Showing papers by "Technical University of Denmark published in 2007"

RNAmmer: consistent and rapid annotation of ribosomal RNA genes

Abstract: The publication of a complete genome sequence is usually accompanied by annotations of its genes. In contrast to protein coding genes, genes for ribosomal RNA (rRNA) are often poorly or inconsistently annotated. This makes comparative studies based on rRNA genes difficult. We have therefore created computational predictors for the major rRNA species from all kingdoms of life and compiled them into a program called RNAmmer. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project. A pre-screening step makes the method fast with little loss of sensitivity, enabling the analysis of a complete bacterial genome in less than a minute. Results from running RNAmmer on a large set of genomes indicate that the location of rRNAs can be predicted with a very high level of accuracy. Novel, unannotated rRNAs are also predicted in many genomes. The software as well as the genome analysis results are available at the CBS web server.

Identification of active edge sites for electrochemical H2 evolution from MoS2 nanocatalysts.

Abstract: The identification of the active sites in heterogeneous catalysis requires a combination of surface sensitive methods and reactivity studies. We determined the active site for hydrogen evolution, a reaction catalyzed by precious metals, on nanoparticulate molybdenum disulfide (MoS2) by atomically resolving the surface of this catalyst before measuring electrochemical activity in solution. By preparing MoS2 nanoparticles of different sizes, we systematically varied the distribution of surface sites on MoS2 nanoparticles on Au(111), which we quantified with scanning tunneling microscopy. Electrocatalytic activity measurements for hydrogen evolution correlate linearly with the number of edge sites on the MoS2 catalyst.

Locating proteins in the cell using TargetP, SignalP and related tools

Abstract: Determining the subcellular localization of a protein is an important first step toward understanding its function. Here, we describe the properties of three well-known N-terminal sequence motifs directing proteins to the secretory pathway, mitochondria and chloroplasts, and sketch a brief history of methods to predict subcellular localization based on these sorting signals and other sequence properties. We then outline how to use a number of internet-accessible tools to arrive at a reliable subcellular localization prediction for eukaryotic and prokaryotic proteins. In particular, we provide detailed step-by-step instructions for the coupled use of the amino-acid sequence-based predictors TargetP, SignalP, ChloroP and TMHMM, which are all hosted at the Center for Biological Sequence Analysis, Technical University of Denmark. In addition, we describe and provide web references to other useful subcellular localization predictors. Finally, we discuss predictive performance measures in general and the performance of TargetP and SignalP in particular.

Integration of biological networks and gene expression data using Cytoscape

Abstract: Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.

Morphology-based black and white filters for topology optimization

Abstract: To ensure manufacturability and mesh independence in density-based topology optimization schemes, it is imperative to use restriction methods. This paper introduces a new class of morphology-based restriction schemes that work as density filters; that is, the physical stiffness of an element is based on a function of the design variables of the neighboring elements. The new filters have the advantage that they eliminate grey scale transitions between solid and void regions. Using different test examples, it is shown that the schemes, in general, provide black and white designs with minimum length-scale constraints on either or both minimum hole sizes and minimum structural feature sizes. The new schemes are compared with methods and modified methods found in the literature.

The prevalence of food allergy: a meta-analysis.

Abstract: Background There is uncertainty about the prevalence of food allergy in communities. Objective To assess the prevalence of food allergy by performing a meta-analysis according to the method of assessment used. Methods The foods assessed were cow's milk, hen's egg, peanut, fish, shellfish, and an overall estimate of food allergy. We summarized the information in 5 categories: self-reported symptoms, specific IgE positive, specific skin prick test positive, symptoms combined with sensitization, and food challenge studies. We systematically searched MEDLINE and EMBASE for publications since 1990. The meta-analysis included only original studies. They were stratified by age groups: infant/preschool, school children, and adults. Results A total of 934 articles were identified, but only 51 were considered appropriate for inclusion. The prevalence of self-reported food allergy was very high compared with objective measures. There was marked heterogeneity between studies regardless of type of assessment or food item considered, and in most analyses this persisted after age stratification. Self-reported prevalence of food allergy varied from 1.2% to 17% for milk, 0.2% to 7% for egg, 0% to 2% for peanuts and fish, 0% to 10% for shellfish, and 3% to 35% for any food. Conclusion There is a marked heterogeneity in the prevalence of food allergy that could be a result of differences in study design or methodology, or differences between populations. Clinical implications We recommend that measurements be made by using standardized methods, if possible food challenge. We need to be cautious in estimates of prevalence based only on self-reported food allergy.

