperaturas con un acuerdo muy bueno. Se muestra que el conocido fenómeno del escape térmico de los puntos cuánticos es de naturaleza fotónica; se debe a los fotones térmicos, que inducen transiciones entre los estados excitados que se encuentran escalonados en energía entre el estado intermedio fundamental y la banda de conducción. En el capítulo final, este modelo realista de equilibrio detallado se combina con el método de simulación de redes de difracción para predecir el efecto que tendría incorporar una red de difracción en una célula solar de banda intermedia y puntos cuánticos. Se ha de optimizar cuidadosamente el periodo de la red para equilibrar el aumento de las diferentes transiciones intermedias, que tienen lugar en serie. Debido a que la absorción en los puntos cuánticos es extremadamente débil, se deduce que el atrapamiento de la luz, por sí solo, no es suficiente para conseguir corrientes apreciables a partir de fotones con energía menor que la banda prohibida en las células con puntos cuánticos. Se requiere una combinación del atrapamiento de la luz con un incremento de la densidad de puntos cuánticos. En el límite radiativo y sin atrapamiento de la luz, se necesitaría que el número de puntos cuánticos de una célula solar se multiplicara por 1000 para superar la eficiencia de una célula de referencia con una sola banda prohibida. En cambio, una célula con red de difracción precisaría un incremento del número de puntos en un factor 10 a 100, dependiendo del nivel de la absorción parásita en el reflector posterior. Abstract The purpose of this thesis is to investigate the benefits that diffractive light trapping can offer to quantum dot intermediate band solar cells and crystalline silicon solar cells. Both solar cell technologies suffer from incomplete photon absorption in some part of the solar spectrum. Quantum dot intermediate band solar cells are theoretically capable of achieving much higher efficiencies than conventional single-gap devices. Present prototypes suffer from extremely weak absorption of subbandgap photons in the quantum dots. This problem has received little attention so far, yet it is a serious barrier to the technology approaching its theoretical efficiency limit. Crystalline silicon solar cells absorb weakly in the near infrared due to their indirect bandgap. This problem has received much attention over recent decades, and all commercial crystalline silicon solar cells employ some form of light trapping. With the industry moving toward thinner and thinner wafers, light trapping is becoming of greater importance and diffractive structures may offer an improvement over the state-of-the-art. We begin by constructing a computational method with which to simulate solar cells equipped with diffraction grating textures. The method employs a wave-optical treatment of the diffraction grating, via rigorous coupled wave analysis, with a geometric-optical treatment of the thick solar cell bulk. These are combined using a steady-state matrix formalism. The method has been implemented computationally, and is found to be efficient and to give results in good agreement with alternative methods from other authors. The theoretical upper limit to absorption enhancement in solar cells using diffractions gratings is calculated using the matrix formalism derived in the previous task. This limit is compared to the so-called Lambertian limit for light trapping with isotropic scatterers, and to the absolute upper limit to light trapping in bulk absorbers. It is found that bi-periodic gratings (square or hexagonal geometry) are capable of offering much better light trapping than uni-periodic line gratings. The upper limit depends strongly on the grating period. For large periods, diffraction gratings are theoretically able to offer light trapping at the absolute upper limit, but only if the scattering efficiencies have a particular form, which is deemed to be beyond present design capabilities. For periods similar to the incident wavelength, diffraction gratings can offer light trapping below the absolute limit but above the Lambertian limit without placing unrealistic demands on the exact form of the scattering efficiencies. This is possible for a reasonably broad wavelength range. The computational method is used to design and optimise diffraction gratings for light trapping in solar cells. The proposed diffraction grating consists of a hexagonal lattice of cylindrical wells etched into the rear of the bulk solar cell absorber. This is encapsulated in a dielectric buffer layer, and capped with a rear reflector. Simulations are made of this grating profile applied to a crystalline silicon solar cell and to a quantum dot intermediate band solar cell. The grating period, well depth, and lateral well dimensions are optimised numerically for both solar cell types. This yields the optimum parameters to be used in fabrication of grating equipped solar cells. The optimum parameters are explained using simple physical concepts, allowing us to make more general statements that can be applied to other solar cell technologies. Diffraction grating textures are fabricated on crystalline silicon substrates using nano-imprint lithography and reactive ion etching. The optimum grating period from the previous task has been used as a design parameter. The substrates have been processed into solar cell precursors for optical measurements. Reflection spectroscopy measurements confirm that bi-periodic square gratings offer better absorption enhancement than uni-periodic line gratings. The fabricated structures have been simulated with the previously developed computation tool, with good agreement between measurement and simulation results. The simulations reveal that a significant amount of the incident photons are absorbed parasitically in the rear reflector, and that this is exacerbated by the non-planarity of the rear reflector. An alternative method of depositing the dielectric buffer layer was developed, which leaves a planar surface onto which the reflector is deposited. It was found that samples prepared in this way suffered less from parasitic reflector absorption. The next task described in the thesis is the study of photon absorption in semiconductor quantum dots. The bound-state energy levels of in InAs/GaAs quantum dots is calculated using the effective mass approximation. A one- and four- band method is applied to the calculation of electron and hole wavefunctions respectively, with an empirical Hamiltonian being employed in the latter case. The strength of optical transitions between the bound states is calculated using the Fermi golden rule. The effect of the quantum dot dimensions on the energy levels and transition strengths is investigated. It is found that a strong direct transition between the ground intermediate state and the conduction band can be promoted by decreasing the quantum dot width from its value in present prototypes. This has the added benefit of reducing the ladder of excited states between the ground state and the conduction band, which may help to reduce thermal escape of electrons from quantum dots: an undesirable phenomenon from the point of view of the open circuit voltage of an intermediate band solar cell. A realistic detailed balance model is developed for quantum dot solar cells, which uses as input the energy levels and transition strengths calculated in the previous task. The model calculates the transition currents between the many intermediate levels and the valence and conduction bands under a given set of conditions. It is distinct from previous idealised detailed balance models, which are used to calculate limiting efficiencies, since it makes realistic assumptions about photon absorption by each transition. The model is used to reproduce published experimental quantum efficiency results at different temperatures, with quite good agreement. The much-studied phenomenon of thermal escape from quantum dots is found to be photonic; it is due to thermal photons, which induce transitions between the ladder of excited states between the ground intermediate state and the conduction band. In the final chapter, the realistic detailed balance model is combined with the diffraction grating simulation method to predict the effect of incorporating a diffraction grating into a quantum dot intermediate band solar cell. Careful optimisation of the grating period is made to balance the enhancement given to the different intermediate transitions, which occur in series. Due to the extremely weak absorption in the quantum dots, it is found that light trapping alone is not sufficient to achieve high subbandgap currents in quantum dot solar cells. Instead, a combination of light trapping and increased quantum dot density is required. Within the radiative limit, a quantum dot solar cell with no light trapping requires a 1000 fold increase in the number of quantum dots to supersede the efficiency of a single-gap reference cell. A quantum dot solar cell equipped with a diffraction grating requires between a 10 and 100 fold increase in the number of quantum dots, depending on the level of parasitic absorption in the rear reflector.

