Composite vertices that lead to soft form factors

The momentum-space cut-off parameter $\Lambda$ of hadronic vertex functions is studied in this paper. We use a composite model where we can measure the contributions of intermediate particle propagations to $\Lambda$. We show that in many cases a composite vertex function has a much smaller cut-off than its constituent vertices, particularly when light constituents such as pions are present in the intermediate state. This suggests that composite meson-baryon-baryon vertex functions are rather soft, i.e., they have \Lambda considerably less than 1 GeV. We discuss the origin of this softening of form factors as well as the implications of our findings on the modeling of nuclear reactions.Comment: REVTex, 19 pages, 5 figs(to be provided on request

Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction.

Tumor heterogeneity is a limiting factor in cancer treatment and in the discovery of biomarkers to personalize it. We describe a computational purification tool, ISOpure, to directly address the effects of variable normal tissue contamination in clinical tumor specimens. ISOpure uses a set of tumor expression profiles and a panel of healthy tissue expression profiles to generate a purified cancer profile for each tumor sample and an estimate of the proportion of RNA originating from cancerous cells. Applying ISOpure before identifying gene signatures leads to significant improvements in the prediction of prognosis and other clinical variables in lung and prostate cancer

Enhancing properties of iron and manganese ores as oxygen carriers for chemical looping processes by dry impregnation

The use of naturally occurring ores as oxygen carriers in CLC processes is attractive because of their relative abundance and low cost. Unfortunately, they typically exhibit lower reactivity and lack the mechanical robustness required, when compared to synthetically produced carriers. Impregnation is a suitable method for enhancing both the reactivity and durability of natural ores when used as oxygen carriers for CLC systems. This investigation uses impregnation to improve the chemical and mechanical properties of a Brazilian manganese ore and a Canadian iron ore. The manganese ore was impregnated with Fe2O3 and the iron ore was impregnated with Mn2O3 with the goal of forming a combined Fe/Mn oxygen carrier. The impregnated ore’s physical characteristics were assessed by SEM, BET and XRD analysis. Measurements of the attrition resistance and crushing strength were used to investigate the mechanical robustness of the oxygen carriers. The impregnated ore’s mechanical and physical properties were clearly enhanced by the impregnation method, with boosts in crushing strength of 11–26% and attrition resistance of 37–31% for the impregnated iron and manganese ores, respectively. Both the unmodified and impregnated ore’s reactivity, for the conversion of gaseous fuel (CH4 and syngas) and gaseous oxygen release (CLOU potential) were investigated using a bench-scale quartz fluidised-bed reactor. The impregnated iron ore exhibited a greater degree of syngas conversion compared to the other samples examined. Iron ore based oxygen carrier’s syngas conversion increases with the number of oxidation and reduction cycles performed. The impregnated iron ore exhibited gaseous oxygen release over extended periods in an inert atmosphere and remained at a constant 0.2% O2 concentration by volume at the end of this inert period. This oxygen release would help ensure the efficient use of solid fuels. The impregnated iron ore’s reactivity for CH4 conversion was similar to the reactivity of its unmodified counterpart. The unmodified manganese ore converted CH4 to the greatest extent of all the samples tested here, while the impregnated manganese ore exhibited a decrease in reactivity with respect to syngas and CH4 conversion.EPSR

Dynamical nonequilibrium molecular dynamics reveals the structural basis for allostery and signal propagation in biomolecular systems

A dynamical approach to nonequilibrium molecular dynamics (D-NEMD), proposed in the 1970s by Ciccotti et al., is undergoing a renaissance and is having increasing impact in the study of biological macromolecules. This D-NEMD approach, combining MD simulations in stationary (in particular, equilibrium) and nonequilibrium conditions, allows for the determination of the time-dependent structural response of a system using the Kubo–Onsager relation. Besides providing a detailed picture of the system’s dynamic structural response to an external perturbation, this approach also has the advantage that the statistical significance of the response can be assessed. The D-NEMD approach has been used recently to identify a general mechanism of inter-domain signal propagation in nicotinic acetylcholine receptors, and allosteric effects in β-lactamase enzymes, for example. It complements equilibrium MD and is a very promising approach to identifying and analysing allosteric effects. Here, we review the D-NEMD approach and its application to biomolecular systems, including transporters, receptors, and enzymes