Quality assessment of protein NMR structures

Biomolecular NMR structures are now routinely used in biology, chemistry, and bioinformatics. Methods and metrics for assessing the accuracy and precision of protein NMR structures are beginning to be standardized across the biological NMR community. These include both knowledge-based assessment metrics, parameterized from the database of protein structures, and model versus data assessment metrics. On line servers are available that provide comprehensive protein structure quality assessment reports, and efforts are in progress by the world-wide Protein Data Bank (wwPDB) to develop a biomolecular NMR structure quality assessment pipeline as part of the structure deposition process. These quality assessment metrics and standards will aid NMR spectroscopists in determining more accurate structures, and increase the value and utility of these structures for the broad scientific community

Phase behaviour of additive binary mixtures in the limit of infinite asymmetry

We provide an exact mapping between the density functional of a binary mixture and that of the effective one-component fluid in the limit of infinite asymmetry. The fluid of parallel hard cubes is thus mapped onto that of parallel adhesive hard cubes. Its phase behaviour reveals that demixing of a very asymmetric mixture can only occur between a solvent-rich fluid and a permeated large particle solid or between two large particle solids with different packing fractions. Comparing with hard spheres mixtures we conclude that the phase behaviour of very asymmetric hard-particle mixtures can be determined from that of the large component interacting via an adhesive-like potential.Comment: Full rewriting of the paper (also new title). 4 pages, LaTeX, uses revtex, multicol, epsfig, and amstex style files, to appear in Phys. Rev. E (Rapid Comm.

Oxygenase Domain of Drosophila melanogaster Nitric Oxide Synthase: Unique Kinetic Parameters Enable a More Efficient NO Release

Although nitric oxide (NO) is important for cell signaling and nonspecific immunity in the fruit fly Drosophila melanogaster, little is known about its single NO synthase (dNOS). We expressed the oxygenase domain of dNOS (dNOSoxy), characterized its spectroscopic, kinetic, and catalytic properties, and interpreted them in light of a global kinetic model for NO synthesis. Single turnover reactions with ferrous dNOSoxy showed it could convert Arg to N'omega-hydroxy-l-arginine (NOHA), or NOHA to citrulline and NO, when it was given 6R-tetrahydrobiopterin and O2. The dNOSoxy catalyzed Arg hydroxylation and NOHA oxidation at rates that matched or exceeded the rates catalyzed by the three mammalian NOSoxy enzymes. Consecutive heme-dioxy, ferric heme-NO, and ferric heme species were observed in the NOHA reaction of dNOSoxy, indicating that its catalytic mechanism is the same as in the mammalian NOS. However, NO dissociation from dNOSoxy was 4 to 9 times faster than that from the mammalian NOS enzymes. In contrast, the dNOSoxy ferrous heme-NO complex was relatively unreactive toward O2 and in this way was equivalent to the mammalian neuronal NOS. Our data show that dNOSoxy has unique settings for the kinetic parameters that determine its NO synthesis. Computer simulations reveal that these unique settings should enable dNOS to be a more efficient and active NO synthase than the mammalian NOS enzymes, which may allow it to function more broadly in cell signaling and immune functions in the fruit fly

The Pseudotransannular Ring Opening of 1-Aminocyclohept-4-ene-derived Epoxides in the Synthesis of Tropane Alkaloids: Total Synthesis of (±)-Ferrugine

We have optimized a synthetic approach to (±)-Ferrugine in 8 steps starting from 5-aminocyclohept-1-ene and using the Brønsted acid-catalyzed pseudotransannular ring-opening of the epoxide derived from this cycloheptene as the key step for the construction of the 8-azabicyclo[3.2.1]octane central core. While attempting the enantioselective synthesis of this natural product from enantiopure 2-hydroxy-8-azabicyclo[3.2.1]octane we have found that this compound shows a pronounced tendency to racemize via an achiral symmetric aziridinium intermediate. This racemization side process has been studied in detail using both experimental and computational methods

Phase behavior of a system of particles with core collapse

The pressure-temperature phase diagram of a one-component system, with particles interacting through a spherically symmetric pair potential in two dimensions is studied. The interaction consists of a hard core plus an additional repulsion at low energies. It is shown that at zero temperature, instead of the expected isostructural transition due to core collapse occurring when increasing pressure, the system passes through a series of ground states that are not triangular lattices. In particular, and depending on parameters, structures with squares, chains, hexagons and even quasicrystalline ground states are found. At finite temperatures the solid-fluid coexistence line presents a zone with negative slope (which implies melting with decreasing in volume) and the fluid phase has a temperature of maximum density, similar to that in water.Comment: 11 pages, 15 figures included. To appear in PRE. Some figures in low quality format. Better ones available upon request from [email protected]

Phase behavior and material properties of hollow nanoparticles

Effective pair potentials for hollow nanoparticles like the ones made from carbon (fullerenes) or metal dichalcogenides (inorganic fullerenes) consist of a hard core repulsion and a deep, but short-ranged, van der Waals attraction. We investigate them for single- and multi-walled nanoparticles and show that in both cases, in the limit of large radii the interaction range scales inversely with the radius, $R$, while the well depth scales linearly with $R$. We predict the values of the radius $R$ and the wall thickness $h$ at which the gas-liquid coexistence disappears from the phase diagram. We also discuss unusual material properties of the solid, which include a large heat of sublimation and a small surface energy.Comment: Revtex, 13 pages with 8 Postscript files included, submitted to Phys. Rev.