Scaling properties of adsorption energies for hydrogen-containing molecules on transition-metal surfaces.

Abstract: Density functional theory calculations are presented for CHx, x=0,1,2,3, NHx, x=0,1,2, OHx, x=0,1, and SHx, x=0,1 adsorption on a range of close-packed and stepped transition-metal surfaces. We find that the adsorption energy of any of the molecules considered scales approximately with the adsorption energy of the central, C, N, O, or S atom, the scaling constant depending only on x. A model is proposed to understand this behavior. The scaling model is developed into a general framework for estimating the reaction energies for hydrogenation and dehydrogenation reactions.

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

Abstract: The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.

A human phenome-interactome network of protein complexes implicated in genetic disorders

Abstract: We performed a systematic, large-scale analysis of human protein complexes comprising gene products implicated in many different categories of human disease to create a phenome-interactome network. This was done by integrating quality-controlled interactions of human proteins with a validated, computationally derived phenotype similarity score, permitting identification of previously unknown complexes likely to be associated with disease. Using a phenomic ranking of protein complexes linked to human disease, we developed a Bayesian predictor that in 298 of 669 linkage intervals correctly ranks the known disease-causing protein as the top candidate, and in 870 intervals with no identified disease-causing gene, provides novel candidates implicated in disorders such as retinitis pigmentosa, epithelial ovarian cancer, inflammatory bowel disease, amyotrophic lateral sclerosis, Alzheimer disease, type 2 diabetes and coronary heart disease. Our publicly available draft of protein complexes associated with pathology comprises 506 complexes, which reveal functional relationships between disease-promoting genes that will inform future experimentation.

Role of ventilation in airborne transmission of infectious agents in the built environment - a multidisciplinary systematic review.

Abstract: There have been few recent studies demonstrating a definitive association between the transmission of airborne infections and the ventilation of buildings. The severe acute respiratory syndrome (SARS) epidemic in 2003 and current concerns about the risk of an avian influenza (H5N1) pandemic, have made a review of this area timely. We searched the major literature databases between 1960 and 2005, and then screened titles and abstracts, and finally selected 40 original studies based on a set of criteria. We established a review panel comprising medical and engineering experts in the fields of microbiology, medicine, epidemiology, indoor air quality, building ventilation, etc. Most panel members had experience with research into the 2003 SARS epidemic. The panel systematically assessed 40 original studies through both individual assessment and a 2-day face-to-face consensus meeting. Ten of 40 studies reviewed were considered to be conclusive with regard to the association between building ventilation and the transmission of airborne infection. There is strong and sufficient evidence to demonstrate the association between ventilation, air movements in buildings and the transmission/spread of infectious diseases such as measles, tuberculosis, chickenpox, influenza, smallpox and SARS. There is insufficient data to specify and quantify the minimum ventilation requirements in hospitals, schools, offices, homes and isolation rooms in relation to spread of infectious diseases via the airborne route. PRACTICAL IMPLICATION: The strong and sufficient evidence of the association between ventilation, the control of airflow direction in buildings, and the transmission and spread of infectious diseases supports the use of negatively pressurized isolation rooms for patients with these diseases in hospitals, in addition to the use of other engineering control methods. However, the lack of sufficient data on the specification and quantification of the minimum ventilation requirements in hospitals, schools and offices in relation to the spread of airborne infectious diseases, suggest the existence of a knowledge gap. Our study reveals a strong need for a multidisciplinary study in investigating disease outbreaks, and the impact of indoor air environments on the spread of airborne infectious diseases.

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis

Abstract: We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the similar to 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.

Regularization Tools Version 4.0 for Matlab 7.3

Abstract: This communication describes version 4.0 of Regularization Tools, a Matlab package for analysis and solution of discrete ill-posed problems. The new version allows for under-determined problems, and it is expanded with several new iterative methods, as well as new test problems and new parameter-choice methods.

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

Abstract: JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR database—the JASPAR CORE sub-database—has increased by 12% in size, and three new specialized sub-databases have been added. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. JASPAR is available at http://jaspar.genereg.net.

Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction

Abstract: Reliable predictions of Cytotoxic T lymphocyte (CTL) epitopes are essential for rational vaccine design. Most importantly, they can minimize the experimental effort needed to identify epitopes. NetCTL is a web-based tool designed for predicting human CTL epitopes in any given protein. It does so by integrating predictions of proteasomal cleavage, TAP transport efficiency, and MHC class I affinity. At least four other methods have been developed recently that likewise attempt to predict CTL epitopes: EpiJen, MAPPP, MHC-pathway, and WAPP. In order to compare the performance of prediction methods, objective benchmarks and standardized performance measures are needed. Here, we develop such large-scale benchmark and corresponding performance measures and report the performance of an updated version 1.2 of NetCTL in comparison with the four other methods. We define a number of performance measures that can handle the different types of output data from the five methods. We use two evaluation datasets consisting of known HIV CTL epitopes and their source proteins. The source proteins are split into all possible 9 mers and except for annotated epitopes; all other 9 mers are considered non-epitopes. In the RANK measure, we compare two methods at a time and count how often each of the methods rank the epitope highest. In another measure, we find the specificity of the methods at three predefined sensitivity values. Lastly, for each method, we calculate the percentage of known epitopes that rank within the 5% peptides with the highest predicted score. NetCTL-1.2 is demonstrated to have a higher predictive performance than EpiJen, MAPPP, MHC-pathway, and WAPP on all performance measures. The higher performance of NetCTL-1.2 as compared to EpiJen and MHC-pathway is, however, not statistically significant on all measures. In the large-scale benchmark calculation consisting of 216 known HIV epitopes covering all 12 recognized HLA supertypes, the NetCTL-1.2 method was shown to have a sensitivity among the 5% top-scoring peptides above 0.72. On this dataset, the best of the other methods achieved a sensitivity of 0.64. The NetCTL-1.2 method is available at http://www.cbs.dtu.dk/services/NetCTL . All used datasets are available at http://www.cbs.dtu.dk/suppl/immunology/CTL-1.2.php .

Density functional theory calculations for the hydrogen evolution reaction in an electrochemical double layer on the Pt(111) electrode.

Abstract: We present results of density functional theory calculations on a Pt(111) slab with a bilayer of water, solvated protons in the water layer, and excess electrons in the metal surface. In this way we model the electrochemical double layer at a platinum electrode. By varying the number of protons/electrons in the double layer we investigate the system as a function of the electrode potential. We study the elementary processes involved in the hydrogen evolution reaction, 2(H+ + e−) → H2, and determine the activation energy and predominant reaction mechanism as a function of electrode potential. We confirm by explicit calculations the notion that the variation of the activation barrier with potential can be viewed as a manifestation of the Bronsted–Evans–Polanyi-type relationship between activation energy and reaction energy found throughout surface chemistry.

NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence.

Abstract: Background. Binding of peptides to Major Histocompatibility Complex (MHC) molecules is the single most selective step in the recognition of pathogens by the cellular immune system. The human MHC class I system (HLA-I) is extremely polymorphic. The number of registered HLA-I molecules has now surpassed 1500. Characterizing the specificity of each separately would be a major undertaking. Principal Findings. Here, we have drawn on a large database of known peptide-HLA-I interactions to develop a bioinformatics method, which takes both peptide and HLA sequence information into account, and generates quantitative predictions of the affinity of any peptide-HLA-I interaction. Prospective experimental validation of peptides predicted to bind to previously untested HLA-I molecules, cross-validation, and retrospective prediction of known HIV immune epitopes and endogenous presented peptides, all successfully validate this method. We further demonstrate that the method can be applied to perform a clustering analysis of MHC specificities and suggest using this clustering to select particularly informative novel MHC molecules for future biochemical and functional analysis. Conclusions. Encompassing all HLA molecules, this high-throughput computational method lends itself to epitope searches that are not only genome- and pathogen-wide, but also HLA-wide. Thus, it offers a truly global analysis of immune responses supporting rational development of vaccines and immunotherapy. It also promises to provide new basic insights into HLA structure-function relationships. The method is available at http://www.cbs.dtu.dk/services/NetMHCpan.

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

Abstract: Antigen presenting cells (APCs) sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II) molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC) and three mouse H2-IA alleles. The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR), we demonstrate a consistent gain in predictive performance by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors. The SMM-align method was shown to outperform other state of the art MHC class II prediction methods. The method predicts quantitative peptide:MHC binding affinity values, making it ideally suited for rational epitope discovery. The method has been trained and evaluated on the, to our knowledge, largest benchmark data set publicly available and covers the nine HLA-DR supertypes suggested as well as three mouse H2-IA allele. Both the peptide benchmark data set, and SMM-align prediction method (NetMHCII) are made publicly available.

