New Intermediate band sulphide nanoparticles acting in the full visible light range spectra as an active photocatalyst

Nowadays one of the challenges of materials science is to find new technologies that will be able to make the most of renewable energies. An example of new proposals in this field are the intermediate-band (IB) materials, which promise higher efficiencies in photovoltaic applications (through the intermediate band solar cells), or in heterogeneous photocatalysis (using nanoparticles of them, for the light-induced degradation of pollutants or for the efficient photoevolution of hydrogen from water). An IB material consists in a semiconductor in which gap a new level is introduced [1], the intermediate band (IB), which should be partially filled by electrons and completely separated of the valence band (VB) and of the conduction band (CB). This scheme (figure 1) allows an electron from the VB to be promoted to the IB, and from the latter to the CB, upon absorption of photons with energy below the band gap Eg, so that energy can be absorbed in a wider range of the solar spectrum and a higher current can be obtained without sacrificing the photovoltage (or the chemical driving force) corresponding to the full bandgap Eg, thus increasing the overall efficiency. This concept, applied to photocatalysis, would allow using photons of a wider visible range while keeping the same redox capacity. It is important to note that this concept differs from the classic photocatalyst doping principle, which essentially tries just to decrease the bandgap. This new type of materials would keep the full bandgap potential but would use also lower energy photons. In our group several IB materials have been proposed, mainly for the photovoltaic application, based on extensively doping known semiconductors with transition metals [2], examining with DFT calculations their electronic structures. Here we refer to In2S3 and SnS2, which contain octahedral cations; when doped with Ti or V an IB is formed according to quantum calculations (see e.g. figure 2). We have used a solvotermal synthesis method to prepare in nanocrystalline form the In2S3 thiospinel and the layered compound SnS2 (which when undoped have bandgaps of 2.0 and 2.2 eV respectively) where the cation is substituted by vanadium at a ?10% level. This substitution has been studied, characterizing the materials by different physical and chemical techniques (TXRF, XRD, HR-TEM/EDS) (see e.g. figure 3) and verifying with UV spectrometry that this substitution introduces in the spectrum the sub-bandgap features predicted by the calculations (figure 4). For both sulphide type nanoparticles (doped and undoped) the photocatalytic activity was studied by following at room temperature the oxidation of formic acid in aqueous suspension, a simple reaction which is easily monitored by UV-Vis spectroscopy. The spectral response of the process is measured using a collection of band pass filters that allow only some wavelengths into the reaction system. Thanks to this method the spectral range in which the materials are active in the photodecomposition (which coincides with the band gap for the undoped samples) can be checked, proving that for the vanadium substituted samples this range is increased, making possible to cover all the visible light range. Furthermore it is checked that these new materials are more photocorrosion resistant than the toxic CdS witch is a well know compound frequently used in tests of visible light photocatalysis. These materials are thus promising not only for degradation of pollutants (or for photovoltaic cells) but also for efficient photoevolution of hydrogen from water; work in this direction is now being pursued.

A function using cubic splines for the analysis of alpha--particles spectra from silicon detectors

A function based on the characteristics of the alpha-particle lines obtained with silicon semiconductor detectors and modi"ed by using cubic splines is proposed to parametrize the shape of the peaks. A reduction in the number of parameters initially considered in other proposals was carried out in order to improve the stability of the optimization process. It was imposed by the boundary conditions for the cubic splines term. This function was then able to describe peaks with highly anomalous shapes with respect to those expected from this type of detector. Some criteria were implemented to correctly determine the area of the peaks and their errors. Comparisons with other well-established functions revealed excellent agreement in the "nal values obtained from both "ts. Detailed studies on reliability of the "tting results were carried out and the application of the function is proposed. Although the aim was to correct anomalies in peak shapes, the peaks showing the expected shapes were also well "tted. Accordingly, the validity of the proposal is quite general in the analysis of alpha-particle spectrometry with semiconductor detectors.