Crack width control in RC elements with recycled steel fibres and applications to integral structures : theoretical and experimental study

El presente trabajo trata de elementos reforzados con barras de armadura y Fibras Metálicas Recicladas (FMR). El objetivo principal es mejorar el comportamiento a fisuración de elementos sometidos a flexión pura y a flexión compuesta, aumentando en consecuencia las prestaciones en servicio de aquellas estructuras con requerimientos estrictos con respecto al control de fisuración. Entre éstas últimas se encuentran las estructuras integrales, es decir aquellas estructuras sin juntas (puentes o edificios), sometidas a cargas gravitatorias y deformaciones impuestas en los elementos horizontales debidas a retracción, fluencia y temperatura. Las FMR son obtenidas a partir de los neumáticos fuera de uso, y puesto que el procedimiento de reciclado se centra en el caucho en vez que en el acero, su forma es aleatoria y con longitud variable. A pesar de que la eficacia del fibrorefuerzo mediante FMR ha sido demostrada en investigaciones anteriores, la innovación que representa este trabajo consiste en proponer la acción combinada de barras convencionales y FMR en la mejora del comportamiento a fisuración. El objetivo es por tanto mejorar la sostenibilidad del proyecto de la estructura en HA al utilizar materiales reciclados por un lado, y aumentando por el otro la durabilidad. En primer lugar, se presenta el estado del arte con respecto a la fisuración en elementos de HA, que sucesivamente se amplía a elementos reforzados con barras y fibras. Asimismo, se resume el método simplificado para el análisis de columnas de estructuras sin juntas ya propuesto por Pérez et al., con particular énfasis en aquellos aspectos que son incompatibles con la acción de las fibras a nivel seccional. A continuación, se presenta un modelo para describir la deformabilidad seccional y la fisuración en elementos en HA, que luego se amplía a aquellos elementos reforzados con barras y fibras, teniendo en cuenta también los efectos debidos a la retracción (tension stiffening negativo). El modelo es luego empleado para ampliar el método simplificado para el análisis de columnas. La aportación consiste por tanto en contar con una metodología amplia de análisis para este tipo de elementos. Seguidamente, se presenta la campaña experimental preliminar que ha involucrado vigas a escala reducida sometidas a flexión simple, con el objetivo de validar la eficiencia y la usabilidad en el hormigón de las FMR de dos diferentes tipos, y su comportamiento con respecto a fibras de acero comerciales. Se describe a continuación la campaña principal, consistente en ensayos sobre ocho vigas en flexión simple a escala 1:1 (variando contenido en FRM, Ø/s,eff y recubrimiento) y doce columnas a flexión compuesta (variando contenido en FMR, Ø/s,eff y nivel de fuerza axil). Los resultados obtenidos en la campaña principal son presentados y comentados, resaltando las mejoras obtenidas en el comportamiento a fisuración de las vigas y columnas, y la rigidez estructural de las columnas. Estos resultados se comparan con las predicciones del modelo propuesto. Los principales parámetros estudiados para describir la fisuración y el comportamiento seccional de las vigas son: la separación entre fisuras, el alargamiento medio de las armaduras y la abertura de fisura, mientras que en los ensayos de las columnas se ha contrastado las leyes momento/curvatura, la tensión en las barras de armadura y la abertura de fisura en el empotramiento en la base. La comparación muestra un buen acuerdo entre las predicciones y los resultados experimentales. Asimismo, se nota la mejora en el comportamiento a fisuración debido a la incorporación de FMR en aquellos elementos con cuantías de armadura bajas en flexión simple, en elementos con axiles bajos y para el control de la fisuración en elementos con grandes recubrimientos, siendo por tanto resultados de inmediato impacto en la práctica ingenieril (diseño de losas, tanques, estructuras integrales, etc.). VIIIComo punto final, se presentan aplicaciones de las FMR en estructuras reales. Se discuten dos casos de elementos sometidos a flexión pura, en particular una viga simplemente apoyada y un tanque para el tratamiento de agua. En ambos casos la adicción de FMR al hormigón lleva a mejoras en el comportamiento a fisuración. Luego, utilizando el método simplificado para el análisis en servicio de columnas de estructuras sin juntas, se calcula la máxima longitud admisible en casos típicos de puentes y edificación. En particular, se demuestra que las limitaciones de la práctica ingenieril actual (sobre todo en edificación) pueden ser aumentadas considerando el comportamiento real de las columnas en HA. Finalmente, los mismos casos son modificados para considerar el uso de MFR, y se presentan las mejoras tanto en la máxima longitud admisible como en la abertura de fisura para una longitud y deformación impuesta. This work deals with elements reinforced with both rebars and Recycled Steel Fibres (RSFs). Its main objective is to improve cracking behaviour of elements subjected to pure bending and bending and axial force, resulting in better serviceability conditions for these structures demanding keen crack width control. Among these structures a particularly interesting type are the so-called integral structures, i.e. long jointless structures (bridges and buildings) subjected to gravitational loads and imposed deformations due to shrinkage, creep and temperature. RSFs are obtained from End of Life Tyres, and due to the recycling process that is focused on the rubber rather than on the steel they come out crooked and with variable length. Although the effectiveness of RSFs had already been proven by previous research, the innovation of this work consists in the proposing the combined action of conventional rebars and RSFs to improve cracking behaviour. Therefore, the objective is to improve the sustainability of RC structures by, on the one hand, using recycled materials, and on the other improving their durability. A state of the art on cracking in RC elements is firstly drawn. It is then expanded to elements reinforced with both rebars and fibres (R/FRC elements). Finally, the simplified method for analysis of columns of long jointless structures already proposed by Pérez et al. is resumed, with a special focus on the points that conflict when taking into account the action of fibres. Afterwards, a model to describe sectional deformability and cracking of R/FRC elements is presented, taking also into account the effect of shrinkage (negative tension stiffening). The model is then used to implement the simplified method for columns. The novelty represented by this is that a comprehensive methodology to analyse this type of elements is presented. A preliminary experimental campaign consisting in small beams subjected to pure bending is described, with the objective of validating the effectiveness and usability in concrete of RSFs of two different types, and their behaviour when compared with commercial steel fibres. With the results and lessons learnt from this campaign in mind, the main experimental campaign is then described, consisting in cracking tests of eight unscaled beams in pure bending (varying RSF content, Ø/s,eff and concrete cover) and twelve columns subjected to imposed displacement and axial force (varying RSF content, Ø/s,eff and squashing load ratio). The results obtained from the main campaign are presented and discussed, with particular focus on the improvement in cracking behaviour for the beams and columns, and structural stiffness for the columns. They are then compared with the proposed model. The main parameters studied to describe cracking and sectional behaviours of the beam tests are crack spacing, mean steel strain and crack width, while for the column tests these were moment/curvature, stress in rebars and crack with at column embedment. The comparison showed satisfactory agreement between experimental results and model predictions. Moreover, it is pointed out the improvement in cracking behaviour due to the addition of RSF for elements with low reinforcement ratios, elements with low squashing load ratios and for crack width control of elements with large concrete covers, thus representing results with a immediate impact in engineering practice (slab design, tanks, integral structures, etc.). Applications of RSF to actual structures are finally presented. Two cases of elements in pure bending are presented, namely a simple supported beam and a water treatment tank. In both cases the addition of RSF to concrete leads to improvements in cracking behaviour. Then, using the simplified model for the serviceability analysis of columns of jointless structures, the maximum achievable jointless length of typical cases of a bridge and building is obtained. In XIIparticular, it is shown how the limitations of current engineering practice (this is especially the case of buildings) can be increased by considering the actual behaviour of RC supports. Then, the same cases are modified considering the use of RSF, and the improvements both in maximum achievable length and in crack width for a given length and imposed strain at the deck/first floor are shown.

