Showing papers by "Technical University of Denmark published in 1996"

CO Chemisorption at Metal Surfaces and Overlayers

Abstract: A database of ab initio calculations of the chemisorption energy of CO over Ni(111), Cu(111), Ru(0001), Pd(111), Ag(111), Pt(111), Au(111), $\mathrm{Cu}{}_{3}$Pt(111), and some metallic overlayer structures is presented. The trends can be reproduced with a simple model describing the interaction between the metal $d$ states and the CO $2{\ensuremath{\pi}}^{*}$ and 5 $\ensuremath{\sigma}$ states, renormalized by the metal $\mathrm{sp}$ continuum. Our model rationalizes the results by Rodriguez and Goodman [Science 257, 897 (1992)] showing a strong correlation between the CO chemisorption energy and the surface core level shift.

Splice Site Prediction in Arabidopsis Thaliana Pre-mRNA by Combining Local and Global Sequence Information

Abstract: Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana. A two step prediction scheme, where a global prediction of the coding potential regulates a cutoff level for a local prediction of splice sites, is refined by rules based on splice site confidence values, prediction scores, coding context and distances between potential splice sites. In this approach, the prediction of splice sites mutually affect each other in a non-local manner. The combined approach drastically reduces the large amount of false positive splice sites normally haunting splice site prediction. An analysis of the errors made by the networks in the first step of the method revealed a previously unknown feature, a frequent T-tract prolongation containing cryptic acceptor sites in the 5' end of exons. The method presented here has been compared with three other approaches, GeneFinder, Gene-Mark and Grail. Overall the method presented here is an order of magnitude better. We show that the new method is able to find a donor site in the coding sequence for the jelly fish Green Fluorescent Protein, exactly at the position that was experimentally observed in A.thaliana transformants. Predictions for alternatively spliced genes are also presented, together with examples of genes from other dicots, monocots and algae. The method has been made available through electronic mail (NetPlantGene@cbs.dtu.dk), or the WWW at http://www.cbs.dtu.dk/NetPlantGene.html

Global illumination using photon maps

Abstract: This paper presents a two pass global illumination method based on the concept of photon maps. It represents a significant improvement of a previously described approach both with respect to speed, accuracy and versatility. In the first pass two photon maps are created by emitting packets of energy (photons) from the light sources and storing these as they hit surfaces within the scene. We use one high resolution caustics photon map to render caustics that are visualized directly and one low resolution photon map that is used during the rendering step. The scene is rendered using a distribution ray tracing algorithm optimized by using the information in the photon maps. Shadow photons are used to render shadows more efficiently and the directional information in the photon map is used to generate optimized sampling directions and to limit the recursion in the distribution ray tracer by providing an estimate of the radiance on all surfaces with the exception of specular and highly glossy surfaces.

Eukaryotic interference with homoserine lactone-mediated prokaryotic signalling.

Abstract: Acylated homoserine lactones (AHLs) play a widespread role in intercellular communication among bacteria. The Australian macroalga Delisea pulchra produces secondary metabolites which have structural similarities to AHL molecules. We report here that these metabolites inhibited AHL-controlled processes in prokaryotes. Our results suggest that the interaction between higher organisms and their surface-associated bacteria may be mediated by interference with bacterial regulatory systems.

Type 1 fimbrial expression enhances Escherichia coli virulence for the urinary tract

Abstract: Type 1 fimbriae are adhesion organelles expressed by many Gram-negative bacteria. They facilitate adherence to mucosal surfaces and inflammatory cells in vitro, but their contribution to virulence has not been defined. This study presents evidence that type 1 fimbriae increase the virulence of Escherichia coli for the urinary tract by promoting bacterial persistence and enhancing the inflammatory response to infection. In a clinical study, we observed that disease severity was greater in children infected with E. coli O1:K1:H7 isolates expressing type 1 fimbriae than in those infected with type 1 negative isolates of the same serotype. The E. coli O1:K1:H7 isolates had the same electrophoretic type, were hemolysin-negative, expressed P fimbriae, and carried the fim DNA sequences. When tested in a mouse urinary tract infection model, the type 1-positive E. coli O1:K1:H7 isolates survived in higher numbers, and induced a greater neutrophil influx into the urine, than O1:K1:H7 type 1-negative isolates. To confirm a role of type 1 fimbriae, a fimH null mutant (CN1016) was constructed from an O1:K1:H7 type 1-positive parent. E. coli CN1016 had reduced survival and inflammatogenicity in the mouse urinary tract infection model. E. coli CN1016 reconstituted with type 1 fimbriae (E. coli CN1018) had restored virulence similar to that of the wild-type parent strain. These results show that type 1 fimbriae in the genetic background of a uropathogenic strain contribute to the pathogenesis of E. coli in the urinary tract.