Highly correlated ab initio study of the far infrared spectra of methyl acetate

Highly correlated ab initio calculations (CCSD(T)) are used to compute gas phase spectroscopic parameters of three isotopologues of the methyl acetate (CH3COOCH3, CD3COOCH3, and CH3COOCD3), searching to help experimental assignments and astrophysical detections. The molecule shows two conformers cis and trans separated by a barrier of 4457 cm−1. The potential energy surface presents 18 minima that intertransform through three internal rotation motions. To analyze the far infrared spectrum at low temperatures, a three-dimensional Hamiltonian is solved variationally. The two methyl torsion barriers are calculated to be 99.2 cm−1 (C–CH3) and 413.1 cm−1 (O–CH3), for the cis-conformer. The three fundamental torsional band centers of CH3COOCH3 are predicted to lie at 63.7 cm−1 (C–CH3), 136.1 cm−1 (O–CH3), and 175.8 cm−1 (C–O torsion) providing torsional state separations. For the 27 vibrational modes, anharmonic fundamentals and rovibrational parameters are provided. Computed parameters are compared with those fitted using experimental data.

Design energy input spectra for high seismicity regions based on Turkish registers

This work proposes design energy spectra in terms of an equivalent velocity, intended for regions with design peak acceleration 0.3 g or higher. These spectra were derived through linear and nonlinear dynamic analyses on a number of selected Turkish strong ground motion records. In the long and mid period ranges the analyses are linear, given the relative insensitivity of the spectra to structural parameters other than the fundamental period; conversely, in the short period range, the spectra are more sensitive to the structural parameters and, hence, nonlinear analyses are required. The selected records are classified in eight groups with respect to soil type (stiff or soft soil), the severity of the earthquake in terms of surface magnitude Ms(Ms≤ 5.5 and Ms> 5.5) and the relevance of the near-source effects (impulsive or vibratory). For each of these groups, median and characteristic spectra are proposed; such levels would respectively correspond to 50 and 95 % percentiles. These spectra have an initial linear growing branch in the short period range, a horizontal branch in the mid period range and a descending branch in the long period range. Empirical criteria for estimating the hysteretic energy from the input energy are suggested. The proposed design spectra are compared with those obtained from other studies.

Neutron spectra and dosimetric assessment around a neutron Howitzer container

The neutron Howitzer container at the Neutron Measurements Laboratory of the Nuclear Engineering Department of the Polytechnic University of Madrid (UPM), is equipped with a 241Am-Be neutron source of 74 GBq in its center. The container allows the source to be in either the irradiation or the storage position. To measure the neutron fluence rate spectra around the Howitzer container, measurements were performed using a Bonner spheres spectrometer and the spectra were unfolded using the NSDann program. A calibrated neutron area monitor LB6411 was used to measure the ambient dose equivalent rates, H*(10). Detailed Monte-Carlo simulations were performed to calculate the measured quantities at the same positions. The maximum relative deviation between simulations and measurements was 19.53%. After validation, the simulated model was used to calculate the equivalent dose rate in several key organs of a voxel phantom. The computed doses in the skin and lenses of the eyes are within the ICRP recommended dose limits, as is the H*(10) value for the storage position.

Elimination of variability sources in NIR spectra for the determination of fat content in olive fruits

Models for prediction of oil content as percentage of dried weight in olive fruits were comput- ed through PLS regression on NIR spectra. Spectral preprocessing was carried out by apply- ing multiplicative signal correction (MSC), Sa vitzky–Golay algorithm, standard normal variate correction (SNV), and detrending (D) to NIR spectra. MSC was the preprocessing technique showing the best performance. Further reduction of variability was performed by applying the Wold method of orthogonal signal correction (OSC). The calibration model achieved a R 2 of 0.93, a SEPc of 1.42, and a RPD of 3.8. The R 2 obtained with the validation set remained 0.93, and the SEPc was 1.41.