El análogo natural de almacenamiento y escape de Co2 de la cuenca de Gañuelas-Mazarrón : implicaciones para el comportamiento y la seguridad de un almacenamiento de Co2 en estaso supercrítico

El aumento de la temperatura media de la Tierra durante el pasado siglo en casi 1 ºC; la subida del nivel medio del mar; la disminución del volumen de hielo y nieve terrestres; la fuerte variabilidad del clima y los episodios climáticos extremos que se vienen sucediendo durante las ultimas décadas; y el aumento de las epidemias y enfermedades infecciosas son solo algunas de las evidencias del cambio climático actual, causado, principalmente, por la acumulación de gases de efecto invernadero en la atmósfera por actividades antropogénicas. La problemática y preocupación creciente surgida a raíz de estos fenómenos, motivo que, en 1997, se adoptara el denominado “Protocolo de Kyoto” (Japón), por el que los países firmantes adoptaron diferentes medidas destinadas a controlar y reducir las emisiones de los citados gases. Entre estas medidas cabe destacar las tecnologías CAC, enfocadas a la captura, transporte y almacenamiento de CO2. En este contexto se aprobó, en octubre de 2008, el Proyecto Singular Estratégico “Tecnologías avanzadas de generación, captura y almacenamiento de CO2” (PSE-120000-2008-6), cofinanciado por el Ministerio de Ciencia e Innovación y el FEDER, el cual abordaba, en su Subproyecto “Almacenamiento Geológico de CO2” (PSS-120000-2008-31), el estudio detallado, entre otros, del Análogo Natural de Almacenamiento y Escape de CO2 de la cuenca de Ganuelas-Mazarrón (Murcia). Es precisamente en el marco de dicho Proyecto en el que se ha realizado este trabajo, cuyo objetivo final ha sido el de predecir el comportamiento y evaluar la seguridad, a corto, medio y largo plazo, de un Almacenamiento Geológico Profundo de CO2 (AGP-CO2), mediante el estudio integral del citado análogo natural. Este estudio ha comprendido: i) la contextualización geológica e hidrogeológica de la cuenca, así como la investigación geofísica de la misma; ii) la toma de muestras de aguas de algunos acuíferos seleccionados con el fin de realizar su estudio hidrogeoquímico e isotópico; iii) la caracterización mineralógica, petrográfica, geoquímica e isotópica de los travertinos precipitados a partir de las aguas de algunos de los sondeos de la cuenca; y iv) la medida y caracterización química e isotópica de los gases libres y disueltos detectados en la cuenca, con especial atención al CO2 y 222Rn. Esta información, desarrollada en capítulos independientes, ha permitido realizar un modelo conceptual de funcionamiento del sistema natural que constituye la cuenca de Ganuelas-Mazarrón, así como establecer las analogías entre este y un AGP-CO2, con posibles escapes naturales y/o antropogénicos. La aplicación de toda esta información ha servido, por un lado, para predecir el comportamiento y evaluar la seguridad, a corto, medio y largo plazo, de un AGP-CO2 y, por otro, proponer una metodología general aplicable al estudio de posibles emplazamientos de AGP-CO2 desde la perspectiva de los reservorios naturales de CO2. Los resultados más importantes indican que la cuenca de Ganuelas-Mazarrón se trata de una cubeta o fosa tectónica delimitada por fallas normales, con importantes saltos verticales, que hunden al substrato rocoso (Complejo Nevado-Filabride), y rellenas, generalmente, por materiales volcánicos-subvolcánicos ácidos. Además, esta cuenca se encuentra rellena por formaciones menos resistivas que son, de muro a techo, las margas miocenas, predominantes y casi exclusivas de la cuenca, y los conglomerados y gravas pliocuaternarias. El acuífero salino profundo y enriquecido en CO2, puesto de manifiesto por la xx exploración geotérmica realizada en dicha cuenca durante la década de los 80 y objeto principal de este estudio, se encuentra a techo de los materiales del Complejo Nevado-Filabride, a una profundidad que podría superar los 800 m, según los datos de la investigación mediante sondeos y geofísica. Por ello, no se descarta la posibilidad de que el CO2 se encuentre en estado supe critico, por lo que la citada cuenca reuniría las características principales de un almacenamiento geológico natural y profundo de CO2, o análogo natural de un AGP-CO2 en un acuífero salino profundo. La sobreexplotación de los acuíferos mas someros de la cuenca, con fines agrícolas, origino, por el descenso de sus niveles piezométricos y de la presión hidrostática, el ascenso de las aguas profundas, salinas y enriquecidas en CO2, las cuales son las responsables de la contaminación de dichos acuíferos. El estudio hidrogeoquímico de las aguas de los acuíferos investigados muestra una gran variedad de hidrofacies, incluso en aquellos de litología similar. La alta salinidad de estas aguas las hace inservibles tanto para el consumo humano como para fines agrícolas. Además, el carácter ligeramente ácido de la mayoría de estas aguas determina que tengan gran capacidad para disolver y transportar, hacia la superficie, elementos pesados y/o tóxicos, entre los que destaca el U, elemento abundante en las rocas volcánicas ácidas de la cuenca, con contenidos de hasta 14 ppm, y en forma de uraninita submicroscópica. El estudio isotópico ha permitido discernir el origen, entre otros, del C del DIC de las aguas (δ13C-DIC), explicándose como una mezcla de dos componentes principales: uno, procedente de la descomposición térmica de las calizas y mármoles del substrato y, otro, de origen edáfico, sin descartar una aportación menor de C de origen mantélico. El estudio de los travertinos que se están formando a la salida de las aguas de algunos sondeos, por la desgasificación rápida de CO2 y el consiguiente aumento de pH, ha permitido destacar este fenómeno, por analogía, como alerta de escapes de CO2 desde un AGP-CO2. El análisis de los gases disueltos y libres, con especial atención al CO2 y al 222Rn asociado, indican que el C del CO2, tanto disuelto como en fase libre, tiene un origen similar al del DIC, confirmándose la menor contribución de CO2 de origen mantélico, dada la relación R/Ra del He existente en estos gases. El 222Rn sería el generado por el decaimiento radiactivo del U, particularmente abundante en las rocas volcánicas de la cuenca, y/o por el 226Ra procedente del U o del existente en los yesos mesinienses de la cuenca. Además, el CO2 actúa como carrier del 222Rn, hecho evidenciado en las anomalías positivas de ambos gases a ~ 1 m de profundidad y relacionadas principalmente con perturbaciones naturales (fallas y contactos) y antropogénicas (sondeos). La signatura isotópica del C a partir del DIC, de los carbonatos (travertinos), y del CO2 disuelto y libre, sugiere que esta señal puede usarse como un excelente trazador de los escapes de CO2 desde un AGPCO2, en el cual se inyectara un CO2 procedente, generalmente, de la combustión de combustibles fósiles, con un δ13C(V-PDB) de ~ -30 ‰. Estos resultados han permitido construir un modelo conceptual de funcionamiento del sistema natural de la cuenca de Ganuelas-Mazarrón como análogo natural de un AGP-CO2, y establecer las relaciones entre ambos. Así, las analogías mas importantes, en cuanto a los elementos del sistema, serian la existencia de: i) un acuífero salino profundo enriquecido en CO2, que seria análoga a la formación almacén de un AGPxxi CO2; ii) una formación sedimentaria margosa que, con una potencia superior a 500 m, se correspondería con la formación sello de un AGP-CO2; y iii) acuíferos mas someros con aguas dulces y aptas para el consumo humano, rocas volcánicas ricas en U y fallas que se encuentran selladas por yesos y/o margas; elementos que también podrían concurrir en un emplazamiento de un AGP-CO2. Por otro lado, los procesos análogos mas importantes identificados serian: i) la inyección ascendente del CO2, que seria análoga a la inyección de CO2 de origen antropogénico, pero este con una signatura isotópica δ13C(V-PDB) de ~ -30 ‰; ii) la disolución de CO2 y 222Rn en las aguas del acuífero profundo, lo que seria análogo a la disolución de dichos gases en la formación almacén de un AGP-CO2; iii) la contaminación de los acuíferos mas someros por el ascenso de las aguas sobresaturadas en CO2, proceso que seria análogo a la contaminación que se produciría en los acuíferos existentes por encima de un AGP-CO2, siempre que este se perturbara natural (reactivación de fallas) o artificialmente (sondeos); iv) la desgasificación (CO2 y gases asociados, entre los que destaca el 222Rn) del acuífero salino profundo a través de sondeos, proceso análogo al que pudiera ocurrir en un AGP-CO2 perturbado; y v) la formación rápida de travertinos, proceso análogo indicativo de que el AGP-CO2 ha perdido su estanqueidad. La identificación de las analogías más importantes ha permitido, además, analizar y evaluar, de manera aproximada, el comportamiento y la seguridad, a corto, medio y largo plazo, de un AGP-CO2 emplazado en un contexto geológico similar al sistema natural estudiado. Para ello se ha seguido la metodología basada en el análisis e identificación de los FEPs (Features, Events and Processes), los cuales se han combinado entre sí para generar y analizar diferentes escenarios de evolución del sistema (scenario analysis). Estos escenarios de evolución identificados en el sistema natural perturbado, relacionados con la perforación de sondeos, sobreexplotación de acuíferos, precipitación rápida de travertinos, etc., serian análogos a los que podrían ocurrir en un AGP-CO2 que también fuera perturbado antropogénicamente, por lo que resulta totalmente necesario evitar la perturbación artificial de la formación sello del AGPCO2. Por último, con toda la información obtenida se ha propuesto una metodología de estudio que pueda aplicarse al estudio de posibles emplazamientos de un AGP-CO2 desde la perspectiva de los reservorios naturales de CO2, sean estancos o no. Esta metodología comprende varias fases de estudio, que comprendería la caracterización geológico-estructural del sitio y de sus componentes (agua, roca y gases), la identificación de las analogías entre un sistema natural de almacenamiento de CO2 y un modelo conceptual de un AGP-CO2, y el establecimiento de las implicaciones para el comportamiento y la seguridad de un AGP-CO2. ABSTRACT The accumulation of the anthropogenic greenhouse gases in the atmosphere is the main responsible for: i) the increase in the average temperature of the Earth over the past century by almost 1 °C; ii) the rise in the mean sea level; iii) the drop of the ice volume and terrestrial snow; iv) the strong climate variability and extreme weather events that have been happening over the last decades; and v) the spread of epidemics and infectious diseases. All of these events are just some of the evidence of current climate change. The problems and growing concern related to these phenomena, prompted the adoption of the so-called "Kyoto Protocol" (Japan) in 1997, in which the signatory countries established different measurements to control and reduce the emissions of the greenhouse gases. These measurements include the CCS technologies, focused on the capture, transport and storage of CO2. Within this context, it was approved, in October 2008, the Strategic Singular Project "Tecnologías avanzadas de generación, captura y almacenamiento de CO2" (PSE-120000-2008-6), supported by the Ministry of Science and Innovation and the FEDER funds. This Project, by means of the Subproject "Geological Storage of CO2" (PSS- 120000-2008-31), was focused on the detailed study of the Natural Analogue of CO2 Storage and Leakage located in the Ganuelas-Mazarron Tertiary basin (Murcia), among other Spanish Natural Analogues. This research work has been performed in the framework of this Subproject, being its final objective to predict the behaviour and evaluate the safety, at short, medium and long-term, of a CO2 Deep Geological Storage (CO2-DGS) by means of a comprehensive study of the abovementioned Natural Analogue. This study comprises: i) the geological and hydrogeological context of the basin and its geophysical research; ii) the water sampling of the selected aquifers to establish their hydrogeochemical and isotopic features; iii) the mineralogical, petrographic, geochemical and isotopic characterisation of the travertines formed from upwelling groundwater of several hydrogeological and geothermal wells; and iv) the measurement of the free and dissolved gases detected in the basin, as well as their chemical and isotopic characterisation, mainly regarding CO2 and 222Rn. This information, summarised in separate chapters in the text, has enabled to build a conceptual model of the studied natural system and to establish the analogies between both the studied natural system and a CO2-DGS, with possible natural and/or anthropogenic escapes. All this information has served, firstly, to predict the behaviour and to evaluate the safety, at short, medium and long-term, of a CO2-DGS and, secondly, to propose a general methodology to study suitable sites for a CO2-DGS, taking into account the lessons learned from this CO2 natural reservoir. The main results indicate that the Ganuelas-Mazarron basin is a graben bounded by normal faults with significant vertical movements, which move down the metamorphic substrate (Nevado-Filabride Complex), and filled with acid volcanic-subvolcanic rocks. Furthermore, this basin is filled with two sedimentary formations: i) the Miocene marls, which are predominant and almost exclusive in the basin; xxiv and ii) the Plio-Quaternary conglomerates and gravels. A deep saline CO2-rich aquifer was evidenced in this basin as a result of the geothermal exploration wells performed during the 80s, located just at the top of the Nevado-Filabride Complex and at a depth that could exceed 800 m, according to the geophysical exploration performed. This saline CO2-rich aquifer is precisely the main object of this study. Therefore, it is not discarded the possibility that the CO2 in this aquifer be in supercritical state. Consequently, the aforementioned basin gathers the main characteristics of a natural and deep CO2 geological storage, or natural analogue of a CO2-DGS in a deep saline aquifer. The overexploitation of the shallow aquifers in this basin for agriculture purposes caused the drop of the groundwater levels and hydrostatic pressures, and, as a result, the ascent of the deep saline and CO2-rich groundwater, which is the responsible for the contamination of the shallow and fresh aquifers. The hydrogeochemical features of groundwater from the investigated aquifers show the presence of very different hydrofacies, even in those with similar lithology. The high salinity of this groundwater prevents the human and agricultural uses. In addition, the slightly acidic character of most of these waters determines their capacity to dissolve and transport towards the surface heavy and/or toxic elements, among which U is highlighted. This element is abundant in the acidic volcanic rocks of the basin, with concentrations up to 14 ppm, mainly as sub-microscopic uraninite crystals. The isotopic study of this groundwater, particularly the isotopic signature of C from DIC (δ13C-DIC), suggests that dissolved C can be explained considering a mixture of C from two main different sources: i) from the thermal decomposition of limestones and marbles forming the substrate; and ii) from edaphic origin. However, a minor contribution of C from mantle degassing cannot be discarded. The study of travertines being formed from upwelling groundwater of several hydrogeological and geothermal wells, as a result of the fast CO2 degassing and the pH increase, has allowed highlighting this phenomenon, by analogy, as an alert for the CO2 leakages from a CO2-DGS. The analysis of the dissolved and free gases, with special attention to CO2 and 222Rn, indicates that the C from the dissolved and free CO2 has a similar origin to that of the DIC. The R/Ra ratio of He corroborates the minor contribution of CO2 from the mantle degassing. Furthermore, 222Rn is generated by the radioactive decay of U, particularly abundant in the volcanic rocks of the basin, and/or by 226Ra from the U or from the Messinian gypsum in the basin. Moreover, CO2 acts as a carrier of the 222Rn, a fact evidenced by the positive anomalies of both gases at ~ 1 m depth and mainly related to natural (faults and contacts) and anthropogenic (wells) perturbations. The isotopic signature of C from DIC, carbonates (travertines), and dissolved and free CO2, suggests that this parameter can be used as an excellent tracer of CO2 escapes from a CO2-DGS, in which CO2 usually from the combustion of fossil fuels, with δ13C(V-PDB) of ~ -30 ‰, will be injected. All of these results have allowed to build a conceptual model of the behaviour of the natural system studied as a natural analogue of a CO2-DGS, as well as to establish the relationships between both natural xxv and artificial systems. Thus, the most important analogies, regarding the elements of the system, would be the presence of: i) a deep saline CO2-rich aquifer, which would be analogous to the storage formation of a CO2-DGS; ii) a marly sedimentary formation with a thickness greater than 500 m, which would correspond to the sealing formation of a CO2-DGS; and iii) shallow aquifers with fresh waters suitable for human consumption, U-rich volcanic rocks, and faults that are sealed by gypsums and/or marls; geological elements that could also be present in a CO2-DGS. On the other hand, the most important analogous processes identified are: i) the upward injection of CO2, which would be analogous to the downward injection of the anthropogenic CO2, this last with a δ13C(V-PDB) of ~ -30 ‰; ii) the dissolution of CO2 and 222Rn in groundwater of the deep aquifer, which would be analogous to the dissolution of these gases in the storage formation of a CO2-DGS; iii) the contamination of the shallow aquifers by the uprising of CO2-oversaturated groundwater, an analogous process to the contamination that would occur in shallow aquifers located above a CO2-DGS, whenever it was naturally (reactivation of faults) or artificially (wells) perturbed; iv) the degassing (CO2 and associated gases, among which 222Rn is remarkable) of the deep saline aquifer through wells, process which could be similar in a perturbed CO2- DGS; v) the rapid formation of travertines, indicating that the CO2-DGS has lost its seal capacity. The identification of the most important analogies has also allowed analysing and evaluating, approximately, the behaviour and safety in the short, medium and long term, of a CO2-DGS hosted in a similar geological context of the natural system studied. For that, it has been followed the methodology based on the analysis and identification of FEPs (Features, Events and Processes) that have been combined together in order to generate and analyse different scenarios of the system evolution (scenario analysis). These identified scenarios in the perturbed natural system, related to boreholes, overexploitation of aquifers, rapid precipitation of travertines, etc., would be similar to those that might occur in a CO2-DGS anthropogenically perturbed, so that it is absolutely necessary to avoid the artificial perturbation of the seal formation of a CO2-DGS. Finally, a useful methodology for the study of possible sites for a CO2-DGS is suggested based on the information obtained from this investigation, taking into account the lessons learned from this CO2 natural reservoir. This methodology comprises several phases of study, including the geological and structural characterisation of the site and its components (water, rock and gases), the identification of the analogies between a CO2 storage natural system and a conceptual model of a CO2-DGS, and the implications regarding the behaviour and safety of a CO2-DGS.