Real‐time Volumetric Deformable Models for Surgery Simulation using Finite Elements and Condensation

Abstract: This paper discusses the application of 3D solid volumetric Finite Element models to surgery simulation. In particular it introduces three new ideas for solving the problem of achieving real-time performance for these models. The simulation system we have developed is described and we demonstrate real-time deformation using the methods developed in the paper.

Estimation of Blood Velocities Using Ultrasound: A Signal Processing Approach

Abstract: Medical ultrasound systems Ultrasound Flow physics Ultrasound's interaction with blood Continuous wave systems Pulsed wave systems Color flow mapping using phase shift estimation Color flow mapping using time shift estimation Experimental systems Bibliography Appendices.

A new Approach to Variable-Topology Shape Design Using a Constraint on the Perimeter

Abstract: This paper introduces a method for variable-topology shape optimization of elastic structures called theperimeter method. An upper-bound constraint on the perimeter of the solid part of the structure ensures a well-posed design problem. The perimeter constraint allows the designer to control the number of holes in the optimal design and to establish their characteristic length scale. Finite element implementations generate practical designs that are convergent with respect to grid refinement. Thus, an arbitrary level of geometric resolution can be achieved, so single-step procedures for topology design and detailed shape design are possible. The perimeter method eliminates the need for relaxation, thereby circumventing many of the complexities and restrictions of other approaches to topology design.

Fast Fluid Registration of Medical Images

Abstract: This paper offers a new fast algorithm for non-rigid Viscous Fluid Registration of medical images that is at least an order of magnitude faster than the previous method by Christensen et al. [4]. The core algorithm in the fluid registration method is based on a linear elastic deformation of the velocity field of the fluid. Using the linearity of this deformation we derive a convolution filter which we use in a scalespace framework. We also demonstrate that the ’demon’-based registration method of Thirion [13] can be seen as an approximation to the fluid registration method and point to possible problems.

Involvement of N‐acyl‐l‐homoserine lactone autoinducers in controlling the multicellular behaviour of Serratia liquefaciens

Abstract: Summary Several bacterial species possess the ability to differentiate into highly motile swarmer cells capable of rapid surface colonization. In Serratia liquefaciens, we demonstrate that initiation of swarmer-cell differentiation involves diffusible signal molecules that are released into the growth medium. Using high-performance liquid chromatography (HPLC), high resolution mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy, we identified N-butanoyl-l-homoserine lactone (BHL) and N-hexanoyl-l-homoserine lactone (HHL) in cell-free Serratia culture supernatants. BHL and HHL are present in a ratio of approximately 10:1 and their structures were unequivocally confirmed by chemical synthesis. The swrlswarmer initiation) gene, the predicted translation product of which exhibits substantial homology to the Luxl family of putative Nacyl homoserine lactone (AHL) synthases is responsible for directing synthesis of both BHL and HHL. In an swrl mutant, swarming motility is abolished but can be restored by the addition of an exogenous AHL. These results add swarming motility to the rapidly expanding list of phenotypes known to be controlled through quorum sensing.

Abiotic Nitrate Reduction to Ammonium: Key Role of Green Rust

Abstract: Leaching of nitrate from soils and sediments can be reduced in anoxic environments due to denitrification to N2O/N2 or reduction of nitrate to ammonium. While microbial dissimilatory reduction of nitrate to ammonia is well known, it is shown here that this conversion can also proceed at appreciable rates in abiotic systems in the presence of green rust compounds [FeII4FeIII2(OH)12SO4·yH2O]. In the reaction nitrate is stoichiometrically reduced to ammonium, and magnetite (Fe3O4) is the sole Fe-containing product. At a constant pH of approximately 8.25 and 25 °C, the rate expression is given as: d[NH4+]/dt = k[Fe(II)]GR[NO3-],where k = 4.93 × 10-5 ± 0.39 × 10-5 L mol-1 s-1. In anoxic soils and sediments, this reaction may also lead to a nitrate to ammonium reduction, at rates of similar magnitude or even higher than microbial reduction rates. Hence green rust should be considered a possible important reductant for nitrate reduction to ammonium in subsoils, sediments, or aquifers where microbially mediated ...

