Energy payback time of grid connected pv systems: comparison between tracking and fixed systems

A review of existing studies about LCA of PV systems has been carried out. The data from this review have been completed with our own figures in order to calculate the Energy Payback Time of double and horizontal axis tracking and fixed systems. The results of this metric span from 2 to 5 years for the latitude and global irradiation ranges of the geographical area comprised between −10◦ to 10◦ of longitude, and 30◦ to 45◦ of latitude. With the caution due to the uncertainty of the sources of information, these results mean that a GCPVS is able to produce back the energy required for its existence from 6 to 15 times during a life cycle of 30 years. When comparing tracking and fixed systems, the great importance of the PV generator makes advisable to dedicate more energy to some components of the system in order to increase the productivity and to obtain a higher performance of the component with the highest energy requirement. Both double axis and horizontal axis trackers follow this way, requiring more energy in metallic structure, foundations and wiring, but this higher contribution is widely compensated by the improved productivity of the system.

Physical parameters in relation to physiological changes of avocado during ripening (20ºc) and cold storage (6ºc) in different conditions.

The application of the response of fruits to low energy for mechanical impacts is described, for evaluation of post-harvest ripening of avocadoes of the variety "Hass". An impactor of 50g of weight, provided with an accelerometer, and free-falling from a height of 4 cm, is used; it is interfaced to a computer and uses a special software for retrieving and analyzing the deceleration data. Impact response parameters of individual fruits were compared to firmness of the pulp, measured by the most used method of double-plate puncture, as well as to other physical and physiological parameters: color, skin puncture ethylene production rate and others. Two groups of fruits were carefully selected, stored at 6º C (60 days) and ripened at 20ºC (11 days), and tested during the storage period. It is shown that, as in other types of fruits, impact response can be a good predictor of firmness in avocadoes, obtaining the same accuracy as with destructive firmness measurements. Mathematical and multiple regression models are calculated and compared to measured data, with which a prediction of storage period can be made for these fruits.

Pressure measurements of the detachment bubble on the Bolund Island

Pressure measurements on the surface of a 1:230 scale model of Bolund Island are presented. The model is smooth and no boundary layer generation has been considered since the experiment is designed as the simplest possible reference case. Measurement have been taken for a range of Reynolds numbers based on the average undisturbed wind speed U? and the maximum height of the island, h [1.7×104 , 8.5×104], and for a range of wind directions. Four minutes time series of pressure in more than 400 points have been acquired and analysed to obtain the spatial distribution of both the time average and the variance of the pressure signal. The horizontal extension of the detachment bubble for the different Reynolds numbers and wind directions is identified by isobars and curves of constant value of pressure variance. The applicability of this technique for evaluating the horizontal topology of high turbulence regions associated to detachment bubbles after escarpments in potential wind farm sites is analysed. The results obtained shows that the behaviour of the mean pressure coefficient, Cp, the std. pressure coefficient, C?p, and the skewness of the pressure, Sp can be used to study the bubble over the island to a certain extent. This experiment is part of the set of different analysis on the Bolund test case that is being undertaken within WAUDIT project by the different scientific groups.

The variability and interdependence of spider viscid line tensile properties

True stress-true strain curves of naturally spun viscid line fibers retrieved directly from the spiral of orb-webs built by Argiope trifasciata spiders were measured using a novel methodology. This new procedure combines a method for removing the aqueous coating of the fibers and a technique that allows the accurate measurement of their cross sectional area. Comparison of the tensile behaviour of different samples indicates that naturally spun viscid lines show a large variability, comparable to that of other silks, such as major ampullate gland silk and silkworm silk. Nevertheless, application of a statistical analysis allowed identifying two independent parameters that underlie the variability and characterize the observed range of true stress-true strain curves. Combination of this result with previous mechanical and microstructural data suggested the assignment of these two independent effects to the degree of alignment of the protein chains and to the local relative humidity which, in turn, depends on the composition of the viscous coating and on the external environmental conditions.

Effect of fire on the microstructure and mechanical response of structural steels for building construction

The research is an exhaustive study of the microstructure and of the stress-strain curves of structural steel S460N at temperatures typical of a fire. It includes a fractographic study of the fracture suifaces of cylindrical specimens, tensile tested at different fire scenarios, explaining the relationship between the failure micromechanisms and temperature. The paper ends with the comparison between the experimentally found strain-stress curves with that one's proposed by the EUROCODE EC3, resulting that in the case of steel S460N these are on the side ofsafety.

Effect of fire on the microstructure and mechanical response of structural steels for building construction

The research is an exhaustive study of the microstructure and of the stress-strain curves of structural steel S460N at temperatures typical of a fire. It includes a fractographic study of the fracture suifaces of cylindrical specimens, tensile tested at different fire scenarios, explaining the relationship between the failure micromechanisms and temperature. The paper ends with the comparison between the experimentally found strain-stress curves with that one's proposed by the EUROCODE EC3, resulting that in the case of steel S460N these are on the side ofsafety.

A parametric, experimental analysis of conical vortices on curved roofs of low-rise buildings

Different methods to reduce the high suction caused by conical vortices have been reported in the literature: vertical parapets, either solid or porous, placed at the roof edges being the most analysed configuration. Another method for alleviating the high suction peaks due to conical vortices is the use of some non-standard parapet configuration like cantilever parapets. In this paper the influence of roof curvature on the conical vortex pattern appearing on a curved roof (Fig. 1) when subject to oblique winds is experimentally analysed by testing the mean pressure distribution on the curved roofs of low-rise building models in a wind tunnel. Also, the efficiency of cantilever parapets to reduce mean suction loads on curved roofs is experimentally checked. Very high suction loads have been measured on curved roofs, the magnitude of these high suction loads being significantly decreased when cantilever parapets are used. Thus, the suitability of these parapets to reduce wind pressure loads on curved roofs is demonstrated.

Experimental and numerical study of cracking of concrete due to reinforcement corrosion

La corrosión del acero es una de las patologías más importantes que afectan a las estructuras de hormigón armado que están expuestas a ambientes marinos o al ataque de sales fundentes. Cuando se produce corrosión, se genera una capa de óxido alrededor de la superficie de las armaduras, que ocupa un volumen mayor que el acero inicial; como consecuencia, el óxido ejerce presiones internas en el hormigón circundante, que lleva a la fisuración y, ocasionalmente, al desprendimiento del recubrimiento de hormigón. Durante los últimos años, numerosos estudios han contribuido a ampliar el conocimiento sobre el proceso de fisuración; sin embargo, aún existen muchas incertidumbres respecto al comportamiento mecánico de la capa de óxido, que es fundamental para predecir la fisuración. Por ello, en esta tesis se ha desarrollado y aplicado una metodología, para mejorar el conocimiento respecto al comportamiento del sistema acero-óxido-hormigón, combinando experimentos y simulaciones numéricas. Se han realizado ensayos de corrosión acelerada en condiciones de laboratorio, utilizando la técnica de corriente impresa. Con el objetivo de obtener información cercana a la capa de acero, como muestras se seleccionaron prismas de hormigón con un tubo de acero liso como armadura, que se diseñaron para conseguir la formación de una única fisura principal en el recubrimiento. Durante los ensayos, las muestras se equiparon con instrumentos especialmente diseñados para medir la variación de diámetro y volumen interior de los tubos, y se midió la apertura de la fisura principal utilizando un extensómetro comercial, adaptado a la geometría de las muestras. Las condiciones de contorno se diseñaron cuidadosamente para que los campos de corriente y deformación fuesen planos durante los ensayos, resultando en corrosión uniforme a lo largo del tubo, para poder reproducir los ensayos en simulaciones numéricas. Se ensayaron series con varias densidades de corriente y varias profundidades de corrosión. De manera complementaria, el comportamiento en fractura del hormigón se caracterizó en ensayos independientes, y se midió la pérdida gravimétrica de los tubos siguiendo procedimientos estándar. En todos los ensayos, la fisura principal creció muy despacio durante las primeras micras de profundidad de corrosión, pero después de una cierta profundidad crítica, la fisura se desarrolló completamente, con un aumento rápido de su apertura; la densidad de corriente influye en la profundidad de corrosión crítica. Las variaciones de diámetro interior y de volumen interior de los tubos mostraron tendencias diferentes entre sí, lo que indica que la deformación del tubo no fue uniforme. Después de la corrosión acelerada, las muestras se cortaron en rebanadas, que se utilizaron en ensayos post-corrosión. El patrón de fisuración se estudió a lo largo del tubo, en rebanadas que se impregnaron en vacío con resina y fluoresceína para mejorar la visibilidad de las fisuras bajo luz ultravioleta, y se estudió la presencia de óxido dentro de las grietas. En todas las muestras, se formó una fisura principal en el recubrimiento, infiltrada con óxido, y varias fisuras secundarias finas alrededor del tubo; el número de fisuras varió con la profundidad de corrosión de las muestras. Para muestras con la misma corrosión, el número de fisuras y su posición fue diferente entre muestras y entre secciones de una misma muestra, debido a la heterogeneidad del hormigón. Finalmente, se investigó la adherencia entre el acero y el hormigón, utilizando un dispositivo diseñado para empujar el tubo en el hormigón. Las curvas de tensión frente a desplazamiento del tubo presentaron un pico marcado, seguido de un descenso constante; la profundidad de corrosión y la apertura de fisura de las muestras influyeron notablemente en la tensión residual del ensayo. Para simular la fisuración del hormigón causada por la corrosión de las armaduras, se programó un modelo numérico. Éste combina elementos finitos con fisura embebida adaptable que reproducen la fractura del hormigón conforme al modelo de fisura cohesiva estándar, y elementos de interfaz llamados elementos junta expansiva, que se programaron específicamente para reproducir la expansión volumétrica del óxido y que incorporan su comportamiento mecánico. En el elemento junta expansiva se implementó un fenómeno de despegue, concretamente de deslizamiento y separación, que resultó fundamental para obtener localización de fisuras adecuada, y que se consiguió con una fuerte reducción de la rigidez tangencial y la rigidez en tracción del óxido. Con este modelo, se realizaron simulaciones de los ensayos, utilizando modelos bidimensionales de las muestras con elementos finitos. Como datos para el comportamiento en fractura del hormigón, se utilizaron las propiedades determinadas en experimentos. Para el óxido, inicialmente se supuso un comportamiento fluido, con deslizamiento y separación casi perfectos. Después, se realizó un ajuste de los parámetros del elemento junta expansiva para reproducir los resultados experimentales. Se observó que variaciones en la rigidez normal del óxido apenas afectaban a los resultados, y que los demás parámetros apenas afectaban a la apertura de fisura; sin embargo, la deformación del tubo resultó ser muy sensible a variaciones en los parámetros del óxido, debido a la flexibilidad de la pared de los tubos, lo que resultó fundamental para determinar indirectamente los valores de los parámetros constitutivos del óxido. Finalmente, se realizaron simulaciones definitivas de los ensayos. El modelo reprodujo la profundidad de corrosión crítica y el comportamiento final de las curvas experimentales; se comprobó que la variación de diámetro interior de los tubos está fuertemente influenciada por su posición relativa respecto a