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in creator/contributor: "Lawrence Berkeley National Laboratory. Physical Biosciences Division."  
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The evolution of Ga and As core levels in the formation of Fe/GaAs (001):A high resolution soft x-ray photoelectron spectroscopic study

Description: A high resolution soft x-ray photoelectron spectroscopic study of Ga and As 3d core levels has been conducted for Fe/GaAs (001) as a function of Fe thickness. This work has provided unambiguous evidence of substrate disrupting chemical reactions induced by the Fe overlayer--a quantitative analysis of the acquired spectra indicates significantly differing behavior of Ga and As during Fe growth, and our observations have been compared with existing theoretical models. Our results demonstrate that… more
Date: July 14, 2008
Creator: Thompson, Jamie; Neal, James; Shen, Tiehan; Morton, Simon; Tobin, James; Waddill, George Dan et al.
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Partner: UNT Libraries Government Documents Department
open access

A model for improving microbial biofuel production using a synthetic feedback loop

Description: Cells use feedback to implement a diverse range of regulatory functions. Building synthetic feedback control systems may yield insight into the roles that feedback can play in regulation since it can be introduced independently of native regulation, and alternative control architectures can be compared. We propose a model for microbial biofuel production where a synthetic control system is used to increase cell viability and biofuel yields. Although microbes can be engineered to produce biofuel… more
Date: July 14, 2011
Creator: Dunlop, Mary; Keasling, Jay & Mukhopadhyay, Aindrila
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Partner: UNT Libraries Government Documents Department
open access

MicrobesOnline: an integrated portal for comparative and functional genomics

Description: Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconst… more
Date: July 14, 2011
Creator: Dehal, Paramvir; Joachimiak, Marcin; Price, Morgan; Bates, John; Baumohl, Jason; Chivian, Dylan et al.
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Partner: UNT Libraries Government Documents Department
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A simple method for enzymatic synthesis of unlabeled and radiolabeled Hydroxycinnamate-CoA

Description: Hydroxycinnamate coenzyme A (CoA) thioesters are substrates for biosynthesis of lignin and hydroxycinna- mate esters of polysaccharides and other polymers. Hence, a supply of these substrates is essential for investigation of cell wall biosynthesis. In this study, three recombinant enzymes, caffeic acid 3-O-methyltransferase, 4-coumarate- CoA ligase 1, and 4-coumarate-CoA ligase 5, were cloned from wheat, tobacco, and Arabidopsis, respectively, and were used to synthesize {sup 14}C-feruloyl-CoA… more
Date: July 20, 2011
Creator: Rautergarten, Carsten; Baidoo, Edward; Keasling, Jay & Vibe Scheller, Henrik
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Partner: UNT Libraries Government Documents Department
open access

Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil

Description: Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading org… more
Date: July 14, 2011
Creator: DeAngelis, Kristen; Allgaier, Martin; Chavarria, Yaucin; Fortney, Julian; Hugenholtz, Phillip; Simmons, Blake et al.
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Partner: UNT Libraries Government Documents Department
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Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Description: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor inte… more
Date: July 31, 2009
Creator: N. Price, Morgan; S. Dehal, Paramvir & P. Arkin, Adam
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Partner: UNT Libraries Government Documents Department
open access

Bayesian Estimates of Free Energies from Nonequilibrium Work Data in the Presence of Instrument Noise

Description: The Jarzynski equality and the fluctuation theorem relate equilibrium free energy differences to nonequilibrium measurements of the work. These relations extend to single-molecule experiments that have probed the finite-time thermodynamics of proteins and nucleic acids. The effects of experimental error and instrument noise have not been considered previously. Here, we present a Bayesian formalism for estimating free energy changes from nonequilibrium work measurements that compensates for inst… more
Date: July 8, 2008
Creator: Maragakis, Paul; Ritort, Felix; Bustamante, Carlos; Karplus, Martin & Crooks, Gavin E.
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Partner: UNT Libraries Government Documents Department
open access