Identification of Ultraviolet radiation induced Gallic acid and Caffeic acid formation in Palm juice (Borassus flabellifer) by HPLC & Mass Spectra Technique.

Palm juice, a common-cheap-antioxidants rich natural plant juice has been investigated for optimizing the effect of UV-radiation on the antioxidant activity using a DPPH free radical scavenging activity method. In this study separate set of samples of raw palm juice has been treated with 365 and 254 nm UV-lights (UVL) respectively for different exposure time. When exposed for 15 min with 365 nm UVL induces concentration factor of caffeic acid, whereas, 254 nm UVL induces gallic acid accumulation, but overall antioxidant activity was higher for 365 nm UVradiation. Caffeic acid and other polyphenol compounds are increased by 5.5 ± 0.5 % than normal palm juice, observed after irradiation with 365 nm UVL. Even after the exposure of UV irradiation for 15 min, did not affect on peptide bond modification of protein molecules present in palm juice, therefore a green effect of UVL is explored for the effective increase of antioxidant activity.

Propiedades ópticas y estructurales de nanoestructuras de Zn(Cd)(Mg)O

En la presente tesis doctoral se ha realizado un estudio utilizando diferentes técnicas de crecimiento (RPE-MOCVD y spray pyrolysis) y estructuras (nanohilos, pozos y puntos cuánticos y capas) con el objetivo de desarrollar dispositivos que cubran desde el rango visible hasta el ultravioleta. Es por esta razón por la que se han elegido materiales basados en ZnO, debido a la posibilidades que estos ofrecen para variar su bandgap en un amplio rango de energías. Prueba de ello es que en este estudio se ha conseguido cubrir un rango espectral desde 1.86 hasta 4.11 eV, estudiandose además fenómenos físicos como son la difusión e incorporaci ón de la aleación o la adsorción de gases en la super_cie, lo que ha permitido la fabricación de diferentes fotodetectores de gran sensibilidad. Por todo ello, los resultados obtenidos en esta tesis suponen una gran contribución al conocimiento de las propiedades físicas de las aleaciones de Zn(Cd)O y Zn(Mg)O para potenciales aplicaciónes en dispositivos que operen en el rango visible y ultravioleta del espectro, respectivamente. En esta memoria se da en primer lugar una visión de las propiedades de materiales basados en ZnO, entrando en detalle en una de las ventajas que este presenta, la facilidad que tiene este material para formar nanoestructuras. En el capítulo 3 se dan los conceptos teóricos necesarios para comprender las propiedades ópticas de este tipo de materiales, mostrando también los resultados más reseñables obtenidos en ZnO. En los capítulos referentes a los resultados se pueden diferenciar dos grandes bloques. En el primer bloque de resultados se han analizado nanohilos y pozos cuánticos de Zn(Cd)O crecidos por la técnica de RPE-MOCVD (Capítulos 4 y 5). En el segundo se expondrá el estudio realizado sobre capas y puntos cuánticos de Zn(Mg)O crecidos por la técnica spray pyrolysis como se describe en mayor detalle a continuación. Nanohilos y pozos cuánticos de Zn(Cd)O crecidos por RPE-MOCVD Teóricamente aleando el ZnO con CdO es posible disminuir el valor del band- gap desde 3.37 eV hasta 0.95 eV, cubriendo por completo el espectro visible. El desarrollo del ternario Zn(Cd)O permitiría la fabricación de heteroestructuras y pozos cuánticos, muy importantes en el desarrollo de dispositivos optoelectrónicos que cubran la parte visible del espectro. Sin embargo, la diferencia de estructura cristalina entre estos dos materiales junto a la baja solubilidad del Cd y su alta presión de vapor, di_culta la obtención de material de alta calidad cristalina con alto contenido en Cd. En esta tesis doctoral se ha realizado una completa caracterización óptica y estructural de nanohilos de Zn(Cd)O credidos por la técnica de RPE-MOCVD. Estos nanohilos tinene unas longitudes comprendidas entre 1 y 3 _m y diámetros entre 100 y 200 nm. La concentración máxima introducida de Cd en estas estructuras ha sido de hasta un 54% manteniendo la estructura wurtzita del ZnO, siendo este el mayor contenido de Cd introducido hasta la fecha en nanostructuras basada en ZnO. Este hecho se traduce en una variación de la energía de emisión entre 3.31 y 1.86 eV con el aumento en Cd. El uso de diferentes técnicas de alta resoluci ón de caracterización estructural ha permitido demostrar la presencia de una sola fase estructural wurtzita sin observarse ningún indicio de separación de fases ni acumulación de Cd a lo largo del nanohilo para todos los contenidos de Cd. Con el propósito de fabricar dispositivos en nanohilos individuales, parte de esta tesis doctoral ha estado dedicada a estudiar el impacto que el recocido térmico tiene en las propiedades ópticas y eléctricas de nanohilos de Zn(Cd)O. El recocido térmico es un proceso clave en la optimización de dispositivos, ya sea para la obtenci ón de contactos óhmicos, reducción de defectos o difusión de dopantes por ejemplo. En este estudio se ha observado una mejora muy signi_cativa de las propiedades de emisión de los nanohilos cuando estos eran recocidos a temperaturas mayores que la de crecimiento (300 oC). En las muestras con Cd se ha observado además que el recocido también produce un desplazamiento de la emisión hacia mayores energías debido a una reducción homogénea del contenido de Cd. Medidas de fotoluminiscencia con resolución temporal muestran el impacto que tiene la localización del excitón en las _uctuaciones de potencial, debidas a una distribución estadística del Cd, en la dinámica de los portadores. Comparando el tiempo de vida de los portadores entre los nanohilos recocidos y sin recocer se ha observado un aumento de este parámetro en las estructuras recocidas. Este aumento es fundamentalmente debido a una reducción de centros de recombinación no radiativa asociados a defectos presentes a lo largo del nanohilo. Además, se ha estudiado la evolución de los tiempos de vida de los portadores en función de la temperatura, registrándose una menor estabilidad con la temperatura de los tiempos de vida en las muestras recocidas. Este resultado sugiere que el recocido térmico consigue reducir parte del desorden de la aleación en la estructura. Tras haber caracterizados los nanohilos se desarrollaron una serie de procesa dos para la fabricación de dispositivos basados en nanohilos individuales. Se fabricaron en concreto fotodetectores sensibles al UV, en los que se observó también la alta sensibilidad que muestran a la adsorción de gases en la super_cie, incrementada por la gran relación super_cie/volúmen característica de las nanoestructuras. Estos procesos de adsorción observados tienen un impacto directo sobre las propiedades ópticas y electricas de los dispositivos como se ha demostrado. Por ello que en esta tesis se hayan estudiado en detalle este tipo de procesos, ideando maneras para tener un mayor control sobre ellos. Finalmente se crecieron estructuras de pozos cuántico de ZnCdO/ZnO en nanohilos con contenidos de Cd nominales de 54 %. Las medidas ópticas realizadas mostraron como al aumentar la anchura del pozo de 0.7 a 10 nm, la emisión relacionada con el pozo se desplazaba entre 3.30 y 1.97 eV. Este gran desplazamiento representa el mayor obtenido hasta la fecha en pozos cuánticos de ZnCdO/ZnO. Sin embargo, al caracterizar estructuralmente estas muestras se observó la presencia de procesos de difusión de Cd entre el pozo y la barrera. Como se ha podido medir, este tipo de procesos reducen sustancialmente la concentración de Cd en el pozo al difundirse parte a la barrera. cambiando completamente la estructura de bandas nominal de estas estructuras. Este estudio demuestra la importancia del impacto de los procesos de difusión en la interpretación de los efectos de con_namiento cuántico para este tipo de estructuras. Capas y puntos cuánticos de Zn(Mg)O crecidos por spray pyrolysis La técnica de spray pyrolysis, debido a su simplicidad, bajo coste y capacidad de crecer sobre grandes áreas conservando una alta calidad cristalina presenta un gran interés en la comunidad cientí_ca para el potencial desarrollo de dispositivos comerciales. En esta tesis se ha estudiado las propiedades ópticas y eléctricas de capas y puntos cuánticos de Zn(Mg)O crecidos por esta técnica. Al contrario que pasa con el Cd, al introducir Mg en la estructura wurtzita de ZnO se consigue aumentar el bandgap del semiconductor. Sin embargo, al igual que pasa con el CdO, la diferencia de estructura cristalina entre el ZnO y el MgO limita la cantidad de Mg que se puede incorporar, haciendo que para una cierta concentración de Mg aparezcan el fenómeno de separación de fases. En esta tesis se ha conseguido incorporar hasta un contenido de Mg del 35% en la estructura wurtzita del ZnO utilizando la técnica de spray pyrolysis, resultado que representa la mayor concentración de Mg publicada hasta la fecha. Este hecho ha posibilitado variar la energía del borde de absorción desde 3.30 a 4.11 eV. En estas capas se ha realizado una completa caracterización óptica observándose una diferencia entre las energías del borde de absorción y del máximo de emisión creciente con el contenido en