Water adsorption on O (2×2 )/Ru (0001): STM experiments and first-principles calculations

We present a combined theoretical and experimental study of water adsorption on Ru(0001) precovered with 0.25 ML (monolayer) of oxygen forming a (2×2) structure. Several structures were analyzed by means of density functional theory calculations for which scanning tunneling microscope (STM) simulations were performed and compared with experimental data. Up to 0.25 ML, the molecules bind to the exposed Ru atoms of the 2×2unit cell via the lone pair orbitals. The molecular plane is almost parallel to the surface with its H atoms pointing toward the chemisorbed O atoms of the 2×2 unit cell forming hydrogen bonds. The existence of these additional hydrogen bonds increases the adsorption energy of the water molecule to approximately 616meV, which is ∼220meV more stable than on the clean Ru(0001) surface with a similar configuration. The binding energy shows only a weak dependence on water coverage, with a shallow minimum for a row structure at 0.125 ML. This is consistent with the STM experiments that show a tendency of the molecules to form linear rows at intermediate coverage. Our calculations also suggest the possible formation of water dimers near 0.25 ML.This work has been supported by the Basque Departamento de Educación, the UPV/EHU Grant No. 9/UPV 00206.215-13639/2001, the Spanish Ministerio de Educación y Ciencia Grant No. FIS2004-06490-C3-00, the European Network of Excellence FP6-NoE NANOQUANTA Grant No. 500198-2, and the projects NANOMATERIALES and NANOTRON funded by the Basque Departamento de Industria, Comercio y Turismo within the ETORTEK program, and the Departamento para la Innovación y la Sociedad del Conocimiento from the Diputación Foral de Guipúzcoa. The experimental work was supported by the Director, Office of Energy Research, Office of Basic Energy Sciences, Materials Sciences Division, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. A.M. was financed by the Marie Curie Outgoing International Foundation, Project No. 514412.Peer reviewe

Chemical reactions of water molecules on Ru(0001) induced by selective excitation of vibrational modes

Tunneling electrons in a scanning tunneling microscope were used to excite specific vibrational quantum states of adsorbed water and hydroxyl molecules on a Ru(0 0 0 1) surface. The excited molecules relaxed by transfer of energy to lower energy modes, resulting in diffusion, dissociation, desorption, and surface-tip transfer processes. Diffusion of H{sub 2}O molecules could be induced by excitation of the O-H stretch vibration mode at 445 meV. Isolated molecules required excitation of one single quantum while molecules bonded to a C atom required at least two quanta. Dissociation of single H{sub 2}O molecules into H and OH required electron energies of 1 eV or higher while dissociation of OH required at least 2 eV electrons. In contrast, water molecules forming part of a cluster could be dissociated with electron energies of 0.5 eV

Structure and reactions of carbon and hydrogen on Ru(0001): A scanning tunneling microscopy study

The interaction between carbon and hydrogen atoms on a Ru(0001) surface was studied using scanning tunneling microscopy (STM), Density Functional Theory (DFT) and STM image calculations. Formation of CH species by reaction between adsorbed H and C was observed to occur readily at 100 K. When the coverage of H increased new complexes of the form CH+nH (n = 1, 2 and 3) were observed. These complexes, never observed before, might be precursors for further hydrogenation reactions. DFT analysis reveals that a considerable energy barrier exists for the CH+H {yields} CH{sub 2} reaction

Atomic species identification at the (101) anatase surface by simultaneous scanning tunnelling and atomic force microscopy

Anatase is a pivotal material in devices for energy-harvesting applications and catalysis. Methods for the accurate characterization of this reducible oxide at the atomic scale are critical in the exploration of outstanding properties for technological developments. Here we combine atomic force microscopy (AFM) and scanning tunnelling microscopy (STM), supported by first-principles calculations, for the simultaneous imaging and unambiguous identification of atomic species at the (101) anatase surface. We demonstrate that dynamic AFM-STM operation allows atomic resolution imaging within the materiala € s band gap. Based on key distinguishing features extracted from calculations and experiments, we identify candidates for the most common surface defects. Our results pave the way for the understanding of surface processes, like adsorption of metal dopants and photoactive molecules, that are fundamental for the catalytic and photovoltaic applications of anatase, and demonstrate the potential of dynamic AFM-STM for the characterization of wide band gap materialsWork supported by the NIMS (AA002 and AF006 projects), by the MEXT KAKENHI Grant Number 26104540, by the Charles University (GAUK 339311) and by the Spanish MINECO (projects PLE2009-0061, MAT2011- 023627 and CSD2010-00024). Computer time was provided by the Spanish Supercomputing Network (RES, Spain) at the MareNostrum III Supercomputer (BCS, Barcelona), and by the PRACE initiative (project RA0986) at the Curie Supercomputer (CEA, France). O.S and V.M. thank the Charles University-NIMS International Cooperative Graduate School Program. J.W.R. thanks NIMS for funding through the NIMS Internship Program and ICIQ for his ICIQ Fellowshi

