Showing papers by "United States Department of Energy published in 2005"

The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode.

Abstract: Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial parasitic nematode Brugia malayi. Although, quantitatively, the genome is even more degraded than those of closely related Rickettsia species, Wolbachia has retained more intact metabolic pathways. The ability to provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely to be Wolbachia's principal contribution to the mutualistic relationship, whereas the host nematode likely supplies amino acids required for Wolbachia growth. Genome comparison of the Wolbachia endosymbiont of B. malayi (wBm) with the Wolbachia endosymbiont of Drosophila melanogaster (wMel) shows that they share similar metabolic trends, although their genomes show a high degree of genome shuffling. In contrast to wMel, wBm contains no prophage and has a reduced level of repeated DNA. Both Wolbachia have lost a considerable number of membrane biogenesis genes that apparently make them unable to synthesize lipid A, the usual component of proteobacterial membranes. However, differences in their peptidoglycan structures may reflect the mutualistic lifestyle of wBm in contrast to the parasitic lifestyle of wMel. The smaller genome size of wBm, relative to wMel, may reflect the loss of genes required for infecting host cells and avoiding host defense systems. Analysis of this first sequenced endosymbiont genome from a filarial nematode provides insight into endosymbiont evolution and additionally provides new potential targets for elimination of cutaneous and lymphatic human filarial disease.

Role of water in electron-initiated processes and radical chemistry: issues and scientific advances.

Abstract: Chemical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352; Department of Chemistry, ShelbyHall, University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336; Notre Dame Radiation Laboratory, University of Notre Dame,Notre Dame, Indiana 46556; Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 0520-8107; Argonne NationalLaboratory, 9700 South Cass Avenue, Argonne, Illinois 60439; Department of Computer Science and Department of Physics, 2710 University Drive,Washington State University, Richland, Washington 99352-1671; Lawrence Berkeley National Laboratory, 1 Cyclotron Road Mailstop 1-0472,Berkeley, California 94720; Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300,Austin, Texas 78712; Office of Basic Energy Sciences, U.S. Department of Energy, SC-141/Germantown Building, 1000 Independence Avenue,S.W., Washington, D.C. 20585-1290; Department of Physics and Engineering Physics, Stevens Institute of Technology, Castle Point on Hudson,Hoboken, New Jersey 07030; Department of Chemistry, Johns Hopkins University, 34th and Charles Streets, Baltimore, Maryland 21218;Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062; Department of Chemistry, The Ohio StateUniversity, 100 West 18th Avenue, Columbus, Ohio 43210-1185; Department of Chemistry, Columbia University, Box 3107, Havemeyer Hall,New York, New York 10027; Department of Chemistry, University of Pittsburgh, Parkman Avenue and University Drive,Pittsburgh, Pennsylvania 15260; Chemistry Department, Brookhaven National Laboratory, Upton, New York 11973-5000; Department of Physics andAstronomy, Rutgers, The State University of New Jersey, 136 Frelinghuysen Road, Piscataway, New Jersey 08854-8019; Department of Chemistry,516 Rowland Hall, University of California, Irvine, Irvine, California 92697-2025; Stanford Synchrotron Radiation Laboratory, Stanford LinearAccelerator Center, 2575 Sand Hill Road, Mail Stop 69, Menlo Park, California 94025; School of Chemistry and Biochemistry, Georgia Institute ofTechnology, 770 State Street, Atlanta, Georgia 30332-0400; Geology Department, University of California, Davis, One Shields Avenue,Davis, California 95616-8605; Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue,Cambridge, Massachusetts 02139-4307; Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084Received July 23, 2004

Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution

Abstract: We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the A pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25-55 million years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species-but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.

On the chemical nature of graphene edges: origin of stability and potential for magnetism in carbon materials.

Abstract: Heretofore disconnected experimental observations are combined with a theoretical study to develop a model of the chemical composition of the edges of graphene sheets in both flat and curved sp2-hybridized carbon materials. It is proposed that under ambient conditions a significant fraction of the oxygen-free edge sites are neither H-terminated nor unadulterated σ free radicals, as universally assumed. The zigzag sites are carbene-like, with the triplet ground state being most common. The armchair sites are carbyne-like, with the singlet ground state being most common. This proposal is not only consistent with the key electronic properties and surface (re)activity behavior of carbons, but it can also explain the recently documented and heretofore puzzling ferromagnetic properties of some impurity-free carbon materials.

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

Abstract: Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolates from diverse areas of the world’s oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3%, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations in Prochlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer membrane synthesis and transport that dominate the flexible genome and set it apart from the core. Besides identifying islands and demonstrating their role throughout the history of Prochlorococcus, reconstruction of past gene gains and losses shows that much of the variability exists at the ‘‘leaves of the tree,’’ between the most closely related strains. Finally, the identification of core and flexible genes from this 12-genome comparison is largely consistent with the relative frequency of Prochlorococcus genes found in global ocean metagenomic databases, further closing the gap between our understanding of these organisms in the lab and the wild.