Classification of mononuclear zinc metal sites in protein structures

Our study of the extended metal environment, particularly of the second shell, focuses in this paper on zinc sites. Key findings include: (i) The second shell of mononuclear zinc centers is generally more polar than hydrophobic and prominently features charged residues engaged in an abundance of hydrogen bonding with histidine ligands. Histidine–acidic or histidine–tyrosine clusters commonly overlap the environment of zinc ions. (ii) Histidine tautomeric metal bonding patterns in ligating zinc ions are mixed. For example, carboxypeptidase A, thermolysin, and sonic hedgehog possess the same ligand group (two histidines, one unibidentate acidic ligand, and a bound water), but their histidine tautomeric geometries markedly differ such that the carboxypeptidase A makes only Nδ1 contacts, thermolysin makes only Nɛ2 contacts, and sonic hedgehog uses one of each. Thus the presence of a similar ligand cohort does not necessarily imply the same topology or function at the active site. (iii) Two close histidine ligands HXmH, m ≤ 5, rarely both coordinate a single metal ion in the Nδ1 tautomeric conformation, presumably to avoid steric conflicts. Mononuclear zinc sites can be classified into six types depending on the ligand composition and geometry. Implications of the results are discussed in terms of divergent and convergent evolution.

Ordered water molecules as key allosteric mediators in a cooperative dimeric hemoglobin

One of the most remarkable structural aspects of Scapharca dimeric hemoglobin is the disruption of a very well-ordered water cluster at the subunit interface upon ligand binding. We have explored the role of these crystallographically observed water molecules by site-directed mutagenesis and osmotic stress techniques. The isosteric mutation of Thr-72 → Val in the interface increases oxygen affinity more than 40-fold with a surprising enhancement of cooperativity. The only significant structural effect of this mutation is to destabilize two ordered water molecules in the deoxy interface. Wild-type Scapharca hemoglobin is strongly sensitive to osmotic conditions. Upon addition of glycerol, striking changes in Raman spectrum of the deoxy form are observed that indicate a transition toward the liganded form. Increased osmotic pressure, which lowers the oxygen affinity in human hemoglobin, raises the oxygen affinity of Scapharca hemoglobin regardless of whether the solute is glycerol, glucose, or sucrose. Analysis of these results provides an estimate of six water molecules lost upon oxygen binding to the dimer, in good agreement with eight predicted from crystal structures. These experiments suggest that the observed cluster of interfacial water molecules plays a crucial role in communication between subunits.

Reconstitution and functional comparison of purified GlpF and AqpZ, the glycerol and water channels from Escherichia coli

A large family of membrane channel proteins selective for transport of water (aquaporins) or water plus glycerol (aquaglyceroporins) has been found in diverse life forms. Escherichia coli has two members of this family—a water channel, AqpZ, and a glycerol facilitator, GlpF. Despite having similar primary amino acid sequences and predicted structures, the oligomeric state and solute selectivity of AqpZ and GlpF are disputed. Here we report biochemical and functional characterizations of affinity-purified GlpF and compare it to AqpZ. Histidine-tagged (His-GlpF) and hemagglutinin-tagged (HA-GlpF) polypeptides encoded by a bicistronic construct were expressed in bacteria. HA-GlpF and His-GlpF appear to form oligomers during Ni-nitrilotriacetate affinity purification. Sucrose gradient sedimentation analyses showed that the oligomeric state of octyl glucoside-solubilized GlpF varies: low ionic strength favors subunit dissociation, whereas Mg2+ stabilizes tetrameric assembly. Reconstitution of affinity-purified GlpF into proteoliposomes increases glycerol permeability more than 100-fold and water permeability up to 10-fold compared with control liposomes. Glycerol and water permeability of GlpF both occur with low Arrhenius activation energies and are reversibly inhibited by HgCl2. Our studies demonstrate that, unlike AqpZ, a water-selective stable tetramer, purified GlpF exists in multiple oligomeric forms under nondenaturing conditions and is highly permeable to glycerol but less well permeated by water.

Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules

We propose a framework to describe the cooperative orientational motions of water molecules in liquid water and around solute molecules in water solutions. From molecular dynamics (MD) simulation a new quantity “site-dipole field” is defined as the averaged orientation of water molecules that pass through each spatial position. In the site-dipole field of bulk water we found large vortex-like structures of more than 10 Å in size. Such coherent patterns persist more than 300 ps although the orientational memory of individual molecules is quickly lost. A 1-ns MD simulation of systems consisting of two amino acids shows that the fluctuations of site-dipole field of solvent are pinned around the amino acids, resulting in a stable dipole-bridge between side-chains of amino acids. The dipole-bridge is significantly formed even for the side-chain separation of 14 Å, which corresponds to five layers of water. The way that dipole-bridge forms sensitively depends on the side-chain orientations and thereby explains the specificity in the solvent-mediated interactions between biomolecules.

Diffractive optics-based heterodyne-detected four-wave mixing signals of protein motion: From “protein quakes” to ligand escape for myoglobin

Ligand transport through myoglobin (Mb) has been observed by using optically heterodyne-detected transient grating spectroscopy. Experimental implementation using diffractive optics has provided unprecedented sensitivity for the study of protein motions by enabling the passive phase locking of the four beams that constitute the experiment, and an unambiguous separation of the Real and Imaginary parts of the signal. Ligand photodissociation of carboxymyoglobin (MbCO) induces a sequence of events involving the relaxation of the protein structure to accommodate ligand escape. These motions show up in the Real part of the signal. The ligand (CO) transport process involves an initial, small amplitude, change in volume, reflecting the transit time of the ligand through the protein, followed by a significantly larger volume change with ligand escape to the surrounding water. The latter process is well described by a single exponential process of 725 ± 15 ns at room temperature. The overall dynamics provide a distinctive signature that can be understood in the context of segmental protein fluctuations that aid ligand escape via a few specific cavities, and they suggest the existence of discrete escape pathways.

Manganese oxide minerals: Crystal structures and economic and environmental significance

Manganese oxide minerals have been used for thousands of years—by the ancients for pigments and to clarify glass, and today as ores of Mn metal, catalysts, and battery material. More than 30 Mn oxide minerals occur in a wide variety of geological settings. They are major components of Mn nodules that pave huge areas of the ocean floor and bottoms of many fresh-water lakes. Mn oxide minerals are ubiquitous in soils and sediments and participate in a variety of chemical reactions that affect groundwater and bulk soil composition. Their typical occurrence as fine-grained mixtures makes it difficult to study their atomic structures and crystal chemistries. In recent years, however, investigations using transmission electron microscopy and powder x-ray and neutron diffraction methods have provided important new insights into the structures and properties of these materials. The crystal structures for todorokite and birnessite, two of the more common Mn oxide minerals in terrestrial deposits and ocean nodules, were determined by using powder x-ray diffraction data and the Rietveld refinement method. Because of the large tunnels in todorokite and related structures there is considerable interest in the use of these materials and synthetic analogues as catalysts and cation exchange agents. Birnessite-group minerals have layer structures and readily undergo oxidation reduction and cation-exchange reactions and play a major role in controlling groundwater chemistry.

Packing at the protein-water interface.

We have determined the packing efficiency at the protein-water interface by calculating the volumes of atoms on the protein surface and nearby water molecules in 22 crystal structures. We find that an atom on the protein surface occupies, on average, a volume approximately 7% larger than an atom of equivalent chemical type in the protein core. In these calculations, larger volumes result from voids between atoms and thus imply a looser or less efficient packing. We further find that the volumes of individual atoms are not related to their chemical type but rather to their structural location. More exposed atoms have larger volumes. Moreover, the packing around atoms in locally concave, grooved regions of protein surfaces is looser than that around atoms in locally convex, ridge regions. This as a direct manifestation of surface curvature-dependent hydration. The net volume increase for atoms on the protein surface is compensated by volume decreases in water molecules near the surface. These waters occupy volumes smaller than those in the bulk solvent by up to 20%; the precise amount of this decrease is directly related to the extent of contact with the protein.