Lake restoration: successes, failures and long‐term effects

Abstract: 1. Eutrophication constitutes a serious threat to many European lakes and many approaches have been used during the past 20–30 years to improve lake water quality. Results from the various lake restoration initiatives are diverse and the long-term effects are not well described. 2. In this study we evaluated data from more than 70 restoration projects conducted mainly in shallow, eutrophic lakes in Denmark and the Netherlands. Special focus was given to the removal of zooplanktivorous and benthivorous fish, by far the most common internal lake measure. 3. In more than half of the biomanipulation projects, Secchi depth increased and chlorophyll a decreased to less than 50% within the first few years. In some of the shallow lakes, total phosphorus and total nitrogen levels decreased considerably, indicating an increased retention or loss by denitrification. The strongest effects seemed to be obtained 4–6 years after the start of fish removal. 4. The long-term effect of restoration initiatives can only be described for a few lakes, but data from biomanipulated lakes indicate a return to a turbid state within 10 years or less in most cases. One of reasons for the lack of long-term effects may be internal phosphorus loading from a mobile pool accumulated in the sediment. 5. Synthesis and applications. Lake restoration, and in particular fish removal in shallow eutrophic lakes, has been widely used in Denmark and the Netherlands, where it has had marked effects on lake water quality in many lakes. Long-term effects ( > 8–10 years) are less obvious and a return to turbid conditions is often seen unless fish removal is repeated. Insufficient external loading reduction, internal phosphorus loading and absence of stable submerged macrophyte communities to stabilize the clear-water state are the most probable causes for this relapse to earlier conditions Eutrophication constitutes a serious threat to many European lakes and many approaches have been used during the past 20-30 years to improve lake water quality. Results from the various lake restoration initiatives are diverse and the long-term effects are not well described. In this study we evaluated data from more than 70 restoration projects conducted mainly in shallow, eutrophic lakes in Denmark and the Netherlands. Special focus was given to the removal of zooplanktivorous and benthivorous fish, by far the most common internal lake measure. In more than half of the biomanipulation projects, Secchi depth increased and chlorophyll a decreased to less than 50% within the first few years. In some of the shallow lakes, total phosphorus and total nitrogen levels decreased considerably, indicating an increased retention or loss by denitrification. The strongest effects seemed to be obtained 4-6 years after the start of fish removal. The long-term effect of restoration initiatives can only be described for a few lakes, but data from biomanipulated lakes indicate a return to a turbid state within 10 years or less in most cases. One of reasons for the lack of long-term effects may be internal phosphorus loading from a mobile pool accumulated in the sediment. Synthesis and applications. Lake restoration, and in particular fish removal in shallow eutrophic lakes, has been widely used in Denmark and the Netherlands, where it has had marked effects on lake water quality in many lakes. Long-term effects (> 8-10 years) are less obvious and a return to turbid conditions is often seen unless fish removal is repeated. Insufficient external loading reduction, internal phosphorus loading and absence of stable submerged macrophyte communities to stabilize the clear-water state are the most probable causes for this relapse to earlier conditions.

Generation and Photonic Guidance of Multi-Octave Optical-Frequency Combs

Abstract: Ultrabroad coherent comb-like optical spectra spanning several octaves are a chief ingredient in the emerging field of attoscience. We demonstrate generation and guidance of a three-octave spectral comb, spanning wavelengths from 325 to 2300 nanometers, in a hydrogen-filled hollow-core photonic crystal fiber. The waveguidance results not from a photonic band gap but from the inhibited coupling between the core and cladding modes. The spectrum consists of up to 45 high-order Stokes and anti-Stokes lines and is generated by driving the confined gas with a single, moderately powerful (10-kilowatt) infrared laser, producing 12-nanosecond-duration pulses. This represents a reduction by six orders of magnitude in the required laser powers over previous equivalent techniques and opens up a robust and much simplified route to synthesizing attosecond pulses.

Evolution of species interactions in a biofilm community

Abstract: Biofilms are specialized environments where communities of microorganisms are insulated from the outside world by an extracellular polymer matrix that they themselves secrete The resulting microbial mats have been compared to tropical rainforests in terms of complexity and biodiversity Selective pressures on such biofilms are likely to demand intense interactions between the individual bacteria, and an experiment with a simple community of two species (soil dwellers Pseudomonas putida and Acinetobacter sp) shows just how close that relationship is The physical structure of the community altered, to the mutual benefit of both species, as a result of a simple mutation in the genome of one of the species In the absence of a partner the mutation (in P putida) would have been deleterious This system demonstrates the importance of interspecies interactions, and may be useful in work on the evolution of these interactions Biofilms are specialized environments where one might predict that evolution demands intense interactions between bacteria However, by using two species, this paper demonstrates that genomic changes occur to favour species working together to enhance fitness Biofilms are spatially structured communities of microbes whose function is dependent on a complex web of symbiotic interactions1,2 Localized interactions within these assemblages are predicted to affect the coexistence of the component species3,4,5, community structure6 and function7,8,9,10, but there have been few explicit empirical analyses of the evolution of interactions11 Here we show, with the use of a two-species community, that selection in a spatially structured environment leads to the evolution of an exploitative interaction Simple mutations in the genome of one species caused it to adapt to the presence of the other, forming an intimate and specialized association The derived community was more stable and more productive than the ancestral community Our results show that evolution in a spatially structured environment can stabilize interactions between species, provoke marked changes in their symbiotic nature and affect community function