Adsorption of CO2 on Zeolites at Moderate Temperatures

Abstract: Pressure swing adsorption (PSA) and temperature swing adsorption (TSA) are potential techniques for removing carbon dioxide (CO2) from high-pressure fuel gas streams. Zeolites are suitable candidate sorbents for use in these processes; however, the systems would be even more energy efficient if the sorbents were operational at moderate or high temperatures, especially for the removal of CO2 from high-pressure gas streams, such as those from integrated gasification combined-cycle (IGCC) systems. Competitive gas adsorption tests with gas mixtures representing both coal combustion and coal gasification gas streams were conducted in an atmospheric flow reactor with five zeolites at 120 °C. Promising results of preferential adsorption of CO2 were observed with two of these zeolites. However, the CO2 adsorption capacity was significantly lower at 120 °C than at ambient temperature. Volumetric gas adsorption tests of CO2 and nitrogen (N2) on these two zeolites were conducted at 120 °C, up to a pressure of 300 ps...

Low Temperature Induction of Arabidopsis CBF1, 2, and 3 Is Gated by the Circadian Clock

Abstract: Exposing Arabidopsis (Arabidopsis thaliana) plants to low temperature results in rapid induction of CBF1, 2, and 3 (CBF1-3; also known as DREB1B, C, and A, respectively), which encode transcriptional activators that induce expression of a battery of genes that increase plant freezing and chilling tolerance. Recently, it has been shown that basal levels of CBF3 transcripts and those of certain CBF-regulated genes exhibit circadian cycling. Here, we further explored the regulation of CBF1-3 by the circadian clock. The results indicated that the extent to which CBF1-3 transcripts accumulated in response to low temperature was dependent on the time of day that the plants were exposed to low temperature and that this was regulated by the circadian clock. The highest and lowest levels of cold-induced CBF1-3 transcript accumulation occurred at 4 and 16 h after subjective dawn, respectively. An analysis of CBF2 promoter-reporter gene fusions indicated that this control included transcriptional regulation. In addition, the cold responsiveness of RAV1 and ZAT12, genes that are cold induced in parallel with CBF1-3, was also subject to circadian regulation. However, whereas the maximum level of cold-induced RAV1 transcript accumulation occurred at the same time of day as did CBF1-3 transcripts, that of ZAT12 was in reverse phase, i.e. the highest level of cold-induced ZAT12 transcript accumulation occurred 16 h after subjective dawn. These results indicate that cold-induced expression of CBF1-3, RAV1, and ZAT12 is gated by the circadian clock and suggest that this regulation likely occurs through at least two nonidentical (though potentially overlapping) signaling pathways.

Adsorption of Gases in Metal Organic Materials: Comparison of Simulations and Experiments

Abstract: Molecular simulations using standard force fields have been carried out to model the adsorption of various light gases on a number of different metal organic framework-type materials. The results have been compared with the available experimental data to test the validity of the model potentials. We observe good agreement between simulations and experiments for a number of different cases and very poor agreement in other cases. Possible reasons for the discrepancy in simulated and measured isotherms are discussed. We predict hydrogen adsorption isotherms at 77 and 298 K in a number of different metal organic framework materials. The importance of quantum diffraction effects and framework charges on the adsorption of hydrogen at 77 K is discussed. Our calculations indicate that at room temperature none of the materials that we have tested is able to meet the requirements for on-board hydrogen storage for fuel cell vehicles. We have calculated the volume available in a given sorbent at a specified adsorption energy (density of states). We discuss how this density of states can be used to assess the effectiveness of a sorbent material for hydrogen storage.

Tip loss corrections for wind turbine computations

Abstract: As an essential ingredient in the blade element momentum theory, the tip loss effect of rotors plays an important role in the prediction of wind turbine performance Various tip loss corrections based on the Prandtl tip loss function are analysed in the article Comparisons with measurements and theoretical analyses show that existing tip loss correction models are inconsistent and fail to predict correctly the physical behaviour in the proximity of the tip A new tip loss correction model is proposed that remedies the inconsistency Comparisons between numerical and experimental data show that the new model results in much better predictions of the loading in the tip region Copyright © 2005 John Wiley & Sons, Ltd

Prediction of hydrogen flux through sulfur-tolerant binary alloy membranes

Abstract: Metal membranes play a vital role in hydrogen purification. Defect-free membranes can exhibit effectively infinite selectivity but must also provide high fluxes, resistance to poisoning, long operational lifetimes, and low cost. Alloying offers one route to improve on membranes based on pure metals such as palladium. We show how ab initio calculations and coarse-grained modeling can accurately predict hydrogen fluxes through binary alloy membranes as functions of alloy composition, temperature, and pressure. Our approach, which requires no experimental input apart from knowledge of bulk crystal structures, is demonstrated for palladium-copper alloys, which show nontrivial behavior due to the existence of face-centered cubic and body-centered cubic crystal structures and have the potential to resist sulfur poisoning. The accuracy of our approach is examined by a comparison with extensive experiments using thick foils at elevated temperatures. Our experiments also demonstrate the ability of these membranes to resist poisoning by hydrogen sulfide.

