Knowledge of the thermophysical properties of materials at extreme pressure and temperature conditions is essential for improving our understanding of many planetary and detonation processes. Significant gaps in what is known about the behavior of materials at high density and high temperature exist, largely due to the limitations and dangers of performing experiments at the necessary extreme conditions. Modeling these systems through the use of equations of state and particle-based simulation methods significantly extends the range of pressures and temperatures that can be safely studied. The reliability of such calculations depends on the accuracy of the models used. Here we present an assessment of the united-atom version of the TraPPE (Transferable Potentials for Phase Equilibria) force field and single-site exp-6 representations for methane, methanol, oxygen, and ammonia at extreme conditions. As shown by Monte Carlo simulations in the isobaric-isothermal ensemble, the TraPPE models, despite being parameterized to the vapor-liquid coexistence curve (i.e. relatively mild conditions), perform remarkably well in the high pressure/high temperature regime. The single-site exp-6 models can fit experimental data in the high pressure/temperature regime very well, but the parameters are less transferable to ambient conditions.

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We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. All three genomes share a conserved double origin of replication and many gene clusters. M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcinae in the region proximal to the origin of replication with interspecies gene similarities as high as 95%. However it is disordered and marked by increased transposase frequency and decreased gene synteny and gene density in the proximal semi-genome. Of the 3680 open reading frames in M. barkeri, 678 had paralogs with better than 80% similarity to both M. acetivorans and M. mazei while 128 nonhypothetical orfs were unique (non-paralogous) amongst these species including a complete formate dehydrogenase operon, two genes required for N-acetylmuramic acid synthesis, a 14 gene gas vesicle cluster and a bacterial P450-specific ferredoxin reductase cluster not previously observed or characterized in this genus. A cryptic 36 kbp plasmid sequence was detected in M. barkeri that contains an orc1 gene flanked by a presumptive origin of replication consisting of 38 tandem repeats of a 143 nt motif. Three-way comparison of these genomes reveals differing mechanisms …

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An understanding of the hydrologic interactions among atmosphere, land surface, and subsurface is one of the keys to understanding the water cycling system that supports life on earth. The inherent coupled processes and complex feedback structures among subsystems make such interactions difficult to simulate. In this paper, we present a model that simulates the land surface and subsurface hydrologic response to meteorological forcing. This model combines a state-of-the-art land-surface model, the NCAR Community Land Model version 3 (CLM3), with a variably saturated groundwater model, TOUGH2, through an internal interface that includes flux and state variables shared by the two submodels. Specifically, TOUGH2 uses infiltration, evaporation, and root-uptake rates, calculated by CLM3, as source/sink terms in its simulation; CLM3 uses saturation and capillary pressure profiles, calculated by TOUGH2, as state variables in its simulation. This new model, CLMT2, preserves the best aspects of both submodels: the state-of-the-art modeling capability of surface energy and hydrologic processes (including snow, runoff, freezing/melting, evapotranspiration, radiation, and biophysiological processes) from CLM3 and the more realistic physical-process-based modeling capability of subsurface hydrologic processes (including heterogeneity, three-dimensional flow, seamless combining of unsaturated and saturated zone, and water table) from TOUGH2. The preliminary simulation results show that the coupled …

Plasma fluxes to the divertor region in ITER near the magnetic separatrix have been modeled extensively in the past. The smaller, but potentially very important fluxes to the main chamber and outer divertor regions are the focus of the present paper. Two main additions to the usual transport modeling are investigated: namely, convective radial transport from intermittent, rapidly propagating ''blob'' events, and inclusion of the magnetic flux-surface region beyond the second X-point that actually contacts the main-chamber wall. The two-dimensional fluid transport code UEDGE is use to model the plasma, while the energy spectrum of charge-exchange neutrals to the main chamber wall is calculated by DEGAS 2 Monte Carlo code. Additionally, the spatial distribution of Be sputtered from the main chamber wall is determined in the fluid limit.

The higher oxidation states of iron (Fe(VI) and Fe(V) in particular) have been shown to be strongly oxidizing in enzymatic systems, where they can carry out aliphatic hydrogen abstraction. In addition, they have been postulated as intermediates in Fenton-type systems. Fe(VI) itself is relatively stable and has been shown to have potential as an oxidant in the so-called ''green'' treatment of polluted waters. By contrast, Fe(V) is a relatively short-lived transient when produced in aqueous solution in the absence of strongly bonding ligands other than hydroxide, a feature that has limited studies of its reactivity. Fe(VI) has been proposed to be useful in battery design and a very interesting study suggested that ferrate may be able to oxidize insoluble chromium to chromate and thus serve to remove chromium contamination in the Hanford radioactive waste tanks.

MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A …