X-ray Absorption Spectroscopy

Description: This review gives a brief description of the theory and application of X-ray absorption spectroscopy, both X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), especially, pertaining to photosynthesis. The advantages and limitations of the methods are discussed. Recent advances in extended EXAFS and polarized EXAFS using oriented membranes and single crystals are explained. Developments in theory in understanding the XANES spectra are described. The… more
Date: July 9, 2009
Creator: Yano, Junko & Yachandra, Vittal K.
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Partner: UNT Libraries Government Documents Department
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electronic Ligand Builder and Optimisation Workbench (eLBOW): A tool for ligand coordinate and restraint generation

Description: The electronic Ligand Builder and Optimisation Workbench (eLBOW) is a program module of the PHENIX suite of computational crystallographic software. It's designed to be a flexible procedure using simple and fast quantum chemical techniques to provide chemically accurate information for novel and known ligands alike. A variety of input formats and options allow for the attainment of a number of diverse goals including geometry optimisation and generation of restraints.
Date: July 1, 2009
Creator: Moriarty, Nigel; Grosse-Kunstleve, Ralf & Adams, Paul
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Partner: UNT Libraries Government Documents Department
open access

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

Description: We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution… more
Date: July 20, 2009
Creator: Hura, Greg L.; Menon, Angeli L.; Hammel, Michal; Rambo, Robert P.; Poole II, Farris L.; Tsutakawa, Susan E. et al.
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Partner: UNT Libraries Government Documents Department
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Spectroscopic Analyses of the Biofuels-Critical Phytochemical Coniferyl Alcohol and Its Enzyme-Catalyzed Oxidation Products

Description: Lignin composition (monolignol types of coniferyl, sinapyl or p-coumaryl alcohol) is causally related to biomass recalcitrance. We describe multiwavelength (220, 228, 240, 250, 260, 290, 295, 300, 310 or 320 nm) absorption spectroscopy of coniferyl alcohol and its laccase- or peroxidase-catalyzed products during real time kinetic, pseudo-kinetic and endpoint analyses, in optical turn on or turn off modes, under acidic or basic conditions. Reactions in microwell plates and 100 mu L volumes demon… more
Date: July 13, 2011
Creator: Achyuthan, Komandoor; Adams, Paul; Simmons, Blake & Singh, Anup
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Partner: UNT Libraries Government Documents Department
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Development of a Markerless Genetic Exchange System in Desulfovibrio vulgaris Hildenborough and Its Use in Generating a Strain with Increased Transformation Efficiency

Description: In recent years, the genetic manipulation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough has seen enormous progress. In spite of this progress, the current marker exchange deletion method does not allow for easy selection of multiple sequential gene deletions in a single strain because of the limited number of selectable markers available in D. vulgaris. To broaden the repertoire of genetic tools for manipulation, an in-frame, markerless deletion system has been develope… more
Date: July 21, 2009
Creator: Keller, Kimberly L.; Bender, Kelly S. & Wall, Judy D.
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Partner: UNT Libraries Government Documents Department
open access

Biofuel Economics

Description: As concerns regarding increasing energy prices, global warming and renewable resources continue to grow, so has scientific discovery into agricultural biomass conversion. Plant Biomass Conversion addresses both the development of plant biomass and conversion technology, in addition to issues surrounding biomass conversion, such as the affect on water resources and soil sustainability. This book also offers a brief overview of the current status of the industry and examples of production plants … more
Date: July 15, 2011
Creator: Klein-Marcuschamer, Daniel; Holmes, Brad; Simmons, Blake & Blanch, Harvey
Item Type: Refine your search to only Book
Partner: UNT Libraries Government Documents Department
open access

On thermodynamic and microscopic reversibility

Description: The word 'reversible' has two (apparently) distinct applications in statistical thermodynamics. A thermodynamically reversible process indicates an experimental protocol for which the entropy change is zero, whereas the principle of microscopic reversibility asserts that the probability of any trajectory of a system through phase space equals that of the time reversed trajectory. However, these two terms are actually synonymous: a thermodynamically reversible process is microscopically reversib… more
Date: July 12, 2011
Creator: Crooks, Gavin E.
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Partner: UNT Libraries Government Documents Department
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