la fisura principal, en concordancia con los resultados experimentales. De la comparación de los resultados experimentales y numéricos, se pudo extraer información sobre las propiedades del óxido que de otra manera no habría podido obtenerse. Corrosion of steel is one of the main pathologies affecting reinforced concrete structures exposed to marine environments or to molten salt. When corrosion occurs, an oxide layer develops around the reinforcement surface, which occupies a greater volume than the initial steel; thus, it induces internal pressure on the surrounding concrete that leads to cracking and, eventually, to full-spalling of the concrete cover. During the last years much effort has been devoted to understand the process of cracking; however, there is still a lack of knowledge regarding the mechanical behavior of the oxide layer, which is essential in the prediction of cracking. Thus, a methodology has been developed and applied in this thesis to gain further understanding of the behavior of the steel-oxide-concrete system, combining experiments and numerical simulations. Accelerated corrosion tests were carried out in laboratory conditions, using the impressed current technique. To get experimental information close to the oxide layer, concrete prisms with a smooth steel tube as reinforcement were selected as specimens, which were designed to get a single main crack across the cover. During the tests, the specimens were equipped with instruments that were specially designed to measure the variation of inner diameter and volume of the tubes, and the width of the main crack was recorded using a commercial extensometer that was adapted to the geometry of the specimens. The boundary conditions were carefully designed so that plane current and strain fields were expected during the tests, resulting in nearly uniform corrosion along the length of the tube, so that the tests could be reproduced in numerical simulations. Series of tests were carried out with various current densities and corrosion depths. Complementarily, the fracture behavior of concrete was characterized in independent tests, and the gravimetric loss of the steel tubes was determined by standard means. In all the tests, the main crack grew very slowly during the first microns of corrosion depth, but after a critical corrosion depth it fully developed and opened faster; the current density influenced the critical corrosion depth. The variation of inner diameter and inner volume of the tubes had different trends, which indicates that the deformation of the tube was not uniform. After accelerated corrosion, the specimens were cut into slices, which were used in post-corrosion tests. The pattern of cracking along the reinforcement was investigated in slices that were impregnated under vacuum with resin containing fluorescein to enhance the visibility of cracks under ultraviolet lightening and a study was carried out to assess the presence of oxide into the cracks. In all the specimens, a main crack developed through the concrete cover, which was infiltrated with oxide, and several thin secondary cracks around the reinforcement; the number of cracks diminished with the corrosion depth of the specimen. For specimens with the same corrosion, the number of cracks and their position varied from one specimen to another and between cross-sections of a given specimen, due to the heterogeneity of concrete. Finally, the bond between the steel and the concrete was investigated, using a device designed to push the tubes of steel in the concrete. The curves of stress versus displacement of the tube presented a marked peak, followed by a steady descent, with notably influence of the corrosion depth and the crack width on the residual stress. To simulate cracking of concrete due to corrosion of the reinforcement, a numerical model was implemented. It combines finite elements with an embedded adaptable crack that reproduces cracking of concrete according to the basic cohesive model, and interface elements so-called expansive joint elements, which were specially designed to reproduce the volumetric expansion of oxide and incorporate its mechanical behavior. In the expansive joint element, a debonding effect was implemented consisting of sliding and separation, which was proved to be essential to achieve proper localization of cracks, and was achieved by strongly reducing the shear and the tensile stiffnesses of the oxide. With that model, simulations of the accelerated corrosion tests were carried out on 2- dimensional finite element models of the specimens. For the fracture behavior of concrete, the properties experimentally determined were used as input. For the oxide, initially a fluidlike behavior was assumed with nearly perfect sliding and separation; then the parameters of the expansive joint element were modified to fit the experimental results. Changes in the bulk modulus of the oxide barely affected the results and changes in the remaining parameters had a moderate effect on the predicted crack width; however, the deformation of the tube was very sensitive to variations in the parameters of oxide, due to the flexibility of the tube wall, which was crucial for indirect determination of the constitutive parameters of oxide. Finally, definitive simulations of the tests were carried out. The model reproduced the critical corrosion depth and the final behavior of the experimental curves; it was assessed that the variation of inner diameter of the tubes is highly influenced by its relative position with respect to the main crack, in accordance with the experimental observations. From the comparison of the experimental and numerical results, some properties of the mechanical behavior of the oxide were disclosed that otherwise could not have been measured.

