Excited-state calculations with quantum Monte Carlo

Quantum Monte Carlo methods are first-principle approaches that approximately solve the Schr\"odinger equation stochastically. As compared to traditional quantum chemistry methods, they offer important advantages such as the ability to handle a large variety of many-body wave functions, the favorable scaling with the number of particles, and the intrinsic parallelism of the algorithms which are particularly suitable to modern massively parallel computers. In this chapter, we focus on the two quantum Monte Carlo approaches most widely used for electronic structure problems, namely, the variational and diffusion Monte Carlo methods. We give particular attention to the recent progress in the techniques for the optimization of the wave function, a challenging and important step to achieve accurate results in both the ground and the excited state. We conclude with an overview of the current status of excited-state calculations for molecular systems, demonstrating the potential of quantum Monte Carlo methods in this field of applications

Dynamic protein methylation in chromatin biology

Post-translational modification of chromatin is emerging as an increasingly important regulator of chromosomal processes. In particular, histone lysine and arginine methylation play important roles in regulating transcription, maintaining genomic integrity, and contributing to epigenetic memory. Recently, the use of new approaches to analyse histone methylation, the generation of genetic model systems, and the ability to interrogate genome wide histone modification profiles has aided in defining how histone methylation contributes to these processes. Here we focus on the recent advances in our understanding of the histone methylation system and examine how dynamic histone methylation contributes to normal cellular function in mammals

Velocity-space sensitivity of the time-of-flight neutron spectrometer at JET

The velocity-space sensitivities of fast-ion diagnostics are often described by so-called weight functions. Recently, we formulated weight functions showing the velocity-space sensitivity of the often dominant beam-target part of neutron energy spectra. These weight functions for neutron emission spectrometry (NES) are independent of the particular NES diagnostic. Here we apply these NES weight functions to the time-of-flight spectrometer TOFOR at JET. By taking the instrumental response function of TOFOR into account, we calculate time-of-flight NES weight functions that enable us to directly determine the velocity-space sensitivity of a given part of a measured time-of-flight spectrum from TOFOR

Relationship of edge localized mode burst times with divertor flux loop signal phase in JET

A phase relationship is identified between sequential edge localized modes (ELMs) occurrence times in a set of H-mode tokamak plasmas to the voltage measured in full flux azimuthal loops in the divertor region. We focus on plasmas in the Joint European Torus where a steady H-mode is sustained over several seconds, during which ELMs are observed in the Be II emission at the divertor. The ELMs analysed arise from intrinsic ELMing, in that there is no deliberate intent to control the ELMing process by external means. We use ELM timings derived from the Be II signal to perform direct time domain analysis of the full flux loop VLD2 and VLD3 signals, which provide a high cadence global measurement proportional to the voltage induced by changes in poloidal magnetic flux. Specifically, we examine how the time interval between pairs of successive ELMs is linked to the time-evolving phase of the full flux loop signals. Each ELM produces a clear early pulse in the full flux loop signals, whose peak time is used to condition our analysis. The arrival time of the following ELM, relative to this pulse, is found to fall into one of two categories: (i) prompt ELMs, which are directly paced by the initial response seen in the flux loop signals; and (ii) all other ELMs, which occur after the initial response of the full flux loop signals has decayed in amplitude. The times at which ELMs in category (ii) occur, relative to the first ELM of the pair, are clustered at times when the instantaneous phase of the full flux loop signal is close to its value at the time of the first ELM

Dimethyl sulphide biogeochemistry within a coccolithophore bloom (DISCO): an overview

This paper presents an overview of dimethyl sulphide biogeochemistry within a coccolithophore bloom (DISCO), an integrated, multidisciplinary Lagrangian process study of the routes, rates and controls on the biogeochemical cycling of dimethyl sulphide (DMS) within a growing bloom of the coccolithophorid alga, Emiliania huxleyi. The Lagrangian study took place between 16 and 26 June 1999 in the northern North Sea. It was preceded by an 8-d survey of ~52,000 km2 of the region to locate an E. huxleyi bloom suitable for study. Although not originally planned, the survey was carried out because heavy cloud cover precluded use of remote sensing to locate a suitable bloom. E. huxleyi blooms, typically common in the region during mid-summer, were unusually sparse in the study area. The bloom chosen for the process study was initially centred ~58°56?N 02°52?E, and a 40-km2 patch of water was labelled for study with ~30 g sulphur hexafluoride (SF6) on 16 June. The original patch was reinfused with further SF6 on 24 June. During the process study, the SF6-labelled patch moved in a south-easterly direction and the study ended when the patch subducted underneath less dense Norwegian coastal water.The process study comprised analyses of the time-varying biological, optical and physical properties of the patch as well as studies of DMS, dimethylsulphonioproprionate (DMSP), dimethylsulphoxide, nutrients, halocarbons, methylamines, carbon monoxide, dissolved organic carbon, and total dissolved nitrogen. The role of viruses, bacteria, phytoplankton, microzooplankton, and mesozooplankton, together with the dynamics of primary, new and bacterial production, plankton respiration, microzooplankton grazing, and sedimentation, were studied in relation to the biogeochemical cycling of DMS. Although the coccolithophore bloom water exhibited high optical backscatter, the algal community present was highly heterogeneous. Flagellates other than E. huxleyi were found to dominate the phytoplankton. A budget of the DMSP pools suggested that E. huxleyi accounted for only 13% of the stocks of particulate DMSP, showing that in this “E. huxleyi bloom”, taxa other than E. huxleyi were important sources of DMSP. In this young bloom, particulate and dissolved DMSP and DMS concentrations averaged 1360, 155 and 60 ?M m?2, respectively, in the surface mixed layer. Surface-water particulate DMSP concentrations increased during the study at a net rate of 13% d?1, as did concentrations of phytoplankton including E. huxleyi, confirming that the bloom was developing. Nutrient conditions were low in the mixed layer throughout the study, maintained by a strong pycnocline across which nitrate upflux was estimated to be ~2 nM dm?3 d?1. Primary production was fuelled by regenerated nutrients, although nitrification rates in surface waters were found to be significant. Microzooplankton grazing accounted for 91% of the particulate DMSP degradation and was considered to be a major control on the DMSP concentration. Vigorous microzooplankton grazing together with rapid uptake of dissolved DMSP by bacteria suggest that microzooplankton were the main route for the production of dissolved DMSP. The bacterial community was dominated by one taxon, an ? proteobacteria related to Roseobacter that satisfied its entire sulphur demand by metabolising dissolved DMSP. Bacteriogenic DMS production amounted to 2 nM d?1 and was considered the main route for DMS production. In vitro DMSPlyase activity was very high, but there was little evidence for high in situ activity. Over the study period, DMS flux to the atmosphere was estimated to be 7 ?M m?2 d?1, equivalent to ~1% of the DMSP sulphur produced in the surface mixed layer. A budget for DMS cycling in the upper mixed layer is presented based on the analytical and experimental measurements made in the DISCO study