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 biofuels, the fuels are often toxic to cell growth, creating a negative feedback loop that limits biofuel production. These toxic effects may be mitigated by expressing efflux pumps that export biofuel from the cell. We developed a model for cell growth and biofuel production and used it to compare several genetic control strategies for their ability to improve biofuel yields. We show that controlling efflux pump expression directly with a biofuel-responsive promoter is a straight forward way of improving biofuel production. In addition, a feed forward loop controller is shown to be versatile at dealing with uncertainty in biofuel production rates.

Oxy-fuel fireside research goals are: (1) determine the effect of oxyfuel combustion on fireside corrosion - flue gas recycle choice, staged combustion ramifications; and (2) develop methods to use chromia solubility in ash as an ash corrosivity measurement - synthetic ashes at first, then boiler and burner rig ashes.

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 reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

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 organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. …

There is a considerable interest to develop new time-of-flight detectors using, for example, micro-channel-plate photodetectors (MCP-PMTs). The question we pose in this paper is if new waveform digitizer ASICs, such as the WaveCatcher and TARGET, operating with a sampling rate of 2-3 GSa/s can compete with 1GHz BW CFD/TDC/ADC electronics. We have performed a series of measurements with these waveform digitizers coupled to MCP-PMTs operating at low gain and with a signal equivalent to {approx}40 photoelectrons. The tests were done with a laser diode on detectors operating under the same condition used previously in SLAC and Fermilab beam tests. Our test results indicate that one can achieve similar resolution with both methods. Although the commercial CFD-based electronics does exist and performs very well, it is difficult to implement on a very large scale, and therefore the custom electronics is needed. In addition, the analog delay line requirement makes it very difficult to incorporate CFD discriminators in ASIC designs.

Two detailed, unit-cell models, a transverse fin design and a longitudinal fin design, of a combined hydride bed and heat exchanger are developed in COMSOL{reg_sign} Multiphysics incorporating and accounting for heat transfer and reaction kinetic limitations. MatLab{reg_sign} scripts for autonomous model generation are developed and incorporated into (1) a grid-based and (2) a systematic optimization routine based on the Nelder-Mead downhill simplex method to determine the geometrical parameters that lead to the optimal structure for each fin design that maximizes the hydrogen stored within the hydride. The optimal designs for both the transverse and longitudinal fin designs point toward closely-spaced, small cooling fluid tubes. Under the hydrogen feed conditions studied (50 bar), a 25 times improvement or better in the hydrogen storage kinetics will be required to simultaneously meet the Department of Energy technical targets for gravimetric capacity and fill time. These models and methodology can be rapidly applied to other hydrogen storage materials, such as other metal hydrides or to cryoadsorbents, in future work.

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Article discussing stromatolites. The authors apply the method of Diffusion Entropy (DE) to the study of stromatolites by means of a two-dimensional procedure that makes it possible for us to compare the DE analysis to the results of a compression method.

Field validation for the long electrode electrical resistivity tomography (LE-ERT) method was attempted in order to demonstrate the performance of the technique in imaging a simple buried target. The experiment was an approximately 1/17 scale mock-up of a region encompassing a buried nuclear waste tank on the Hanford site. The target of focus was constructed by manually forming a simulated plume within the vadose zone using a tank waste simulant. The LE-ERT results were compared to ERT using conventional point electrodes on the surface and buried within the survey domain. Using a pole-pole array, both point and long electrode imaging techniques identified the lateral extents of the pre-formed plume with reasonable fidelity, but the LE-ERT was handicapped in reconstructing the vertical boundaries. The pole-dipole and dipole-dipole arrays were also tested with the LE-ERT method and were shown to have the least favorable target properties, including the position of the reconstructed plume relative to the known plume and the intensity of false positive targets. The poor performance of the pole-dipole and dipole-dipole arrays was attributed to an inexhaustive and non-optimal coverage of data at key electrodes, as well as an increased noise for electrode combinations with high geometric factors. However, when …