Carbon dioxide capture by diamine-grafted SBA-15: A combined Fourier transform infrared and mass spectrometry study

Abstract: The adsorption and desorption of CO2 on diamine-grafted SBA-15 have been studied by infrared spectroscopy coupled with mass spectrometry. Diamine was grafted onto the SBA-15 surface by the reaction of [N-(2-aminoethyl)-3-aminopropyl]trimethoxysilane with the surface OH. CO2 is adsorbed on the diamine-grafted SBA-15 as bidentate carbonate and bidentate and monodentate bicarbonates at 25 °C. Bidentate carbonate and monodentate bicarbonates are the major surface species formed and decomposed during the concentration-swing adsorption/desorption process at 25 °C. Temperature-programmed desorption revealed that the monodentate and bidentate bicarbonates bound stronger to the diamine-grafted SBA-15 surface than the bidentate carbonate. The amount of CO2 desorbed from the carbonate and bicarbonate between 30 and 120 °C is 2 times more than that of CO2 adsorbed/desorbed during each cycle of the concentration-swing adsorption/desorption. Desorption at 120 °C removes the majority of the captured CO2 and regenerates ...

Optimization of Pressure Swing Adsorption and Fractionated Vacuum Pressure Swing Adsorption Processes for CO2 Capture

Abstract: This work focuses on the optimization of cyclic adsorption processes to improve the performance of CO2 capture from flue gas, consisting of nitrogen and carbon dioxide. The adopted processes are the PSA (pressure swing adsorption) process and the FVPSA (fractionated vacuum pressure swing adsorption) process, modified from the FVSA (fractionated vacuum swing adsorption) process developed by Air Products and Chemicals, Inc. The system models are currently bench scale and adopt zeolite13X as an adsorbent. The high-temperature PSA is better for high purity of product (CO2), and the high-temperature FVPSA is much better than the normal-temperature PSA processes. The main goal of this study is to improve the purity and recovery of carbon dioxide. The Langmuir isotherm parameters were calculated from experimental data taken at National Energy Technology Laboratory (Siriwardane, R.; NETL, DOE, 2004). Moreover, efficient optimization strategies are essential to compare these processes. To perform optimization work...

International comparison of requirements for connection of wind turbines to power systems

Abstract: Power production from wind turbines has increased considerably during the lost decade. Therefore today's wind turbines, which are typically set up in wind farms, have a significant influence on the ...

Estimation of WECC system inertia using observed frequency transients

Abstract: Computer models being developed to understand the interaction between demand-response technology, power system deregulation, and market transformation depend in part on understanding the relationship between system frequency and load control. Frequency, load, and plant outage events data collected over the last several years have permitted analysis to determine the Western Electricity Coordination Council system's inertia during each event. This data were used to evaluate the relationship of system inertia to total load, which is used to model system response to load curtailment programs in next-generation power system simulations.

The Specter of Fuel-Based Lighting

Abstract: Contemporary questions about sustainable energy and development converge in unexpected ways around a technology that is at once an echo of the past and yet very much a part of the present: fuel-based lighting in the developing world. An emerging opportunity for reducing the global costs and greenhouse gas emissions associated with this highly inefficient form of lighting energy use is to replace fuel-based lamps with white solid-state ("LED") lighting, described in this Policy Forum, which can be affordably solar-powered. Doing so would allow those without access to electricity in the developing world to affordably leapfrog over the prevailing incandescent and fluorescent lighting technologies in use today throughout the electrified world.

Dialkylaminopyridine-Functionalized Mesoporous Silica Nanosphere as an Efficient and Highly Stable Heterogeneous Nucleophilic Catalyst

Abstract: A new nucleophilic catalytic system comprised of dialkylaminopyridine-functionalized mesoporous silica nanosphere (DMAP-MSN) has been synthesized and characterized. We have demonstrated that this material is an efficient heterogeneous catalyst for Baylis-Hillman, acylation, and silylation reactions with good reactivity, product selectivity, and recyclability. We envision that this DMAP-functionalized mesoporous silica material can also serve as an effective heterogeneous catalyst for many other catalytic nucleophilic reactions.

Uncatalyzed and wall‐catalyzed forward water–gas shift reaction kinetics

Abstract: The kinetics of the high-temperature (1070–1134 K), low- and high-pressure gas-phase forward water–gas shift reaction (fWGSR) were evaluated in an empty quartz reactor and a quartz reactor packed with quartz particles. The power-law expression for the reaction rate was consistent with the Bradford mechanism and was invariant with respect to pressure. The experimental rate constant was lower than that published by Graven and Long, and slightly higher than estimates obtained using the reaction rate expression derived from the Bradford mechanism in conjunction with values of reaction rate constants obtained from the GRI database. Similar experiments conducted using a reactor composed of Inconel® 600, a representative reactor shell material, exhibited substantially enhanced rates of reaction. A simple power-law rate expression was incorporated into a surface-catalyzed plug flow reactor (PFR) model to correlate the results between 600 and 900 K. Palladium and palladium–copper alloy surfaces, representative of hydrogen membranes, were also shown to enhance the fWGSR rate, but not as much as the Inconel® 600 surfaces. © 2005 American Institute of Chemical Engineers AIChE J, 2005