Role of autolysin-mediated DNA release in biofilm formation of Staphylococcus epidermidis

Abstract: Staphylococcus epidermidis has become a serious nosocomial pathogen frequently causing infections associated with implanted foreign materials. Biofilm formation is considered a major factor determining S. epidermidis pathogenicity in such device-associated infections. Here, evidence is presented that extracellular DNA is important for the initial phase of biofilm development by S. epidermidis on polystyrene or glass surfaces under static or hydrodynamic conditions. Comparative PCR amplification from S. epidermidis chromosomal and extracellular DNA indicated that the extracellular DNA is similar to chromosomal DNA. Experiments involving the S. epidermidis wild-type and an isogenic atlE mutant indicated that most of the extracellular DNA in S. epidermidis cultures and biofilms is generated through activity of the autolysin AtlE. The presented results suggest that extracellular DNA is generated in S. epidermidis populations through AtlE-mediated lysis of a subpopulation of the bacteria, and that the extracellular DNA promotes biofilm formation of the remaining population.

Current Status of Veterinary Vaccines

Abstract: The major goals of veterinary vaccines are to improve the health and welfare of companion animals, increase production of livestock in a cost-effective manner, and prevent animal-to-human transmission from both domestic animals and wildlife. These diverse aims have led to different approaches to the development of veterinary vaccines from crude but effective whole-pathogen preparations to molecularly defined subunit vaccines, genetically engineered organisms or chimeras, vectored antigen formulations, and naked DNA injections. The final successful outcome of vaccine research and development is the generation of a product that will be available in the marketplace or that will be used in the field to achieve desired outcomes. As detailed in this review, successful veterinary vaccines have been produced against viral, bacterial, protozoal, and multicellular pathogens, which in many ways have led the field in the application and adaptation of novel technologies. These veterinary vaccines have had, and continue to have, a major impact not only on animal health and production but also on human health through increasing safe food supplies and preventing animal-to-human transmission of infectious diseases. The continued interaction between animals and human researchers and health professionals will be of major importance for adapting new technologies, providing animal models of disease, and confronting new and emerging infectious diseases.

A turbulent jet in crossflow analysed with proper orthogonal decomposition

Abstract: Detailed instantaneous velocity fields of a jet in crossflow have been measured with stereoscopic particle image velocimetry (PIV). The jet originated from a fully developed turbulent pipe flow and entered a crossflow with a turbulent boundary layer. The Reynolds number based on crossflow velocity and pipe diameter was 2400 and the jet to crossflow velocity ratios were R=3.3 and R=1.3. The experimental data have been analysed by proper orthogonal decomposition (POD). For R=3.3, the results in several different planes indicate that the wake vortices are the dominant dynamic flow structures and that they interact strongly with the jet core. The analysis identifies jet shear-layer vortices and finds that these vortical structures are more local and thus less dominant. For R=1.3, on the other hand, jet shear-layer vortices are the most dominant, while the wake vortices are much less important. For both cases, the analysis finds that the shear-layer vortices are not coupled to the dynamics of the wake vortices. Finally, the hanging vortices are identified and their contribution to the counter-rotating vortex pair (CVP) and interaction with the newly created wake vortices are described.

Insights into the reactivity of supported Au nanoparticles: combining theory and experiments

Abstract: The origin of the extraordinary catalytic activity of gold nanoparticles is discussed on the basis of density-functional calculations, adsorption studies on single crystal surfaces, and activity measurements on well characterized supported gold particles. A number of factors are identified contributing to the activity, and it is suggested that it is useful to consider low-coordinated Au atoms as the active sites, for example, CO oxidation and that the effect of the support can be viewed as structural and electronic promotion. We identify the adsorption energy of oxygen and the Au-support interface energy as important parameters determining the catalytic activity.