A method to obtain the thermal parameters and the photothermal transduction efficiency in an optical hyperthermia device based on laser irradiation of gold nanoparticles

Optical hyperthermia systems based on the laser irradiation of gold nanorods seem to be a promising tool in the development of therapies against cancer. After a proof of concept in which the authors demonstrated the efficiency of this kind of systems, a modeling process based on an equivalent thermal-electric circuit has been carried out to determine the thermal parameters of the system and an energy balance obtained from the time-dependent heating and cooling temperature curves of the irradiated samples in order to obtain the photothermal transduction efficiency. By knowing this parameter, it is possible to increase the effectiveness of the treatments, thanks to the possibility of predicting the response of the device depending on the working configuration. As an example, the thermal behavior of two different kinds of nanoparticles is compared. The results show that, under identical conditions, the use of PEGylated gold nanorods allows for a more efficient heating compared with bare nanorods, and therefore, it results in a more effective therapy.

Influence of the Fiber Alignment in the Ballistic Performance of Dyneema Non-Woven Fabrics

The aim of this study was the determination of the deforming micromechanisms of needlepunched felts subjected to impact loads. A large experimental campaign has been carried out to analyze the influence of the fiber alignment in the ballistic performance. Ballistic limit curves of predeformed samples were compared. The fiber realignment was experimentally measure by means of 2D X-Ray diffraction. Higher specific absorption was observed for samples with a more isotropic mechanical response. A constitutive physicallybased model was developed within the context of the finite element method, which provided the constitutive response for a mesodomain including micromechanical aspects as fiber alignment, fiber sliding and pull-out. The macroscopic response has been validated with the experimental results, showing a very good agreement. The absorbed energy by the material during the impact was predicted and the fiber realignment evolution was also obtained.

Análisis dinámico experimental y numérico de una presa bóveda : ajuste del modelo

El objetivo de este trabajo es analizar las propiedades dinámicas de una presa bóveda de doble curvatura (presa de La Tajera, Guadalajara) para ajustar un modelo de elementos finitos. Para ello se han utilizado acelerómetros de alta sensibilidad sincronizados inalámbricamente. Se han obtenido las frecuencias, amortiguamientos y formas modales frente a los efectos de las acciones de tipo ambiental (viento, paso de vehículos). Se ha modelado mediante elementos finitos la presa y su cimiento incorporando el efecto del nivel del embalse. Con las propiedades dinámicas de la estructura halladas numéricamente se ha realizado un plan de medidas en los puntos que se consideraban más significativos. Tras realizar las medidas, se ha procedido al análisis de resultados mediante un Análisis Modal Operacional. Ello permite estimar los parámetros modales (frecuencias, amortiguamientos y formas modales) experimentalmente y se ha valorado el alcance de los mismos. Posteriormente viene la parte fundamental de este trabajo, que es el ajuste del modelo de elementos finitos inicial considerando el comportamiento dinámico obtenido experimentalmente. El modelo actualizado puede utilizarse dentro de un sistema de detección de daños, o por ejemplo, para el estudio del comportamiento ante un sismo considerando la interacción presa-embalse-cimiento. The purpose of this paper is to study the dynamic characteristics of a double curvature arch dam (La Tajera arch dam) for a Finite Element Model Updating. To achieve it, high sensitivity accelerometers synchronized wirelessly have been used. The system modal dampings, natural frequencies mode shapes are identified using output only identification techniques under environmental loads (wind, vehicles). Firstly, a finite element model of the dam-reservoir-foundation system was created. Once the dynamic properties of the structure were numerically obtained, a testing plan was then carried out identifying the most significant test points. After the measurements were carried out, an Operational Modal Analysis was performed to obtain experimentally the structure dynamic properties: natural frequencies, modal dampings and mode shapes. experimentally and to assess its reach. Then, the finite element model updating of the initial model was carried out to match the recorded dynamic behavior. The updated model may be used within a structural health monitoring and damage detection system or, as it is proposed on this thesis, for the analysis of the seismic response of arch dam-reservoir-foundation coupled systems

La memoria en el proceso creativo de Juan Muñoz = Memory in the creative process of Juan Muñoz

Esta tesis integra un estudio reflexivo sobre la relación de dependencia entre la creación y la memoria a través del análisis de la última obra del escultor Juan Muñoz: Double Bind (Tate Modern, Londres, 2001). Desde esta posición es obligado replantear el análisis de la obra, lo que hace necesario su estudio cubriendo el mayor espectro posible de información accesible más allá de la obra en sí, para aproximarse a la convergencia entre memoria y creación. La perspectiva de análisis propuesta abre camino a nuevas consideraciones so¬bre la relevancia del conocimiento en el desarrollo del proceso creativo. Este análisis no debe tan sólo suponer una aportación al conocimiento del trabajo de Juan Muñoz. Debe también desprenderse de él la innegable participación y necesaria lectura del pasado en el presente. La amnesia de los tiempos pasados impide completar el atlas de imágenes en las que se apoya la creación impidiendo el conocimiento del origen de las fuentes de inspi¬ración y las bases de la creación de una determinada obra. Este hecho limita y distorsiona sus posibles interpretaciones. Pretendo un acercamiento al entendimiento de la forma de mirar y de crear a través del tiempo que es memoria. La memoria tiene un cometido de crucial importancia para la actividad mental y juega un papel fundamental en la conducta y en la creación. La obra es el resultado de la búsqueda de una idea que exprese algo que el creador no puede ex¬presar de otra manera. Es la necesidad de expresar las ideas mediante un lenguaje que se desarrolla en el tiempo y en el espacio, reflejo del ser que responde al pensamiento. Es una forma de experiencia donde subyacen las sendas del pasado y donde se plantea el futuro. Sólo el creador accede a la obra desde dentro, el observador llega a ella desde el exterior y mediante su propia subjetividad. Las obras son formas de experiencia de sus autores, comunicar el mensaje de dicha experiencia supone por tanto interpretar. Persiguiendo la necesidad de saber y entender, pretender explicar el sentido de una cosa implica una apreciación intencionada asociada al entendimiento del intérprete. Las obras son produc¬tos que portan un mensaje y que contienen en su estructura las trazas del tiempo vivido por su creador. Si se quiere adquirir un acercamiento que represente la posición de un autor, será necesario no solo mirar a través de ella, si no introducirse en el contexto de su historia. Mirar hacia atrás, hacia la profundidad del presente para tener conciencia del pensamiento presente y futuro. Recorrer de este modo la instalación Double Bind de Juan Muñoz proporciona una síntesis de sus preocupaciones e intereses a la vez que aporta un conocimiento no necesariamente inmediato, pero relevante y trascendente de la obra, su creador y la historia. ABSTRACT This thesis comprises a reflective study of the dependence relationship between creation and memory through the analysis of the latest work by the sculptor Juan Muñoz: Double Bind (Tate Modern, London, 2001). From this position, it is mandatory to rethink the analysis of the work, making it necessary to cover the widest possible range of information available beyond the work itself, in order to obtain a closer view of the convergence between memory and creation. The proposed analytical approach opens up new considerations on the relevance of knowledge during the development of the creative process. This analysis should not only make a contribution to the knowledge of the work of Juan Muñoz. It should also infer the undeniable involvement and the necessary reading of the past in the present. Amnesia regarding past makes it impossible to complete the atlas of images on which the creation is based, blocking knowledge of the origin of the sources of inspiration and the basis for the creation of a specific work. This fact limits and distorts its possible interpretations. My intention is an approach to how to understand memory as the way of looking and creating over time. Memory has a crucial role to mental activity and plays a key role in behaviour and creation. The work is the result of finding an idea that expresses something that the creator can not express otherwise. It is the need to express ideas by means of a language that develops throughout time and space, a reflection of the being that responds to the thought. It is a way of experience underlying the paths of the past and where the future is set out. Only the creator can access the work from the inside. The observer sees it from the outside and in accordance with his/her own subjectivity. The works form a part of the experience of their authors, thus implying the interpretation of the message of their experience being passed on. The pursuit of knowledge and understanding, and trying to explain the meaning of something implies a deliberate appreciation associated with the understanding of the interpreter. The works are products bearing a message and containing in their structure traces of the time lived by their creator. If one wants to come close to what the author’s posture represents, it will not only be necessary to penetrate it, but also to introduce oneself into the context of its history. Take a look back, towards the depth of the present in order to become aware of present and future thinking. To go across the installation of Double Bind by Juan Muñoz in this way offers a synthesis of his concerns and interests while also providing a not necessarily immediate knowledge, but one which is relevant and important to the work, its creator and history.

