Showing papers by "Technical University of Denmark published in 2002"

Density-functional method for nonequilibrium electron transport

Abstract: We describe an ab initio method for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias. Our method is based on the density-functional theory (DFT) as implemented in the well tested SIESTA approach (which uses nonlocal norm-conserving pseudopotentials to describe the effect of the core electrons, and linear combination of finite-range numerical atomic orbitals to describe the valence states). We fully deal with the atomistic structure of the whole system, treating both the contact and the electrodes on the same footing. The effect of the finite bias (including self-consistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. We relate the nonequilibrium Green's function expressions to the more transparent scheme involving the scattering states. As an illustration, the method is applied to three systems where we are able to compare our results to earlier ab initio DFT calculations or experiments, and we point out differences between this method and existing schemes. The systems considered are: (i) single atom carbon wires connected to aluminum electrodes with extended or finite cross section, (ii) single atom gold wires, and finally (iii) large carbon nanotube systems with point defects.

An introduction to frames and Riesz bases

Abstract: Frames in Finite-dimensional Inner Product Spaces.- Infinite-dimensional Vector Spaces and Sequences.- Bases.- Bases and their Limitations.- Frames in Hilbert Spaces.- Tight Frames and Dual Frame Pairs.- Frames versus Riesz Bases.- Selected Topics in Frame Theory.- Frames of Translates.- Shift-Invariant Systems in l2(R).- Gabor Frames in L2(R).- Gabor Frames and Duality.- Selected Topics on Gabor Frames.- Gabor Frames in â 2(Z),L2(0,L),CL.- General Wavelet Frames in L2(R).- Dyadic Wavelet Frames for L2(R).- Frame Multiresolution Analysis.- Wavelet Frames via Extension Principles.- Selected Topics on Wavelet Frames.- Generalized Shift-Invariant Systems in L2(Rd).- Frames on Locally Compact Abelian Groups.- Perturbation of Frames.- Approximation of the Inverse Frame Operator.- Expansions in Banach Spaces. Appendix.

Extracellular DNA Required for Bacterial Biofilm Formation

Abstract: Bacterial biofilms are structured communities of cells enclosed in self-produced hydrated polymeric matrix adherent to an inert or living surface ([1][1]). Formation of these sessile communities and their inherent resistance to antibiotics and host immune attack are at the root of many persistent

The genome sequence of Schizosaccharomyces pombe

Abstract: We have sequenced and annotated the genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.

An object-oriented scripting interface to a legacy electronic structure code

Abstract: The authors have created an object-oriented scripting interface to a mature density functional theory code. The interface gives users a high-level, flexible handle on the code without rewriting the underlying number-crunching code. The authors also discuss the design issues and advantages of homogeneous interfaces.

Numerical modeling of wind turbine wakes

Abstract: An aerodynamical model for studying three-dimensional flow fields about wind turbine rotors is presented. The developed algorithm combines a three-dimensional Navier-Stokes solver with a so-called actuator line technique in which the loading is distributed along lines representing the blade forces. The loading is determined iteratively using a bladeelement approach and tabulated airfoil data. Computations are carried out for a 500 kW Nordtank wind turbine equipped with three LM19.1 blades. The computations give detailed information about basic features of wind turbine wakes, including distributions of interference factors and vortex structures. The model serves in particular to analyze and verify the validity of the basic assumptions employed in the simple engineering models

Inhibition of quorum sensing in Pseudomonas aeruginosa biofilm bacteria by a halogenated furanone compound.