Mg. Esta diferencia, conocida como desplazamiento de Stokes, es debida en parte a la presencia de _uctuaciones de potencial producidas por un desorden estadístico de la aleación. Se han fabricado fotodetectores MSM de alta calidad utilizando las capas de Zn(Mg)O previamente caracterizadas, observándose un desplazamiento del borde de absorción con el aumento en Mg desde 3.32 a 4.02 eV. Estos dispositivos muestran altos valores de responsividad (10-103 A/W) y altos contrastes entre la responsividad bajo iluminación y oscuridad (10-107). Estos resultados son en parte debidos a la presencia de mecanismos de ganancia y una reducción de la corriente de oscuridad en las muestras con alto contenido de Mg. Utilizando esta misma técnica de crecimiento se han crecido puntos de Zn(Mg)O con concentraciones nominales de Mg entre 0 y 100 %, con dimensiones medias entre 4 y 6 nm. Las medidas estructurales realizadas muestran que hasta un valor de Mg de 45 %, los puntos están compuestos por una única fase estructural, wurtzita. A partir de esa concentración de Mg aparece una fase cúbica en los puntos, coexistiendo con la fase hexagonal hasta una concentración nominales del 85 %. Para concentraciones mayores de Mg, los puntos muestran una única fase estructural cúbica. Medidas de absorción realizadas en estos puntos de Zn(Mg)O muestran un desplazamiento del borde de absorción entre 3.33 y 3.55 eV cuando la concentraci ón de Mg en los puntos aumenta hasta el 40 %. Este desplazamiento observado es debido solamente a la fase wurtzita del Zn(Mg)O donde se incorpora el Mg. ABSTRACT This PhD theis presents a study using di_erent growth techniques (RPEMOCVD and spray pyrolysis) and structures (nanowires, quantum dots and wells and layers) in order to develop devices that extend from the visible to the ultraviolet range. For this reason ZnO based materials have been choosen, because they o_er the possibility to tunne the bandgap in this energy range. Proof of this is that this study has managed to cover a spectral range from 1.86 to 4.11 eV, also being studied physical phenomena such as di_usion and incorporation of alloy or adsorption of gases on the surface, allowing the develop di_erent highly sensitive photodetectors. Therefore, the results obtained in this thesis are a great contribution two large blockso the knowledge of the physical properties of alloys Zn(Cd)O and Zn(Mg)O for potential applications in devices that operate in the visible and ultraviolet range, respectively. In the _rst chapter, the general properties of ZnO-based materials are presented, showing the facilities that these kind of materials o_er to obtain di_erent nanoestructures. In Chapter 3, optical theoretical concepts are given to understand the optical properties of these materials, also showing the most signi_cant results of ZnO. In the chapters related with the results, two blocks could be distinguish. In the _rst one, Zn(Cd)O nanowires and quantum wells grown by RPE-MOCVD have been analyzed (Chapters 4 and 5). The second block of results shows the study performed in Zn(Mg)O _lms and quantum dots grown by spray pyrolysis. Zn(Cd)O nanowires and quantum wells grown by RPE-MOCVD In summary, the results of the PhD thesis are a great contribution to the knowledge of the physical properties of Zn(Cd)O and Zn(Mg)O alloys and their application for high performance devices operating in the visible and UV ranges, respectively. The performance of the device is still limited due to alloy solubility and p-doping stability, which opens a door for future research in this _eld. Theoretically, annealing ZnO with CdO allows to reduce the bandgap from 3.37 to 0.95 eV, covering the whole visible spectrum. The development of ZnCdO alloys allows the fabrication of heterostructures and quantum wells, necessary for the development of high performance optoelectronic devices. However, the di_erent crystal structures between CdO and ZnO and the low solubility of Cd and its high vapor pressure, hinders the growth of ZnCdO alloys with high Cd contents. In this PhD thesis Zn(Cd)O nanowires have been optically and structurally characterized, obtaining a maximum Cd content of 54% while maintaining their wurtzite structure. This Cd content, which allows lowering the bandgap down to 1.86 eV, is the highest concentration ever reported in nanostructures based on ZnO. The combination of optical and structural characterization techniques used during this thesis has allowed the demonstration of the presence of a single wurtzite structure, without observing any indication of phase separation or Cd accumulation along the