Kinetic simulations of X-B and O-X-B mode conversion

We have performed fully-kinetic simulations of X-B and O-X-B mode conversion in one and two dimensional setups using the PIC code EPOCH. We have recovered the linear dispersion relation for electron Bernstein waves by employing relatively low amplitude incoming waves. The setups presented here can be used to study non-linear regimes of X-B and O-X-B mode conversion.Comment: 4 pages, 3 figure

Validation of GBS plasma turbulence simulation of the TJ-K stellarator

We present a validation of a three-dimensional, two-fluid simulation of plasma turbulence in the TJ-K stellarator, a low temperature plasma experiment ideally suited for turbulence measurements. The simulation is carried out by the GBS code, recently adapted to simulate 3D magnetic fields. The comparison shows that GBS retrieves the main turbulence properties observed in the device, namely the fact that transport is dominated by fluctuations with low poloidal mode number. The poloidal dependence of the radial $\text{E}\times\text{B}$ turbulent flux is compared on a poloidal plane with elliptical flux surfaces, where a very good agreement between experiment and simulation is observed, and on another with triangular flux surfaces, which shows a poorer comparison. The fluctuation levels in both cases are underestimated in the simulations. The equilibrium density profile is well retrieved by the simulation, while the electron temperature and the electrostatic potential profiles, which are very sensitive to the strength and localization of the sources, do not agree well with the experimental measurements

Software that goes with the flow in systems biology

A recent article in BMC Bioinformatics describes new advances in workflow systems for computational modeling in systems biology. Such systems can accelerate, and improve the consistency of, modeling through automation not only at the simulation and results-production stages, but also at the model-generation stage. Their work is a harbinger of the next generation of more powerful software for systems biologists

Polarisation Sensitive Single Molecule Fluorescence Detection with Linear Polarised Excitation Light and Modulated Polarisation Direction Applied to Multichromophoric Entities

Recently, investigations of the fluorescence properties of a multichromophoric dendritic entity at the single molecule level have revealed multiple fluorescence levels, collective off-states, variations of the polarisation, large shifts in the spectral position and changes in the fluorescence decay time. In order to further elucidate the multiple processes taking place in this entity, measurements were done in which the polarisation direction of the linear polarised excitation light was modulated. The detection was sensitive for the s- and p-components of the emitted light. The patterns of modulation and relative intensity in the acquired traces reflect the energy transfer processes occurring in this multichromophoric molecule. In-phase modulation and no modulation are the typical modulation patterns that were observed. Simulations involving several models for energy transfer between the chromophores have been carried out taking into account identical conditions as for the performed measurements. The comparison of the modulation patterns and polarisation histograms to the measured data rules out certain models and refines the photophysical model for the multichromophoric entity

Palladium-catalyzed stereoselective domino arylation-acylation:an entry to chiral tetrahydrofluorenone scaffolds

A palladium-catalyzed domino arylation-cyclization of biocatalytically derived cyclic 1,3-dienes is demonstrated. The reaction introduces a high degree of structural complexity in a single step, giving access to tricyclic tetrahydrofluorenones with full regio- and stereoselectivity. The transformation proceeds through a novel acylation-terminated Heck-type sequence, and quantum chemical calculations indicate that C-H activation is involved in the terminating acylation step

Ruthenium catalyzed remote C4-selective C–H functionalisation of carbazoles via σ-activation

We report the C4-selective C–H alkylation of carbazole derivatives furnished with a pyrimidine directing group at N9. This was realized using ruthenium catalyzed r-activation methodology, whereby C–H activation at C1 enables the interaction of this ruthenacycle, at the para position to the metal center, with tertiary alkyl radical