On the toughness of ductile adhesive joints

Abstract: Crack propagation along one of the interfaces between a thin ductile adhesive layer and the elastic substrates it joins is considered. The layer is taken as being elastic-plastic, and the fracture process of the interface is modeled by a traction-separation law, characterized by the peak separation stress 6 and the work of separation per unit area To. Crack growth resistance curves for mode I loading of the adhesive joint are computed, with emphasis on steady-state toughness, as a function of three extrinsic effects : layer thickness, layer-substrate modulus mismatch, and initial residual stress in the layer. Conditions under which separation first occurs well ahead of the initial crack tip are discussed. 1. SPECIFICATION OF THE MODEL This paper continues the study begun by Tvergaard and Hutchinson (1994) in which an embedded fracture zone model is applied to the mode I fracture of an adhesive joint comprised of a thin elastic-plastic metal layer joining two elastic substrates. The present work employs the model to investigate the influence on joint toughness of both the elastic mismatch between the layer and the substrates and the residual stress in the layer. As in the earlier study, the thickness of the ductile layer is another extrinsic variable which comes into play. The approach adopted was first introduced by Needleman (1987) to study particle debonding in metal matrices and subsequently by Tvergaard and Hutchinson (1992, 1993) to model crack growth resistance in homogeneous solids and along interfaces. A traction-separation law simulating the fracture process is embedded within an elastic-plastic continuum as a boundary condition along the line extending ahead of the crack. In the case of an interface joining dissimilar materials, the separation law necessarily involves both the normal and shear tractions and the two associated relative displacements of the surfaces across the interface.

European Indoor Air Quality Audit Project in 56 Office Buildings

Abstract: A European project started at the end of 1992, in which, in addition to current methods, trained sensory panels were used to investigate office buildings all over Europe. The main aim of this EC-Audit was to develop assessment procedures and guid-ance on ventilation and source control, to help optimize energy use in buildings while assuring good indoor air quality. In each of nine countries, six or more office buildings were select-ed. Measurements were performed at five selected locations in each building. The buildings were studied while normally occu-pied and ventilated to identify the pollution sources in the spaces and to quantify the total pollution load caused by the occupants and their activities, as well as the ventilation systems. The investi-gation included physical and chemical measurements, assessment of the perceived air quality in the spaces by a trained sensory pan-el, and measurement of the outdoor air supply to the spaces. A questionnaire for evaluating retrospective and immediate symp-toms and perceptions was given to the occupants of the buildings. The building characteristics were described by use of a check-list. The annual energy consumption of the buildings and the weather conditions were registered. This paper presents results and conclusions of the audit in 56 buildings in Europe. However, the analysis and discussions of the results are a summary of the work done, and are focused mainly on comparison between sensory assessments and the other meas-urements performed. Furthermore, this paper brings the results of the study based on a two-factor analysis. A paper dealing with results on a multifacto-rial analysis is in preparation.

Cleavage site analysis in picornaviral polyproteins: discovering cellular targets by neural networks.

Abstract: Picornaviral proteinases are responsible for maturation cleavages of the viral polyprotein, but also catalyze the degradation of cellular targets. Using graphical visualization techniques and neural network algorithms, we have investigated the sequence specificity of the two proteinases 2Apro and 3Cpro. The cleavage of VP0 (giving rise to VP2 and VP4), which is carried out by a so-far unknown proteinase, was also examined. In combination with a novel surface exposure prediction algorithm, our neural network approach successfully distinguishes known cleavage sites from noncleavage sites and yields a more consistent definition of features common to these sites. The method is able to predict experimentally determined cleavage sites in cellular proteins. We present a list of mammalian and other proteins that are predicted to be possible targets for the viral proteinases. Whether these proteins are indeed cleaved awaits experimental verification. Additionally, we report several errors detected in the protein databases. A computer server for prediction of cleavage sites by picornaviral proteinases is publicly available at the e-mail address NetPicoRNA@cbs.dtu.dk or via WWW at http:@www.cbs.dtu.dk/services/NetPicoRNA/.