nanowire. Annealing processes are essential in the fabrication of optoelectronic devices. For this reason, a complete study of the annealing e_ects in the optical and electrical properties of Zn(Cd)O nanowires has been performed. In the _rst place, annealing nanowires at higher temperatures than their growth temperature (300 oC) allows a signi_cant improvement of their emission properties. However, in the samples that contain Cd a shift in the emission towards higher energies has been observed due to a homogeneous reduction of the Cd content in the nanowires. Time resolved photoluminescence measurements show the impact of the exciton localization in the potential _uctuations due to a statistical alloy disorder. An increase in the carrier lifetime has been obtained for the annealed nanowires. This increase is mainly due to the reduction of non-radiative recombination centers associated with the defects present in the material. Furthermore, temperature dependent time resolved photoluminescence measurements suggest a reduction of the alloy disorder in the annealed samples. In this thesis, single nanowire photodetectors with a high responsivity in the UV range have been demonstrated. Due to the high surface/volume ratio, these structures are very sensitive to gas adsorption at the surface, which largely de_nes the optical and electrical properties of the material and, therefore, of the device. With the aim of obtaining time stable devices, the dynamic adsorption-desorption processes have been studied, developing di_erent approaches that allow a higher control over them. Finally, ZnCdO/ZnO quantum wells have been grown with a nominal Cd concentration of 54% inside the well. The performed optical measurements show that increasing the well width from 0.7 to 10 nm, shifts the emission related with the well from 3.30 to 1.97 eV. This result represents the highest shift reported in the literature. However, a detailed structural characterization shows the presence of di_usion phenomena which substantially reduce the concentration of Cd in the well, while increasing it in the barrier. This type of phenomena should be considered when ac curately interpretating the quantum con_nement e_ects in Zn(Cd)O/ZnO quantum wells. Theoretically, annealing ZnO with CdO allows to decrease the bandgap from 3.37 to 0.95 eV, covering the whole visible spectrum. Zn(Mg)O _lms and quantum dots grown by spray pyrolysis Due to its simplicity, low-cost and capacity to grow over large areas conserving a high crystal quality, spray pyrolysis technique presents a great interest in the scienti_c community for developing comercial devices. In this thesis, a complete study of the optical and structural properties of Zn(Mg)O _lms and quantum dots grown by spray pyrolysis has been performed. Contrary to Zn(Cd)O alloys, when introducing Mg in the ZnO wurtzite structure an increase in the bandgap in obtained. Once again, the di_erence in the crystal structure of ZnO and MgO limits the amount of Mg that can be introduced before phase separation appears. In this PhD thesis, a maximum Mg content of 35% has been incorporated in the wurtzite structure using spray pyrolysis. This variation in the Mg content translates into an increase of the absorption edge from 3.30 to 4.11 eV. Up to this date, this result represents the highest Mg content introduced by spray pyrolysis in a ZnO wurzite structure reported in the literature. The comparison of the emission and absorption spectra shows the presence of an increasing Stokes shift with Mg content. This phenomenon is partialy related with the presence of potential _uctuations due to an statistic alloy disorder. MSM photodetectors have been processed on previously characterized Zn(Mg)O _lms. These devices have shown a shift in the absorption edge from 3.32 to 4.02 eV with the increase in Mg content, high responsivity values (10-103 A/W) and high contrast ratios between illuminated and dark responsivities (10-107). These values are explained by the presence of a gain mechanism and a reduction of dark current in the ZnMgO samples. Zn(Mg)O quantum dots have also been grown using spray pyrolysis with Mg concentrations between 0 and 100% and with average widths ranging 4 to 6 nm. Structural measurements show that at a Mg concentration of 45% the cubic phase appears, coexisting with the hexagonal phase up to an 85% concentration of Mg content. From 85% onwards the quantum dots show only the cubic phase. Absorption measurements performed in these structures reveal a shift in the absorption edge from 3.33 to 3.55 eV when the Mg content increases up to 40 %.

Nonhydrogenic exciton spectrum in perovskite CH3NH3PbI3

The excitons in the orthorhombic phase of the perovskite CH3NH3PbI3 are studied using the effective mass approximation. The electron–hole interaction is screened by a distance-dependent dielectric function, as described by the Haken potential or the Pollmann–Büttner potential. The energy spectrum and the eigenfunctions are calculated for both cases. The results show that the Pollmann–Büttner model, using the corresponding parameters obtained from ab initio calculations, provides better agreement with the experimental results.

Altered spectra of hypermutation in antibodies from mice deficient for the DNA mismatch repair protein PMS2

Mutations are introduced into rearranged Ig variable genes at a frequency of 10−2 mutations per base pair by an unknown mechanism. Assuming that DNA repair pathways generate or remove mutations, the frequency and pattern of mutation will be different in variable genes from mice defective in repair. Therefore, hypermutation was studied in mice deficient for either the DNA nucleotide excision repair gene Xpa or the mismatch repair gene Pms2. High levels of mutation were found in variable genes from XPA-deficient and PMS2-deficient mice, indicating that neither nucleotide excision repair nor mismatch repair pathways generate hypermutation. However, variable genes from PMS2-deficient mice had significantly more adjacent base substitutions than genes from wild-type or XPA-deficient mice. By using a biochemical assay, we confirmed that tandem mispairs were repaired by wild-type cells but not by Pms2−/− human or murine cells. The data indicate that tandem substitutions are produced by the hypermutation mechanism and then processed by a PMS2-dependent pathway.

Multiple pathways for ultrafast transduction of light energy in the photosynthetic reaction center of Rhodobacter sphaeroides

A pathway of electron transfer is described that operates in the wild-type reaction center (RC) of the photosynthetic bacterium Rhodobacter sphaeroides. The pathway does not involve the excited state of the special pair dimer of bacteriochlorophylls (P*), but instead is driven by the excited state of the monomeric bacteriochlorophyll (BA*) present in the active branch of pigments along which electron transfer occurs. Pump-probe experiments were performed at 77 K on membrane-bound RCs by using different excitation wavelengths, to investigate the formation of the charge separated state P+HA−. In experiments in which P or BA was selectively excited at 880 nm or 796 nm, respectively, the formation of P+HA− was associated with similar time constants of 1.5 ps and 1.7 ps. However, the spectral changes associated with the two time constants are very different. Global analysis of the transient spectra shows that a mixture of P+BA− and P* is formed in parallel from BA* on a subpicosecond time scale. In contrast, excitation of the inactive branch monomeric bacteriochlorophyll (BB) and the high exciton component of P (P+) resulted in electron transfer only after relaxation to P*. The multiple pathways for primary electron transfer in the bacterial RC are discussed with regard to the mechanism of charge separation in the RC of photosystem II from higher plants.