Electroconvulsive shock and lidocaine reveal rapid consolidation of spatial working memory in the water maze.

Head trauma leading to concussion and electroconvulsive shock (ECS) in humans causes amnesia for events that occurred shortly before the injury (retrograde amnesia). The present experiment investigated the amnesic effect of lidocaine and ECS in 25 rats trained on a working memory version of the Morris water task. Each day, the escape platform was moved to a new location; learning was evidenced by a decrease in the latency to find the platform from the first to the second trial. "Consolidation" of this newly encoded spatial engram was disrupted by bilateral inactivation of the dorsal hippocampus with 1 microliter of 4% lidocaine applied as soon as possible after the first trial. When trial 2 was given after recovery from the lidocaine (30 min after the injection), a normal decrease in latency indicated that the new engram was not disrupted. When trial 2 was given under the influence of lidocaine (5 min after injection), absence of latency decrease demonstrated both the success of the inactivation and the importance of hippocampus for the task. To examine the role of events immediately after learning, ECS (30 or 100 mA, 50 Hz, 1.2 sec) was applied 0 sec to 45 sec after a single escape to the new platform location. A 2-h delay between ECS and trial 2 allowed the effects of ECS to dissipate. ECS applied 45 sec or 30 sec after trial 1 caused no retrograde amnesia: escape latencies on trial 2 were the same as in control rats. However, ECS applied 0 sec or 15 sec after trial 1 induced clear retrograde amnesia: escape latencies on trial 2 were no shorter than on trial 1. It is concluded that the consolidation of a newly formed memory for spatial location can only be disrupted by ECS within 30 sec after learning.

Visualization of intermediate and transition-state structures in protein-tyrosine phosphatase catalysis.

Engineering site-specific amino acid substitutions into the protein-tyrosine phosphatase (PTPase) PTP1 and the dual-specific vaccinia H1-related phosphatase (VHR), has kinetically isolated the two chemical steps of the reaction and provided a rare opportunity for examining transition states and directly observing the phosphoenzyme intermediate. Changing serine to alanine in the active-site sequence motif HCXXGXXRS shifted the rate-limiting step from intermediate formation to intermediate hydrolysis. Using phosphorus 31P NMR, the covalent thiol-phosphate intermediate was directly observed during catalytic turnover. The importance of the conserved aspartic acid (D92 in VHR and D181 in PTP1) in both chemical steps was established. Kinetic analysis of D92N and D181N mutants indicated that aspartic acid acts as a general acid by protonating the leaving-group phenolic oxygen. Structure-reactivity experiments with native and aspartate mutant enzymes established that proton transfer is concomitant with P-O cleavage, such that no charge develops on the phenolic oxygen. Steady- and presteady-state kinetics, as well as NMR analysis of the double mutant D92N/S131A (VHR), suggested that the conserved aspartic acid functions as a general base during intermediate hydrolysis. As a general base, aspartate would activate a water molecule to facilitate nucleophilic attack. The amino acids involved in transition-state stabilization for cysteinylphosphate hydrolysis were confirmed by the x-ray structure of the Yersinia PTPase complexed with vanadate, a transition-state mimic that binds covalently to the active-site cysteine. Consistent with the NMR, x-ray, biochemical, and kinetic data, a unifying mechanism for catalysis is proposed.

Significance of bound water to local chain conformations in protein crystals.

We examine how the polypeptide chain in protein crystal structures exploits the multivalent hydrogen-bonding potential of bound water molecules. This shows that multiple interactions with a single water molecule tend to occur locally along the chain. A distinctive internal-coordinate representation of the local water-binding segments reveals several consensus conformations. The fractional water occupancy of each was found by comparison of the total number of conformations in the database regardless of the presence or absence of bound water. The water molecule appears particularly frequently in type II beta-turn geometries and an N-terminal helix feature. This work constitutes a first step into assessing not only the generality but also the significance of specific water binding in globular proteins.

Trapping of branched DNA in microfabricated structures.

We have observed electrostatic trapping of tribranched DNA molecules undergoing electrophoresis in a microfabricated pseudo-two-dimensional array of posts. Trapping occurs in a unique transport regimen in which the electrophoretic mobility is extremely sensitive to polymer topology. The arrest of branched polymers is explained by considering their center-of-mass motion; in certain conformations, owing to the constraints imposed by the obstacles a molecule cannot advance without the center of mass first moving a short distance backwards. The depth of the resulting local potential well can be much greater than the thermal energy so that escape of an immobilized molecule can be extremely slow. We summarize the expected behavior of the mobility as a function of field strength and topology and point out that the microfabricated arrays are highly suitable for detecting an extremely small number of branched molecules in a very large population of linear molecules.

Computer determination of peptide conformations in water: different roads to structure.

Fragments of proteins (short peptides) that "fold" suggest a mechanism of how complete conformational search in protein folding is avoided. We used a computational method to determine structures of two foldable peptides in explicit water: RVEW and CSVTC. The optimization starts from random structures and no experimental constraints are used. In agreement with NMR data, the simulations find a hydrophobic pair (Val/Trp) in REVW. The structure of CSVTC is induced by a surface water that bridges two amide hydrogens, a drive to structure hypothesized by Ben-Naim [Ben-Naim, A. (1990) J. Chem. Phys. 93, 8196-8210] that is largely ignored in studies of folding. Tendency to structure in short peptide chains suggests a mechanism for the formation of short-range nucleation sites in protein folding.