Abstract: Novel molecular tools have been constructed which allow for in situ detection of N-acyl homoserine lactone (AHL)-mediated quorum sensing in Pseudomonas aeruginosa biofilms. The reporter responds to AHL activation of LasR by expression of an unstable version of the green-fluorescent protein (Gfp). Gfp-based reporter technology has been applied for non-destructive, single-cell-level detection of quorum sensing in laboratory-based P. aeruginosa biofilms. It is reported that a synthetic halogenated furanone compound, which is a derivative of the secondary metabolites produced by the Australian macroalga Delisea pulchra, is capable of interfering with AHL-mediated quorum sensing in P. aeruginosa. It is demonstrated that the furanone compound specifically represses expression of a PlasB-gfp reporter fusion without affecting growth or protein synthesis. In addition, it reduces the production of important virulence factors, indicating a general effect on target genes of the las quorum sensing circuit. The furanone was applied to P. aeruginosa biofilms established in biofilm flow chambers. The Gfp-based analysis reveals that the compound penetrates microcolonies and blocks cell signalling and quorum sensing in most biofilm cells. The compound did not affect initial attachment to the abiotic substratum. It does, however, affect the architecture of the biofilm and enhances the process of bacterial detachment, leading to a loss of bacterial biomass from the substratum.

Volunteering as Red Queen Mechanism for Cooperation in Public Goods Games

Abstract: The evolution of cooperation among nonrelated individuals is one of the fundamental problems in biology and social sciences. Reciprocal altruism fails to provide a solution if interactions are not repeated often enough or groups are too large. Punishment and reward can be very effective but require that defectors can be traced and identified. Here we present a simple but effective mechanism operating under full anonymity. Optional participation can foil exploiters and overcome the social dilemma. In voluntary public goods interactions, cooperators and defectors will coexist. We show that this result holds under very diverse assumptions on population structure and adaptation mechanisms, leading usually not to an equilibrium but to an unending cycle of adjustments (a Red Queen type of evolution). Thus, voluntary participation offers an escape hatch out of some social traps. Cooperation can subsist in sizable groups even if interactions are not repeated, defectors remain anonymous, players have no memory, and assortment is purely random.

Lactobacilli Differentially Modulate Expression of Cytokines and Maturation Surface Markers in Murine Dendritic Cells

Abstract: Dendritic cells (DC) play a pivotal immunoregulatory role in the Th1, Th2, and Th3 cell balance and are present throughout the gastrointestinal tract. Thus, DC may be targets for modulation by gut microbes, including ingested probiotics. In the present study, we tested the hypothesis that species of Lactobacillus, important members of the gut flora, differentially activate DC. Bone marrow-derived murine DC were exposed to various lethally irradiated Lactobacillus spp. and resultant culture supernatants were analyzed for IL-6, IL-10, IL-12, and TNF-alpha. Substantial differences were found among strains in the capacity to induce IL-12 and TNF-alpha production in the DC. Similar but less pronounced differences were observed among lactobacilli in the induction of IL-6 and IL-10. Although all strains up-regulated surface MHC class II and B7-2 (CD86), which is indicative of DC maturation, those lactobacilli with greatest capacity to induce IL-12 were most effective. Remarkably, Lactobacillus reuteri DSM12246, a poor IL-12 inducer, inhibited IL-12, IL-6, and TNF-alpha induction by the otherwise strong cytokine inducer L. casei CHCC3139, while IL-10 production remained unaltered. In analogous fashion, L. reuteri reduced L. casei-induced up-regulation of B7-2. These results suggest that different species of Lactobacillus exert very different DC activation patterns and, furthermore, at least one species may be capable of inhibiting activities of other species in the genus. Thus, the potential exists for Th1/Th2/Th3-driving capacities of the gut DC to be modulated according to composition of gut microflora, including ingested probiotics.

On the safety of Aspergillus niger - a review

Abstract: Aspergillus niger is one of the most important microorganisms used in biotechnology. It has been in use already for many decades to produce extracellular (food) enzymes and citric acid. In fact, citric acid and many A. niger enzymes are considered GRAS by the United States Food and Drug Administration. In addition, A. niger is used for biotransformations and waste treatment. In the last two decades, A. niger has been developed as an important transformation host to over-express food enzymes. Being pre-dated by older names, the name A. niger has been conserved for economical and information retrieval reasons and there is a taxonomical consensus based on molecular data that the only other common species closely related to A. niger in the Aspergillus series Nigri is A. tubingensis. A. niger, like other filamentous fungi, should be treated carefully to avoid the formation of spore dust. However, compared with other filamentous fungi, it does not stand out as a particular problem concerning allergy or mycopathology. A few medical cases, e.g. lung infections, have been reported, but always in severely immunocompromised patients. In tropical areas, ear infections (otomycosis) do occur due to A. niger invasion of the outer ear canal but this may be caused by mechanical damage of the skin barrier. A. niger strains produce a series of secondary metabolites, but it is only ochratoxin A that can be regarded as a mycotoxin in the strict sense of the word. Only 3-10% of the strains examined for ochratoxin A production have tested positive under favourable conditions. New and unknown isolates should be checked for ochratoxin A production before they are developed as production organisms. It is concluded, with these restrictions, that A. niger is a safe production organism.

Catalytic CO oxidation by a gold nanoparticle: A density functional study

Abstract: Gold is usually considered very noble. It does not oxidize, and the surface of gold cannot adsorb most molecules from the gas phase. Yet it has been found that nanometer size gold particles on different oxide supports can act as catalysts even at or below room temperature. We present self-consistent density functional calculations showing that even an isolated Au10 cluster should be able to catalyze the CO oxidation reaction even below room temperature. We use the calculations to analyze the origin of this effect and suggest that the extraordinary reactivity can be traced back to special reaction geometries available at small particles in combination with an enhanced ability of low coordinated gold atoms to interact with molecules from the surroundings.

Halogenated furanones inhibit quorum sensing through accelerated LuxR turnover.

Abstract: N-acyl-L-homoserine lactones (AHLs) are co-regulatory ligands required for control of the expression of genes encoding virulence traits in many Gram-negative bacterial species. Recent studies have indicated that AHLs modulate the cellular concentrations of LuxR-type regulatory proteins by binding and fortifying these proteins against proteolytic degradation (Zhu & Winans, 2001 R43 ). Halogenated furanones produced by the macroalga Delisea pulchra inhibit AHL-dependent gene expression. This study assayed for an in vivo interaction between a tritiated halogenated furanone and the LuxR protein of Vibrio fischeri overproduced in Escherichia coli. Whilst a stable interaction between the algal metabolite and the bacterial protein was not found, it was noted by Western analysis that the half-life of the protein is reduced up to 100-fold in the presence of halogenated furanones. This suggests that halogenated furanones modulate LuxR activity but act to destabilize, rather than protect, the AHL-dependent transcriptional activator. The furanone-dependent reduction in the cellular concentration of the LuxR protein was associated with a reduction in expression of a plasmid encoded P luxI –gfp(ASV) fusion suggesting that the reduction in LuxR concentration is the mechanism by which furanones control expression of AHL-dependent phenotypes. The mode of action by which halogenated furanones reduce cellular concentrations of the LuxR protein remains to be characterized.

Quorum-sensing cross talk: isolation and chemical characterization of cyclic dipeptides from Pseudomonas aeruginosa and other gram-negative bacteria.

Abstract: In cell-free Pseudomonas aeruginosa culture supernatants, we identified two compounds capable of activating an N-acylhomoserine lactone (AHL) biosensor. Mass spectrometry and NMR spectroscopy revealed that these compounds were not AHLs but the diketopiperazines (DKPs), cyclo(ΔAla-l-Val) and cyclo(l-Pro-l-Tyr) respectively. These compounds were also found in cell-free supernatants from Proteus mirabilis, Citrobacter freundii and Enterobacter agglomerans [cyclo(ΔAla-l-Val) only]. Although both DKPs were absent from Pseudomonas fluorescens and Pseudomonas alcaligenes, we isolated, from both pseudomonads, a third DKP, which was chemically characterized as cyclo(l-Phe-l-Pro). Dose–response curves using a LuxR-based AHL biosensor indicated that cyclo(ΔAla-l-Val), cyclo(l-Pro-l-Tyr) and cyclo(l-Phe-l-Pro) activate the biosensor in a concentration-dependent manner, albeit at much higher concentrations than the natural activator N-(3-oxohexanoyl)-l-homoserine lactone (3-oxo-C6-HSL). Competition studies showed that cyclo(ΔAla-l-Val), cyclo(l-Pro-l-Tyr) and cyclo(l-Phe-l-Pro) antagonize the 3-oxo-C6-HSL-mediated induction of bioluminescence, suggesting that these DKPs may compete for the same LuxR-binding site. Similarly, DKPs were found to be capable of activating or antagonizing other LuxR-based quorum-sensing systems, such as the N-butanoylhomoserine lactone-dependent swarming motility of Serratia liquefaciens. Although the physiological role of these DKPs has yet to be established, their activity suggests the existence of cross talk among bacterial signalling systems.

A new non-linear normalization method for reducing variability in DNA microarray experiments

Abstract: Microarray data are subject to multiple sources of variation, of which biological sources are of interest whereas most others are only confounding. Recent work has identified systematic sources of variation that are intensity-dependent and non-linear in nature. Systematic sources of variation are not limited to the differing properties of the cyanine dyes Cy5 and Cy3 as observed in cDNA arrays, but are the general case for both oligonucleotide microarray (Affymetrix GeneChips) and cDNA microarray data. Current normalization techniques are most often linear and therefore not capable of fully correcting for these effects. We present here a simple and robust non-linear method for normalization using array signal distribution analysis and cubic splines. These methods compared favorably to normalization using robust local-linear regression (lowess). The application of these methods to oligonucleotide arrays reduced the relative error between replicates by 5-10% compared with a standard global normalization method. Application to cDNA arrays showed improvements over the standard method and over Cy3-Cy5 normalization based on dye-swap replication. In addition, a set of known differentially regulated genes was ranked higher by the t-test. In either cDNA or Affymetrix technology, signal-dependent bias was more than ten times greater than the observed print-tip or spatial effects. Intensity-dependent normalization is important for both high-density oligonucleotide array and cDNA array data. Both the regression and spline-based methods described here performed better than existing linear methods when assessed on the variability of replicate arrays. Dye-swap normalization was less effective at Cy3-Cy5 normalization than either regression or spline-based methods alone.

Gaussian Process Priors with Uncertain Inputs Application to Multiple-Step Ahead Time Series Forecasting

Abstract: We consider the problem of multi-step ahead prediction in time series analysis using the non-parametric Gaussian process model. k-step ahead forecasting of a discrete-time non-linear dynamic system can be performed by doing repeated one-step ahead predictions. For a state-space model of the form yt = f(yt-1,...,yt-L), the prediction of y at time t + k is based on the point estimates of the previous outputs. In this paper, we show how, using an analytical Gaussian approximation, we can formally incorporate the uncertainty about intermediate regressor values, thus updating the uncertainty on the current prediction.

Collapse arrest and soliton stabilization in nonlocal nonlinear media.

Abstract: We investigate the properties of localized waves in cubic nonlinear materials with a symmetric nonlocal nonlinear response of arbitrary shape and degree of nonlocality, described by a general nonlocal nonlinear Schrodinger type equation. We prove rigorously by bounding the Hamiltonian that nonlocality of the nonlinearity prevents collapse in, e.g., Bose-Einstein condensates and optical Kerr media in all physical dimensions. The nonlocal nonlinear response must be symmetric and have a positive definite Fourier spectrum, but can otherwise be of completely arbitrary shape and degree of nonlocality. We use variational techniques to find the soliton solutions and illustrate the stabilizing effect of nonlocality.

Ventilation and health in non-industrial indoor environments: report from a European multidisciplinary scientific consensus meeting (EUROVEN).

Abstract: Scientific literature on the effects of ventilation on health, comfort, and productivity in non-industrial indoor environments (offices, schools, homes, etc.) has been reviewed by a multidisciplinary group of European scientists, called EUROVEN, with expertise in medicine, epidemiology, toxicology, and engineering. The group reviewed 105 papers published in peer-reviewed scientific journals and judged 30 as conclusive, providing sufficient information on ventilation, health effects, data processing, and reporting, 14 as providing relevant background information on the issue, 43 as relevant but non-informative or inconclusive, and 18 as irrelevant for the issue discussed. Based on the data in papers judged conclusive, the group agreed that ventilation is strongly associated with comfort (perceived air quality) and health [Sick Building Syndrome (SBS) symptoms, inflammation, infections, asthma, allergy, short-term sick leave], and that an association between ventilation and productivity (performance of office work) is indicated. The group also concluded that increasing outdoor air supply rates in non-industrial environments improves perceived air quality; that outdoor air supply rates below 25 l/s per person increase the risk of SBS symptoms, increase short-term sick leave, and decrease productivity among occupants of office buildings; and that ventilation rates above 0.5 air changes per hour (h-1) in homes reduce infestation of house dust mites in Nordic countries. The group concluded additionally that the literature indicates that in buildings with air-conditioning systems there may be an increased risk of SBS symptoms compared with naturally or mechanically ventilated buildings, and that improper maintenance, design, and functioning of air-conditioning systems contributes to increased prevalence of SBS symptoms.

The glycolytic flux in Escherichia coli is controlled by the demand for ATP.

Abstract: The nature of the control of glycolytic flux is one of the central, as-yet-uncharacterized issues in cellular metabolism. We developed a molecular genetic tool that specifically induces ATP hydrolysis in living cells without interfering with other aspects of metabolism. Genes encoding the F1 part of the membrane-bound (F1F0) H+-ATP synthase were expressed in steadily growing Escherichia coli cells, which lowered the intracellular [ATP]/[ADP] ratio. This resulted in a strong stimulation of the specific glycolytic flux concomitant with a smaller decrease in the growth rate of the cells. By optimizing additional ATP hydrolysis, we increased the flux through glycolysis to 1.7 times that of the wild-type flux. The results demonstrate why attempts in the past to increase the glycolytic flux through overexpression of glycolytic enzymes have been unsuccessful: the majority of flux control (>75%) resides not inside but outside the pathway, i.e., with the enzymes that hydrolyze ATP. These data further allowed us to answer the question of whether catabolic or anabolic reactions control the growth of E. coli. We show that the majority of the control of growth rate resides in the anabolic reactions, i.e., the cells are mostly “carbon” limited. Ways to increase the efficiency and productivity of industrial fermentation processes are discussed.

A new Boussinesq method for fully nonlinear waves from shallow to deep water

Abstract: A new method valid for highly dispersive and highly nonlinear water waves is presented. It combines a time-stepping of the exact surface boundary conditions with an approximate series expansion solution to the Laplace equation in the interior domain. The starting point is an exact solution to the Laplace equation given in terms of infinite series expansions from an arbitrary z-level. We replace the infinite series operators by finite series (Boussinesq-type) approximations involving up to fifth-derivative operators. The finite series are manipulated to incorporate Pade approximants providing the highest possible accuracy for a given number of terms. As a result, linear and nonlinear wave characteristics become very accurate up to wavenumbers as high as kh = 40, while the vertical variation of the velocity field becomes applicable for kh up to 12. These results represent a major improvement over existing Boussinesq-type formulations in the literature. A numerical model is developed in a single horizontal dimension and it is used to study phenomena such as solitary waves and their impact on vertical walls, modulational instability in deep water involving recurrence or frequency downshift, and shoaling of regular waves up to breaking in shallow water.