Systematic Relationship between Phospholipase A2 Activity and Dynamic Lipid Bilayer Microheterogeneity

Abstract: A standing hypothesis in membrane biology implies that the collective physical properties of the lipid bilayer component of biological membranes can modulate the activity of membrane-associated proteins. We provide strong support for this hypothesis by exploring a model system, phospholipase A2 catalyzed hydrolysis of one-component phospholipid vesicles. For vesicles of lipids with different chain lengths we observe, as a function of temperature and chain length, a systematic variation of the characteristic lag time for the onset of rapid phospholipase A2 hydrolysis. These results, combined with theoretical results obtained from computer simulation of the gel-to-fluid phase transition in the unhydrolyzed lipid bilayers, enable us to demonstrate a strong correlation between the lag time and the degree of bilayer microheterogeneity in the phase transition region. Insight into the nature of this correlation suggests rational ways of modulating enzyme activity by modifying the physical properties of the lipid bilayer.

Activity and three-dimensional distribution of toluene-degrading Pseudomonas putida in a multispecies biofilm assessed by quantitative in situ hybridization and scanning confocal laser microscopy.

Abstract: As a representative member of the toluene-degrading population in a biofilter for waste gas treatment, Pseudomonas putida was investigated with a 16S rRNA targeting probe. The three-dimensional distribution of P. putida was visualized in the biofilm matrix by scanning confocal laser microscopy, demonstrating that P. putida was present throughout the biofilm. Acridine orange staining revealed a very heterogeneous structure of the fully hydrated biofilm, with cell-free channels extending from the surface into the biofilm. This indicated that toluene may penetrate to deeper layers of the biofilm, and consequently P. putida may be actively degrading toluene in all regions of the biofilm. Furthermore, measurements of growth rate-related parameters for P. putida showed reduced rRNA content and cell size (relative to that in a batch culture), indicating that the P. putida population was not degrading toluene at a maximal rate in the biofilm environment. Assuming that the rRNA content reflected the cellular activity, a lower toluene degradation rate for P. putida present in the biofilm could be estimated. This calculation indicated that P. putida was responsible for a significant part (65%) of the toluene degraded by the entire community.

Design and fabrication of compliant micromechanisms and structures with negative Poisson's ratio

Abstract: This paper describes a new way to design and fabricate compliant micromechanisms and material structures with negative Poisson's ratio (NPR). The design of compliant mechanisms and material structures is accomplished in an automated way using a numerical topology optimization method. The procedure allows the user to specify the elastic properties of materials or the mechanical or geometrical advantages of compliant mechanisms and returns the optimal structures. The topologies obtained by the numerical procedure require practically no interaction by the engineer before they can be transferred to the fabrication unit. Fabrication is carried out by patterning a sputtered silicon on a PECVD-glass with a laser micromachining set-up. Subsequently the structures are etched into the underlying PECVD-glass and the glass are underetched, all in one two-step RIE process. The components are tested using a probe placed on an xy-stage. This fast prototyping allows newly developed topologies to be fabricated and tested within the same day.

Phase Behavior of Pure Diblocks and Binary Diblock Blends of Poly(ethylene)−Poly(ethylethylene)

Abstract: We have determined the phase behavior of a series of model poly(ethylene)−poly(ethylethylene) (PE−PEE) diblock copolymers with poly(ethylene) block volume fractions (fPE) ranging from 0.25 to 0.46. Four ordered microstructures make contact with the ODT: spheres arranged on a body-centered cubic lattice (Im3m space group), cylinders packed on a hexagonal lattice, a bicontinuous structure of space group Ia3d, and lamellae. A fifth ordered phase, tentatively identified as hexagonally perforated layers (HPL), separates the cylindrical and lamellar morphologies at moderate or greater degrees of segregation. Binary blends of fPE = 0.37 and 0.46 diblocks were used to investigate the bicontinuous cubic phase region in greater detail; these experiments indicate that this phase extends as much as 100 °C below the ODT for 〈fPE〉 values in the blend from 0.385 to 0.420.

Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments.

Abstract: The prediction of protein secondary structure by use of carefully structured neural networks and multiple sequence alignments has been investigated. Separate networks are used for predicting the three secondary structures α-helix, β-strand, and coil. The networks are designed using a priori knowledge of amino acid properties with respect to the secondary structure and the characteristic periodicity in α-helices. Since these single-structure networks all have less than 600 adjustable weights, overfitting is avoided. To obtain a three-state prediction of α-helix, β-strand, or coil, ensembles of single-structure networks are combined with another neural network. This method gives an overall prediction accuracy of 66.3% when using 7-fold cross-validation on a database of 126 nonhomologous globular proteins. Applying the method to multiple sequence alignments of homologous proteins increases the prediction accuracy significantly to 71.3% with corresponding Matthew's correlation coefficients Cα = 0.59,...