Distinct spectra of somatic mutations accumulated with age in mouse heart and small intestine

Somatic mutation accumulation has been implicated as a major cause of cancer and aging. By using a transgenic mouse model with a chromosomally integrated lacZ reporter gene, mutational spectra were characterized at young and old age in two organs greatly differing in proliferative activity, i.e., the heart and small intestine. At young age the spectra were nearly identical, mainly consisting of G·C to A·T transitions and 1-bp deletions. At old age, however, distinct patterns of mutations had developed. In small intestine, only point mutations were found to accumulate, including G·C to T·A, G·C to C·G, and A·T to C·G transversions and G·C to A·T transitions. In contrast, in heart about half of the accumulated mutations appeared to be large genome rearrangements, involving up to 34 centimorgans of chromosomal DNA. Virtually all other mutations accumulating in the heart appeared to be G·C to A·T transitions at CpG sites. These results suggest that distinct mechanisms lead to organ-specific genome deterioration and dysfunction at old age.

Mitochondrial mutational spectra in human cells and tissues

We have found that human organs such as colon, lung, and muscle, as well as their derived tumors, share nearly all mitochondrial hotspot point mutations. Seventeen hotspots, primarily G → A and A → G transitions, have been identified in the mitochondrial sequence of base pairs 10,030–10,130. Mutant fractions increase with the number of cell generations in a human B cell line, TK6, indicating that they are heritable changes. The mitochondrial point mutation rate appears to be more than two orders of magnitude higher than the nuclear point mutation rate in TK6 cells and in human tissues. The similarity of the hotspot sets in vivo and in vitro leads us to conclude that human mitochondrial point mutations in the sequence studied are primarily spontaneous in origin and arise either from DNA replication error or reactions of DNA with endogenous metabolites. The predominance of transition mutations and the high number of hotspots in this short sequence resembles spectra produced by DNA polymerases in vitro.

Action spectra for phytochrome A- and B-specific photoinduction of seed germination in Arabidopsis thaliana.

We have examined the seed germination in Arabidopsis thaliana of wild type (wt), and phytochrome A (PhyA)- and B (PhyB)-mutants in terms of incubation time and environmental light effects. Seed germination of the wt and PhyA-null mutant (phyA) was photoreversibly regulated by red and far-red lights of 10-1,000 micromol m-2 when incubated in darkness for 1-14 hr, but no germination occurred in PhyB-null mutant (phyB). When wt seeds and the phyB mutant seeds were incubated in darkness for 48 hr, they synthesized PhyA during dark incubation and germinated upon exposure to red light of 1-100 nmol m-2 and far-red light of 0.5-10 micromol m-2, whereas the phyA mutant showed no such response. The results indicate that the seed germination is regulated by PhyA and PhyB but not by other phytochromes, and the effects of PhyA and PhyB are separable in this assay. We determined action spectra separately for PhyA- and PhyB-specific induction of seed germination at Okazaki large spectrograph. Action spectra for the PhyA response show that monochromatic 300-780 nm lights of very low fluence induced the germination, and this induction was not photoreversible in the range examined. Action spectra for the PhyB response show that germination was photoreversibly regulated by alternate irradiations with light of 0.01-1 mmol m-2 at wavelengths of 540-690 nm and 695-780 nm. The present work clearly demonstrated that PhyA photoirreversibly triggers the germination upon irradiations with ultraviolet, visible and far-red light of very low fluence, while PhyB controls the photoreversible effects of low fluence.