A mutant of Mycobacterium smegmatis defective in the biosynthesis of mycolic acids accumulates meromycolates

Mycolic acids are a major constituent of the mycobacterial cell wall, and they form an effective permeability barrier to protect mycobacteria from antimicrobial agents. Although the chemical structures of mycolic acids are well established, little is known on their biosynthesis. We have isolated a mycolate-deficient mutant strain of Mycobacterium smegmatis mc2-155 by chemical mutagenesis followed by screening for increased sensitivity to novobiocin. This mutant also was hypersensitive to other hydrophobic compounds such as crystal violet, rifampicin, and erythromycin. Entry of hydrophobic probes into mutant cells occurred much more rapidly than that into the wild-type cells. HPLC and TLC analysis of fatty acid composition after saponification showed that the mutant failed to synthesize full-length mycolic acids. Instead, it accumulated a series of long-chain fatty acids, which were not detected in the wild-type strain. Analysis by 1H NMR, electrospray and electron impact mass spectroscopy, and permanganate cleavage of double bonds showed that these compounds corresponded to the incomplete meromycolate chain of mycolic acids, except for the presence of a β-hydroxyl group. This direct identification of meromycolates as precursors of mycolic acids provides a strong support for the previously proposed pathway for mycolic acid biosynthesis involving the separate synthesis of meromycolate chain and the α-branch of mycolic acids, followed by the joining of these two branches.

The theoretical limits of DNA sequence discrimination by linked polyamides

Linked polyamides bind in the minor groove of double-stranded DNA in a partially sequence-specific manner. This report analyzes the theoretical limits of DNA sequence discrimination by linked polyamides composed of two to four different types of heterocyclic rings, determining (i) the optimal choice of base-binding specificity for each ring and (ii) the optimal design for a polyamide composed of these rings to target a given DNA sequence and designed to maximize the fraction of the total polyamide binding to the specified target sequence relative to all other sequences. The results show that, fortuitously, polyamides composed of pyrrole, a naturally occurring G-excluding element, and imidazole, a rationally designed G-favoring element, have features similar to the theoretical optimum design for polyamides composed of two different rings. The results also show that, in polyamides composed of two or three types of heterocyclic rings, choosing a nonspecific “placeholder” ring, which binds equally strongly to each of the four bases, along with one or two base-specific rings will often enhance sequence specificity over a polyamide composed entirely of base-specific rings.

Heteroduplex joint formation in Escherichia coli recombination is initiated by pairing of a 3′-ending strand

The formation of heteroduplex joints in Escherichia coli recombination is initiated by invasion of double-stranded DNA by a single-stranded homologue. To determine the polarity of the invasive strand, linear molecules with direct terminal repeats were released by in vivo restriction of infecting chimeric phage DNA and heteroduplex products of intramolecular recombination were analyzed. With this substrate, the invasive strand is expected to be incorporated into the circular crossover product and the complementary strand is expected to be incorporated into the reciprocal linear product. Strands of both polarities were incorporated into heteroduplex structures, but only strands ending 3′ at the break were incorporated into circular products. This result indicates that invasion of the 3′-ending strand initiates the heteroduplex joint formation and that the complementary 5′-ending strand is incorporated into heteroduplex structures in the process of reciprocal strand exchange. The polarity of the invasive strand was not affected by recD, recJ, or xonA mutations. However, xonA and recJ mutations increased the proportion of heteroduplexes containing 5′-ending strands. This observation suggests that RecJ exonuclease and exonuclease I may enhance recombination by degrading the displaced strands during branch migration and thereby causing strand exchange to be unidirectional.