Propulsion integration study of civil aero-engine nacelles

It is envisaged that future civil aero-engines will operate with ultra-high bypass ratios to reduce the specific fuel consumption. To achieve the expected benefits from the new engine cycles, these new powerplants may mount compact nacelles. For these new configurations the aerodynamic coupling between the powerplant and the airframe may increase. For this reason, it is required to quantify and further understand the effects of aircraft integration for compact aero-engine nacelles. This study provides an insight of the changes in flow aerodynamics as well as quantification of the most relevant performance metrics of the powerplant, airframe and the combined aircraft system across a range of different installation positions. Relative to a conventional architecture, there is an aerodynamic benefit in net vehicle force of about 1.2% for a compact powerplant when installed in forward positions. This is the same improvement that was identified when the aero-engine nacelles were in isolation. However, for close-coupled installation positions, the aerodynamic benefit in net vehicle force erodes to 0.44% due to the larger effects of aircraft integration on compact nacelles

Artificial neural network for preliminary design and optimisation of civil aero-engine nacelles

Within the context of preliminary aerodynamic design with low order models, the methods have to meet requirements for rapid evaluations, accuracy and sometimes large design space bounds. This can be further compounded by the need to use geometric and aerodynamic degrees of freedom to build generalised models with enough flexibility across the design space. For transonic applications, this can be challenging due to the non-linearity of these flow regimes. This paper presents a nacelle design method with an artificial neural network (ANN) for preliminary aerodynamic design. The ANN uses six intuitive nacelle geometric design variables and the two key aerodynamic properties of Mach number and massflow capture ratio. The method was initially validated with an independent dataset in which the prediction error for the nacelle drag was 2.9% across the bounds of the metamodel. The ANN was also used for multi-point, multi-objective optimisation studies. Relative to computationally expensive CFD-based optimisations, it is demonstrated that the surrogate-based approach with ANN identifies similar nacelle shapes and drag changes across a design space that covers conventional and future civil aero-engine nacelles. The proposed method is an enabling and fast approach for preliminary nacelle design studies.The authors thank Rolls-Royce plc for supporting this research. Partial financial support was received from the INNOVATE UK FANFARE and the INNOVATIVE UK iFAN projects

Tratamiento de agua residual con elevado contenido de nitratos utilizando reactores biomembrana aireados

[ES] Se describe la eliminación conjunta de carbono y nitrógeno de un agua residual, llevada a cabo en reactores biomembrana de laboratorio. El agua residual sintética tuvo una composición similar a la que resultaría de la mezcla, en determinadas proporciones, de agua residual urbana con agua de acuífero rica en nitratos. Se utilizaron dos reactores en paralelo, con igual superficie de soporte pero distinto volumen. Aunque se insufló aire a la biopelícula a través del soporte, el seno del agua permaneció anóxico. La eliminación de nitratos resultó ser una función de la carga orgánica aplicada, estando en un rango de 4 a 6 g N-NO3 elim./(m2•d) para carga aplicada de 120 g DQO/(m2•d), y de 8 a 10 g N-NO3 elim./(m2•d) para carga aplicada de 240 g DQO/(m2•d). La carga orgánica eliminada fue de 87 a 180 g DQO/(m2•d). Se observó que el incremento de nitratos en el agua problema no produjo una mayor desnitrificación, sino una producción y acumulación de nitritos en el reactor. Una sola etapa no permite el máximo aprovechamiento de materia orgánica para desnitrificación, lo cual se podría obtener utilizando dos etapas en serie: una de desnitrificación (para los nitratos del afluente aportados por el agua de acuífero), y la otra de nitrificación-desnitrificación simultáneas (para eliminar el nitrógeno amoniacal afluente aportado por el agua residual urbana). Así, la materia orgánica sería eliminada parcialmente en cada etapa.Lolmede, P.; Jácome, A.; Vidart, T.; Tejero Monzón, I. (2000). Tratamiento de agua residual con elevado contenido de nitratos utilizando reactores biomembrana aireados. Ingeniería del Agua. 7(3):243-254. https://doi.org/10.4995/ia.2000.284724325473Abdel-Warith A.S., Williamson K.J., Strand S.E. (1990). Substratum aerated biofilm reactor. Proceedings of the Environmental Engineering 1990 Specialty Conference (ASCE), Airlington, Virginia on July 8-11. pp. 360-365.Amieva J.J. (1987). 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(Noyes Data Corporation, N. Jersey, USA. ISBN 0-8155-0963-