Bombardment of Graphite and Amorphous Carbon Surfaces Using Molecular Dynamics Simulations: Toward A More Realistic Experimental Model

Molecular dynamics (MD) simulations are a useful computational tool in fields such as fusion research. Small but vital portions of fusion reactors are essential to their correct operation and longevity. Using the reactive bond order (REBO) and adaptive intermolecular REBO potentials, it is possible to model carbon-based systems, such as graphite diverter plates, under simulated bombardment. The degradation of these plates due to random bombardments from plasma can eventually incur costly shut downs. To gain a better understanding of the atomic-level dynamics that occur when a graphite and amorphous carbon surface undergo energetic, serial bombardment by atoms such as hydrogen, deuterium, and tritium, these two systems were evolved with the REBO and AIREBO potentials. It was found that the AIREBO potential gave different results with regards to surface evolution, sputter yield, and steady state formation. Graphite surfaces evolved to a much different steady state when compared to amorphous carbon, which lead to varied surface structure and may also lead to differing sputtering yields. An additional round of simulations was performed on graphite surfaces that were deeper in the direction normal to the surface. Based on the previous results, the AIREBO potential and two different bombardment energies were used, and the additional layers added allowed for greater fluences, defined by the number of impacts per unit area, to be achieved. As an additional improvement of the previous work, thermostats were set by using zones of control rather than employing the thermostat on the entire system, achieving atomic layer control of the thermostatted regions during the simulation. After employing these changes and evolving the simulations for only slightly larger fluences than previous simulations, the formation of voids within the graphite layers, or \u27bubbles\u27, was produced. Particle build-up consisting of gaseous D, D2, and other small molecules near the penetration depth caused the formation of these bubbles. It was found for 20 eV impact energies the penetration depth is well defined, because of the lower energy of insertion. The stopping power of the potential on these low energy insertions leads to a noticable build-up of D atoms near the penetration depth. For the 80 eV simulations, the penetration depth is broadened when compared with the 20 eV simulations. The impacts penetrate more layers with increased impact energy, with bubble formation occurring away from the average penetration depth. A comparison of retention ratios is also discussed, and found that the 80 eV simulations retained more D than the 20 eV simulations. To attempt to avoid the issue of bubble formation, and to expand on the capabilities of the MD code, graphite surfaces were expanded in the directions perpendicular to the insertion direction, and the ability to bombard the surface with multiple atom types was implemented. Another improvement was introduced in the code to allow the variable time step algorithm to be used in conjunction with the thermostat. These systems yielded a closer model to experimental conditions, where the energy of interaction between the layers of graphite is larger than the insertion energy of the incident particles. While only smaller fluences compared to previous work have been achieved for these systems, the systems have shown promise in terms of their surface evolution and behavior

Calculateur d’impact pour la transition énergétique

Ce travail de Bachelor est réalisé en été 2016 par Guillaume Fallet, étudiant à la HES- SO Valais/Wallis en filière informatique de gestion et est suivi par M. Arnaud Zufferey, professeur dans cette même école. L’idée est venue du professeur Philippe Jacquod de l’ISI. L’objectif principal est de développer un calculateur en ligne qui permet la visualisation de la transition énergétique en Suisse jusqu’à l’année 2050. Ce calculateur est composé d’une série de paramètres que l’utilisateur peut modifier pour ensuite afficher sous forme de graphiques l’évolution de la consommation ainsi que la production des différentes sources d’électricité. Le calculateur est entièrement développé en « HTML / CSS / JavaScript » et est donc accessible depuis un navigateur web

Cisplatin exposure alters tRNA-derived small RNAs but does not affect epimutations in C. elegans

Background The individual lifestyle and environment of an organism can influence its phenotype and potentially the phenotype of its offspring. The different genetic and non-genetic components of the inheritance system and their mutual interactions are key mechanisms to generate inherited phenotypic changes. Epigenetic changes can be transmitted between generations independently from changes in DNA sequence. In Caenorhabditis elegans, epigenetic differences, i.e. epimutations, mediated by small non-coding RNAs, particularly 22G-RNAs, as well as chromatin have been identified, and their average persistence is three to five generations. In addition, previous research showed that some epimutations had a longer duration and concerned genes that were enriched for multiple components of xenobiotic response pathways. These results raise the possibility that environmental stresses might change the rate at which epimutations occur, with potential significance for adaptation. Results In this work, we explore this question by propagating C. elegans lines either in control conditions or in moderate or high doses of cisplatin, which introduces genotoxic stress by damaging DNA. Our results show that cisplatin has a limited effect on global small non-coding RNA epimutations and epimutations in gene expression levels. However, cisplatin exposure leads to increased fluctuations in the levels of small non-coding RNAs derived from tRNA cleavage. We show that changes in tRNA-derived small RNAs may be associated with gene expression changes. Conclusions Our work shows that epimutations are not substantially altered by cisplatin exposure but identifies transient changes in tRNA-derived small RNAs as a potential source of variation induced by genotoxic stress

Proteome analysis of the Escherichia coli heat shock response under steady-state conditions

In this study a proteomic approach was used to investigate the steady-state response of Escherichia coli to temperature up-shifts in a cascade of two continuously operated bioreactors. The first reactor served as cell source with optimal settings for microbial growth, while in the second chemostat the cells were exposed to elevated temperatures. By using this reactor configuration, which has not been reported to be used for the study of bacterial stress responses so far, it is possible to study temperature stress under well-defined, steady-state conditions. Specifically the effect on the cellular adaption to temperature stress using two-dimensional gel electrophoresis was examined and compared at the cultivation temperatures of 37°C and 47.5°C. As expected, the steady-state study with the double bioreactor configuration delivered a different protein spectrum compared to that obtained with standard batch experiments in shaking flasks and bioreactors. Setting a high cut-out spot-to-spot size ratio of 5, proteins involved in defence against oxygen stress, functional cell envelope proteins, chaperones and proteins involved in protein biosynthesis, the energy metabolism and the amino acid biosynthesis were found to be differently expressed at high cultivation temperatures. The results demonstrate the complexity of the stress response in a steady-state culture not reported elsewhere to date

Differentiation of protective B cell responses in chronic viral infection

Immune subversion represents a hallmark of persistent infection, but microbial suppression of B cell responses remains mechanistically ill-defined. Adoptive transfer experiments in a chronic viral infection model evidenced the rapid and profound decimation of B cells that responded to virus or to concomitantly administered protein. Decimation affected naïve and memory B cells and resulted from biased differentiation into short-lived antibody-secreting cells. It was driven by type I interferon (IFN-I) signaling to several cell types including dendritic cells, T cells and myeloid cells. Durable B cell responses were restored upon IFN-I receptor blockade or, partially, when depleting myeloid cells or key IFN-I-induced cytokines. B cell decimation represents a molecular mechanism of humoral immune subversion and reflects an unsustainable “all-in” response of B cells in IFN-I-driven inflammation