Comparison of atomic scale dynamics for the middle and late transition metal nanocatalysts

Catalysis of chemical reactions by nanosized clusters of transition metals holds the key to the provision of sustainable energy and materials. However, the atomistic behaviour of nanocatalysts still remains largely unknown due to uncertainties associated with the highly labile metal nanoclusters changing their structure during the reaction. In this study, we reveal and explore reactions of nm-sized clusters of 14 technologically important metals in carbon nano test tubes using time-series imaging by atomically-resolved transmission electron microscopy (TEM), employing the electron beam simultaneously as an imaging tool and stimulus of the reactions. Defect formation in nanotubes and growth of new structures promoted by metal nanoclusters enable the ranking of the different metals both in order of their bonding with carbon and their catalytic activity, showing significant variation across the Periodic Table of Elements. Metal nanoclusters exhibit complex dynamics shedding light on atomistic workings of nanocatalysts, with key features mirroring heterogeneous catalysis

EhMAPK, the Mitogen-Activated Protein Kinase from Entamoeba histolytica Is Associated with Cell Survival

Mitogen Activated Protein Kinases (MAPKs) are a class of serine/threonine kinases that regulate a number of different cellular activities including cell proliferation, differentiation, survival and even death. The pathogen Entamoeba histolytica possess a single homologue of a typical MAPK gene (EhMAPK) whose identification was previously reported by us but its functional implications remained unexplored. EhMAPK, the only mitogen-activated protein kinase from the parasitic protist Entamoeba histolytica with Threonine-X-Tyrosine (TXY) phosphorylation motif was cloned, expressed in E. coli and functionally characterized under different stress conditions. The expression profile of EhMAPK at the protein and mRNA level remained similar among untreated, heat shocked and hydrogen peroxide-treated samples in all cases of dose and time. But a significant difference was obtained in the phosphorylation status of the protein in response to different stresses. Heat shock at 43°C or 0.5 mM H2O2 treatment enhanced the phosphorylation status of EhMAPK and augmented the kinase activity of the protein whereas 2.0 mM H2O2 treatment induced dephosphorylation of EhMAPK and loss of kinase activity. 2.0 mM H2O2 treatment reduced parasite viability significantly but heat shock and 0.5 mM H2O2 treatment failed to adversely affect E. histolytica viability. Therefore, a distinct possibility that activation of EhMAPK is associated with stress survival in E. histolytica is seen. Our study also gives a glimpse of the regulatory mechanism of the protein under in vivo conditions. Since the parasite genome lacks any typical homologue of mammalian MEK, the dual specificity kinases which are the upstream activators of MAPK, indications of the existence of some alternate regulatory mechanisms of the EhMAPK activity is perceived. These may include the autophosphorylation activity of the protein itself in combination with some upstream phosphatases which are not yet identified

An empirical Bayesian approach for model-based inference of cellular signaling networks

Background A common challenge in systems biology is to infer mechanistic descriptions of biological process given limited observations of a biological system. Mathematical models are frequently used to represent a belief about the causal relationships among proteins within a signaling network. Bayesian methods provide an attractive framework for inferring the validity of those beliefs in the context of the available data. However, efficient sampling of high-dimensional parameter space and appropriate convergence criteria provide barriers for implementing an empirical Bayesian approach. The objective of this study was to apply an Adaptive Markov chain Monte Carlo technique to a typical study of cellular signaling pathways. Results As an illustrative example, a kinetic model for the early signaling events associated with the epidermal growth factor (EGF) signaling network was calibrated against dynamic measurements observed in primary rat hepatocytes. A convergence criterion, based upon the Gelman-Rubin potential scale reduction factor, was applied to the model predictions. The posterior distributions of the parameters exhibited complicated structure, including significant covariance between specific parameters and a broad range of variance among the parameters. The model predictions, in contrast, were narrowly distributed and were used to identify areas of agreement among a collection of experimental studies. Conclusion In summary, an empirical Bayesian approach was developed for inferring the confidence that one can place in a particular model that describes signal transduction mechanisms and for inferring inconsistencies in experimental measurements

Dynamic behavior of single Fe atoms embedded in graphene

The effect of electron irradiation on the dynamic behavior of Fe atoms, embedded into monoS vacancy (Fe@MV) and diSvacancy (Fe@DV) defects in graphene, has been investigated using ab initio molecular dynamics. This study reveals the detailed mechanisms of transformation and migration of the Fe@MV and Fe@DV defects in graphene recently observed in aberration-corrected highSresolution transmission electron microscopy (ACSHRTEM) experiments [Nano Lett. 2013, 13, 1468]. An important atomicSscale insight into the dynamics of atomic Fe on graphene, unavailable to ACSHRTEM observations, has been provided. It was found that structural changes of the studied defects are induced by electron impacts on carbon atoms bonded to Fe. The threshold energies for ejection of these carbon atoms are significantly lower compared to that in pristine graphene. For electron impacts with the subSthreshold transferred energies, migration of the defects and flipping of Fe atoms between different sides of the graphene plane can occur. The stability of the Fe@MV defect under electron irradiation strongly depends on the substrate side position of Fe atom with respect to the direction of the electron beam. The Fe@DV → Fe@MV transformations take place spontaneously in the presence of carbon adSatoms, which are available in abundance on graphene in ACSHRTEM. The present study facilitates a greater general understanding of the dynamic behavior of substitutional metal atoms in graphene

Reconfigurations and diffusion of trivacancy in silicon

Disappearance of the divacancy (V 2) and trivacancy (V 3) complexes upon isochronal and isothermal annealing of electron irradiated Si:O crystals has been studied by means of deep level transient spectroscopy. The annealing studies have shown that the V 2 and V 3 defects are mobile in Si at T>200 °C and in oxygen-rich material are trapped by interstitial oxygen atoms so resulting in the appearance of V 2O and V 3O defects. The activation energies for diffusion of the V 2 and V 3 centers have been determined. Density functional modeling calculations have been carried out to investigate the migration and reorientation mechanisms of V 3 in large silicon supercells. It is proposed that these comprise a sequence of transformations between V 3(D 3) and V 3(C 2v) configurations. © 2011 Elsevier B.V. All rights reserved