Meta-analytic approach to the accurate prediction of secreted virulence effectors in gram-negative bacteria

<p>Abstract</p> <p>Background</p> <p>Many pathogens use a type III secretion system to translocate virulence proteins (called effectors) in order to adapt to the host environment. To date, many prediction tools for effector identification have been developed. However, these tools are insufficiently accurate for producing a list of putative effectors that can be applied directly for labor-intensive experimental verification. This also suggests that important features of effectors have yet to be fully characterized.</p> <p>Results</p> <p>In this study, we have constructed an accurate approach to predicting secreted virulence effectors from Gram-negative bacteria. This consists of a support vector machine-based discriminant analysis followed by a simple criteria-based filtering. The accuracy was assessed by estimating the average number of true positives in the top-20 ranking in the genome-wide screening. In the validation, 10 sets of 20 training and 20 testing examples were randomly selected from 40 known effectors of <it>Salmonella enterica </it>serovar Typhimurium LT2. On average, the SVM portion of our system predicted 9.7 true positives from 20 testing examples in the top-20 of the prediction. Removal of the N-terminal instability, codon adaptation index and ProtParam indices decreased the score to 7.6, 8.9 and 7.9, respectively. These discrimination features suggested that the following characteristics of effectors had been uncovered: unstable N-terminus, non-optimal codon usage, hydrophilic, and less aliphathic. The secondary filtering process represented by coexpression analysis and domain distribution analysis further refined the average true positive counts to 12.3. We further confirmed that our system can correctly predict known effectors of <it>P. syringae </it>DC3000, strongly indicating its feasibility.</p> <p>Conclusions</p> <p>We have successfully developed an accurate prediction system for screening effectors on a genome-wide scale. We confirmed the accuracy of our system by external validation using known effectors of <it>Salmonella </it>and obtained the accurate list of putative effectors of the organism. The level of accuracy was sufficient to yield candidates for gene-directed experimental verification. Furthermore, new features of effectors were revealed: non-optimal codon usage and instability of the N-terminal region. From these findings, a new working hypothesis is proposed regarding mechanisms controlling the translocation of virulence effectors and determining the substrate specificity encoded in the secretion system.</p

Increased Risk of Temporomandibular Joint Closed Lock: A Case-Control Study of ANKH Polymorphisms

Objectives: This study aimed to carry out a histological examination of the temporomandibular joint (TMJ) in ank mutant mice and to identify polymorphisms of the human ANKH gene in order to establish the relationship between the type of temporomandibular disorders (TMD) and ANKH polymorphisms.\ud \ud Materials and Methods: Specimens from the TMJ of ank mutant and wild-type mice were inspected with a haematoxylin and eosin staining method. A sample of 55 TMD patients were selected. Each was examined with standard clinical procedures and genotyping techniques.\ud \ud Results: The major histological finding in ank mutant mice was joint space narrowing. Within TMD patients, closed lock was more prevalent among ANKH-OR homozygotes (p = 0.011, OR = 7.7, 95% CI 1.6–36.5) and the elder (p = 0.005, OR = 2.4, 95% CI 1.3–4.3).\ud \ud Conclusions: Fibrous ankylosis was identified in the TMJ of ank mutant mice. In the human sample, ANKH-OR polymorphism was found to be a genetic marker associated with TMJ closed lock. Future investigations correlating genetic polymorphism to TMD are indicated

Surface species formed by the adsorption and dissociation of water molecules on Ru(0001) surface containing a small coverage of carbon atoms studied by scanning tunneling microscopy

The adsorption and dissociation of water on a Ru(0001) surface containing a small amount ({le} 3 %) of carbon impurities was studied by scanning tunneling microscopy (STM). Various surface species are formed depending on the temperature. These include molecular H{sub 2}O, H{sub 2}O-C complexes, H, O, OH and CH. Clusters of either pure H{sub 2}O or mixed H{sub 2}O-OH species are also formed. Each of these species produces a characteristic contrast in the STM images and can be identified by experiment and by ab initio total energy calculations coupled with STM image simulations. Manipulation of individual species via excitation of vibrational modes with the tunneling electrons has been used as supporting evidence

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead