Showing papers by "Technical University of Denmark published in 2001"

FLUXNET: A New Tool to Study the Temporal and Spatial Variability of Ecosystem-Scale Carbon Dioxide, Water Vapor, and Energy Flux Densities

Abstract: FLUXNET is a global network of micrometeorological flux measurement sites that measure the exchanges of carbon dioxide, water vapor, and energy between the biosphere and atmosphere. At present over 140 sites are operating on a long-term and continuous basis. Vegetation under study includes temperate conifer and broadleaved (deciduous and evergreen) forests, tropical and boreal forests, crops, grasslands, chaparral, wetlands, and tundra. Sites exist on five continents and their latitudinal distribution ranges from 70°N to 30°S. FLUXNET has several primary functions. First, it provides infrastructure for compiling, archiving, and distributing carbon, water, and energy flux measurement, and meteorological, plant, and soil data to the science community. (Data and site information are available online at the FLUXNET Web site, http://www-eosdis.ornl.gov/FLUXNET/.) Second, the project supports calibration and flux intercomparison activities. This activity ensures that data from the regional networks are intercomparable. And third, FLUXNET supports the synthesis, discussion, and communication of ideas and data by supporting project scientists, workshops, and visiting scientists. The overarching goal is to provide information for validating computations of net primary productivity, evaporation, and energy absorption that are being generated by sensors mounted on the NASA Terra satellite. Data being compiled by FLUXNET are being used to quantify and compare magnitudes and dynamics of annual ecosystem carbon and water balances, to quantify the response of stand-scale carbon dioxide and water vapor flux densities to controlling biotic and abiotic factors, and to validate a hierarchy of soil–plant–atmosphere trace gas exchange models. Findings so far include 1) net CO 2 exchange of temperate broadleaved forests increases by about 5.7 g C m −2 day −1 for each additional day that the growing season is extended; 2) the sensitivity of net ecosystem CO 2 exchange to sunlight doubles if the sky is cloudy rather than clear; 3) the spectrum of CO 2 flux density exhibits peaks at timescales of days, weeks, and years, and a spectral gap exists at the month timescale; 4) the optimal temperature of net CO 2 exchange varies with mean summer temperature; and 5) stand age affects carbon dioxide and water vapor flux densities.

A 99 line topology optimization code written in Matlab

Abstract: The paper presents a compact Matlab implementation of a topology optimization code for compliance minimization of statically loaded structures. The total number of Matlab input lines is 99 including optimizer and Finite Element subroutine. The 99 lines are divided into 36 lines for the main program, 12 lines for the Optimality Criteria based optimizer, 16 lines for a mesh-independency filter and 35 lines for the finite element code. In fact, excluding comment lines and lines associated with output and finite element analysis, it is shown that only 49 Matlab input lines are required for solving a well-posed topology optimization problem. By adding three additional lines, the program can solve problems with multiple load cases. The code is intended for educational purposes. The complete Matlab code is given in the Appendix and can be down-loaded from the web-site http://www.topopt.dtu.dk.

Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18

Abstract: Salmonella enterica serovar Typhi (S. typhi) is the aetiological agent of typhoid fever, a serious invasive bacterial disease of humans with an annual global burden of approximately 16 million cases, leading to 600,000 fatalities. Many S. enterica serovars actively invade the mucosal surface of the intestine but are normally contained in healthy individuals by the local immune defence mechanisms. However, S. typhi has evolved the ability to spread to the deeper tissues of humans, including liver, spleen and bone marrow. Here we have sequenced the 4,809,037-base pair (bp) genome of a S. typhi (CT18) that is resistant to multiple drugs, revealing the presence of hundreds of insertions and deletions compared with the Escherichia coli genome, ranging in size from single genes to large islands. Notably, the genome sequence identifies over two hundred pseudogenes, several corresponding to genes that are known to contribute to virulence in Salmonella typhimurium. This genetic degradation may contribute to the human-restricted host range for S. typhi. CT18 harbours a 218,150-bp multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2), which shows recent common ancestry with a virulence plasmid of Yersinia pestis.

Fuel ethanol production from lignocellulose: a challenge for metabolic engineering and process integration.

Abstract: With industrial development growing rapidly, there is a need for environmentally sustainable energy sources. Bioethanol (ethanol from biomass) is an attractive, sustainable energy source to fuel transportation. Based on the premise that fuel bioethanol can contribute to a cleaner environment and with the implementation of environmental protection laws in many countries, demand for this fuel is increasing. Efficient ethanol production processes and cheap substrates are needed. Current ethanol production processes using crops such as sugar cane and corn are well-established; however, utilization of a cheaper substrate such as lignocellulose could make bioethanol more competitive with fossil fuel. The processing and utilization of this substrate is complex, differing in many aspects from crop-based ethanol production. One important requirement is an efficient microorganism able to ferment a variety of sugars (pentoses, and hexoses) as well as to tolerate stress conditions. Through metabolic engineering, bacterial and yeast strains have been constructed which feature traits that are advantageous for ethanol production using lignocellulose sugars. After several rounds of modification/evaluation/modification, three main microbial platforms, Saccharomyces cerevisiae, Zymomonas mobilis, and Escherichia coli, have emerged and they have performed well in pilot studies. While there are ongoing efforts to further enhance their properties, improvement of the fermentation process is just one of several factors-that needs to be fully optimized and integrated to generate a competitive lignocellulose ethanol plant.

Filters in topology optimization

Abstract: In this article, a modified (‘filtered’) version of the minimum compliance topology optimization problem is studied. The direct dependence of the material properties on its pointwise density is replaced by a regularization of the density field by the mean of a convolution operator. In this setting it is possible to establish the existence of solutions. Moreover, convergence of an approximation by means of finite elements can be obtained. This is illustrated through some numerical experiments. The ‘filtering’ technique is also shown to cope with two important numerical problems in topology optimization, checkerboards and mesh dependent designs. Copyright © 2001 John Wiley & Sons, Ltd.

Oxygen vacancies as active sites for water dissociation on rutile TiO(2)(110).

Abstract: Through an interplay between scanning tunneling microscopy experiments and density functional theory calculations, we determine unambiguously the active surface site responsible for the dissociation of water molecules adsorbed on rutile ${\mathrm{TiO}}_{2}(110)$. Oxygen vacancies in the surface layer are shown to dissociate ${\mathrm{H}}_{2}\mathrm{O}$ through the transfer of one proton to a nearby oxygen atom, forming two hydroxyl groups for every vacancy. The amount of water dissociation is limited by the density of oxygen vacancies present on the clean surface exclusively. The dissociation process sets in as soon as molecular water is able to diffuse to the active site.

Quinolone and Macrolide Resistance in Campylobacter jejuni and C. coli: Resistance Mechanisms and Trends in Human Isolates

Abstract: The incidence of human Campylobacter jejuni and C. coli infections has increased markedly in many parts of the world in the last decade as has the number of quinolone-resistant and, to a lesser extent, macrolide-resistant Campylobacter strains causing infections. We review macrolide and quinolone resistance in Campylobacter and track resistance trends in human clinical isolates in relation to use of these agents in food animals. Susceptibility data suggest that erythromycin and other macrolides should remain the drugs of choice in most regions, with systematic surveillance and control measures maintained, but fluoroquinolones may now be of limited use in the empiric treatment of Campylobacter infections in many regions.

Prediction of glycosylation across the human proteome and the correlation to protein function.

Abstract: The addition of a carbohydrate moeity to the side chain of a residue in a protein chain in uences the physicochemical properties of the protein Gly cosylation is known to alter proteolytic resistance protein solubility stability local structure lifetime in circulation and immunogenicity Of the various forms of protein glycosylation found in eukaryotic systems the most important types are N linked O linked GalNAc mucin type and O linked GlcNAc intracellular nuclear glycosylation N linked glycosylation is a co translational process involving the transfer of the precursor oligosac charide GlcNAc Man Glc to asparagine residues in the protein chain The asparagine usually occurs in a sequon Asn Xaa Ser Thr where Xaa is not Proline This is however not a speci c consensus since not all such sequons are modi ed in the cell O linked glycosylation involves the post translational transfer of an oligosaccharide to a serine or threonine residue In this case there is no well de ned motif for the acceptor site other than the near vicinity of proline and valine residues We have developed glycosylation site prediction methods for these three types of glycosylation using arti cial neural networks that examine correla tions in the local sequence context and surface accessibility In this paper we have used glycosylation site information on human proteins to illustrate the contribution of glycosylation to protein function and assess how widespread this modi cation is across the human proteome

Alginate Overproduction Affects Pseudomonas aeruginosa Biofilm Structure and Function

Abstract: During the course of chronic cystic fibrosis (CF) infections, Pseudomonas aeruginosa undergoes a conversion to a mucoid phenotype, which is characterized by overproduction of the exopolysaccharide alginate. Chronic P. aeruginosa infections involve surface-attached, highly antibiotic-resistant communities of microorganisms organized in biofilms. Although biofilm formation and the conversion to mucoidy are both important aspects of CF pathogenesis, the relationship between them is at the present unclear. In this study, we report that the overproduction of alginate affects biofilm development on an abiotic surface. Biofilms formed by an alginate-overproducing strain exhibit a highly structured architecture and are significantly more resistant to the antibiotic tobramycin than a biofilm formed by an isogenic nonmucoid strain. These results suggest that an important consequence of the conversion to mucoidy is an altered biofilm architecture that shows increasing resistance to antimicrobial treatments.

One-Dimensional Metallic Edge States in MoS2

Abstract: By the use of density functional calculations it is shown that the edges of a two-dimensional slab of insulating ${\mathrm{MoS}}_{2}$ exhibit several metallic states. These edge states can be viewed as one-dimensional conducting wires, and we show that they can be observed directly using scanning tunneling microscopy for single-layer ${\mathrm{MoS}}_{2}$ nanoparticles grown on a support.

Highly birefringent index-guiding photonic crystal fibers

Abstract: Photonic crystal fibers (PCFs) offer new possibilities of realizing highly birefringent fibers due to a higher intrinsic index contrast compared to conventional fibers. In this letter, we analyze theoretically the levels of birefringence that can be expected using relatively simple PCF designs. While extremely high degrees of birefringence may be obtained for the fibers, we demonstrate that careful design with respect to multimode behavior must be performed. We further discuss the cutoff properties of birefringent PCFs and present experimental results in agreement with theoretical predictions on both single- and multimode behavior and on levels of birefringence.

Waveguiding in surface plasmon polariton band gap structures.

Abstract: Using near-field optical microscopy, we investigate propagation and scattering of surface plasmon polaritons (SPP’s) excited in the wavelength range of 780 – 820 nm at nanostructured gold-film surfaces with areas of 200-nm-wide scatterers arranged in a 400-nm-period triangular lattice containing line defects. We observe the SPP reflection by such an area and SPP guiding along line defects at 782 nm, as well as significant deterioration of these effects is 815 nm, thereby directly demonstrating the SPP band gap effect and showing first examples of SPP channel waveguides in surface band gap structures.

Carbon Nanotube Templated Growth of Mesoporous Zeolite Single Crystals

Abstract: Carbon nanotubes are shown to be useful materials for introduction of nanopores with a controlled diameter into zeolite single crystals. The intracrystalline nanopores are created by crystallization of the zeolite around the carbon nanotubes that are subsequently removed by combustion.

Topology synthesis of large‐displacement compliant mechanisms

Abstract: This paper describes the use of topology optimization as a synthesis tool for the design of large-displacement compliant mechanisms. An objective function for the synthesis of large-displacement mechanisms is proposed together with a formulation for synthesis of path-generating compliant mechanisms. The responses of the compliant mechanisms are modelled using a total Lagrangian finite element formulation, the sensitivity analysis is performed using the adjoint method and the optimization problem is solved using the method of moving asymptotes. Procedures to circumvent some numerical problems are discussed. Copyright © 2001 John Wiley & Sons, Ltd.

Mechanical Properties and Formation Mechanisms of a Wire of Single Gold Atoms

Abstract: A scanning tunneling microscope supplemented with a force sensor is used to study the mechanical properties of a novel metallic nanostructure: a freely suspended chain of single gold atoms. We find that the bond strength of the nanowire is about twice that of a bulk metallic bond. We perform ab initio calculations of the force at chain fracture and compare quantitatively with experimental measurements. The observed mechanical failure and nanoelastic processes involved during atomic wire fabrication are investigated using molecular dynamics simulations, and we find that the total effective stiffness of the nanostructure is strongly affected by the detailed local atomic arrangement at the chain bases.

Network Identification and Flux Quantification in the Central Metabolism of Saccharomyces cerevisiae under Different Conditions of Glucose Repression

Abstract: The network structure and the metabolic fluxes in central carbon metabolism were characterized in aerobically grown cells of Saccharomyces cerevisiae. The cells were grown under both high and low glucose concentrations, i.e., either in a chemostat at steady state with a specific growth rate of 0.1 h−1 or in a batch culture with a specific growth rate of 0.37 h−1. Experiments were carried out using [1-13C]glucose as the limiting substrate, and the resulting summed fractional labelings of intracellular metabolites were measured by gas chromatography coupled to mass spectrometry. The data were used as inputs to a flux estimation routine that involved appropriate mathematical modelling of the central carbon metabolism of S. cerevisiae. The results showed that the analysis is very robust, and it was possible to quantify the fluxes in the central carbon metabolism under both growth conditions. In the batch culture, 16.2 of every 100 molecules of glucose consumed by the cells entered the pentose-phosphate pathway, whereas the same relative flux was 44.2 per 100 molecules in the chemostat. The tricarboxylic acid cycle does not operate as a cycle in batch-growing cells, in contrast to the chemostat condition. Quantitative evidence was also found for threonine aldolase and malic enzyme activities, in accordance with published data. Disruption of the MIG1 gene did not cause changes in the metabolic network structure or in the flux pattern.

Phosphoric acid doped polybenzimidazole membranes: Physiochemical characterization and fuel cell applications

Abstract: A polymer electrolyte membrane fuel cell operational at temperatures around 150–200 °C is desirable for fast electrode kinetics and high tolerance to fuel impurities For this purpose polybenzimidazole (PBI) membranes have been prepared and H3PO4-doped in a doping range from 300 to 1600 mol % Physiochemical properties of the membrane electrolyte have been investigated by measurements of water uptake, acid doping level, electric conductivity, mechanical strength and water drag coefficient Electrical conductivity is found to be insensitive to humidity but dependent on the acid doping level At 160 °C a conductivity as high as 013 S cm−1 is obtained for membranes of high doping levels Mechanical strength measurements show, however, that a high acid doping level results in poor mechanical properties At operational temperatures up to 190 °C, fuel cells based on this polymer membrane have been tested with both hydrogen and hydrogen containing carbon monoxide

Mechanisms of Proton Conductance in Polymer Electrolyte Membranes

Abstract: We provide a phenomenological description of proton conductance in polymer electrolyte membranes, based on contemporary views of proton transfer processes in condensed media and a model for heterogeneous polymer electrolyte membrane structure. The description combines the proton transfer events in a single pore with the total pore-network performance and, thereby, relates structural and kinetic characteristics of the membrane. The theory addresses specific experimentally studied issues such as the effect of the density of proton localization sites (equivalent weight) of the membrane material and the water content of the pores. The effect of the average distance between the sulfonate groups, which changes during membrane swelling, is analyzed in particular, and the factors which determine the temperature dependence of the macroscopic membrane conductance are disclosed. Numerical estimates of the specific membrane conductivity obtained from the theory agree very well with typical experimental data, thereby confirming the appropriateness of the theoretical concepts. Moreover, the versatility of the models offers a useful and transparent frame for combining the analysis of both experimental data and the results of molecular dynamics simulations.

gfp-Based N-Acyl Homoserine-Lactone Sensor Systems for Detection of Bacterial Communication

Abstract: In order to perform single-cell analysis and online studies ofN-acyl homoserine lactone (AHL)-mediated communication among bacteria, components of the Vibrio fischeri quorum sensor encoded by luxR-PluxI have been fused to modified versions of gfpmut3∗ genes encoding unstable green fluorescent proteins. Bacterial strains harboring this green fluorescent sensor detected a broad spectrum of AHL molecules and were capable of sensing the presence of 5 nMN-3-oxohexanoyl-l-homoserine lactone in the surroundings. In combination with epifluorescent microscopy, the sensitivity of the sensor enabled AHL detection at the single-cell level and allowed for real-time measurements of fluctuations in AHL concentrations. This green fluorescent AHL sensor provides a state-of-the-art tool for studies of communication between the individuals present in mixed bacterial communities.

Modulational instability in nonlocal nonlinear Kerr media.

Abstract: We study modulational instability (MI) of plane waves in nonlocal nonlinear Kerr media. For a focusing nonlinearity we show that, although the nonlocality tends to suppress MI, it can never remove it completely, irrespective of the particular profile of the nonlocal response function. For a defocusing nonlinearity the stability properties depend sensitively on the response function profile: for a smooth profile (e.g., a Gaussian) plane waves are always stable, but MI may occur for a rectangular response. We also find that the reduced model for a weak nonlocality predicts MI in defocusing media for arbitrary response profiles, as long as the intensity exceeds a certain critical value. However, it appears that this regime of MI is beyond the validity of the reduced model, if it is to represent the weakly nonlocal limit of a general nonlocal nonlinearity, as in optics and the theory of Bose-Einstein condensates.

Shedding light on disulfide bond formation: engineering a redox switch in green fluorescent protein.

Abstract: To visualize the formation of disulfide bonds in living cells, a pair of redox-active cysteines was introduced into the yellow fluorescent variant of green fluorescent protein. Formation of a disulfide bond between the two cysteines was fully reversible and resulted in a >2-fold decrease in the intrinsic fluorescence. Inter conversion between the two redox states could thus be followed in vitro as well as in vivo by non-invasive fluorimetric measurements. The 1.5 A crystal structure of the oxidized protein revealed a disulfide bond-induced distortion of the beta-barrel, as well as a structural reorganization of residues in the immediate chromophore environment. By combining this information with spectroscopic data, we propose a detailed mechanism accounting for the observed redox state-dependent fluorescence. The redox potential of the cysteine couple was found to be within the physiological range for redox-active cysteines. In the cytoplasm of Escherichia coli, the protein was a sensitive probe for the redox changes that occur upon disruption of the thioredoxin reductive pathway.