Grand canonical approach to modeling hydrogen trapping at vacancies in α-Fe

Vacancies in iron are hydrogen traps, important in the understanding of hydrogen embrittlement of steel. We present a grand canonical approach to computing the trap occupancy as a function of both temperature and hydrogen concentration from practically zero to super-saturation. Our method couples a purpose-made machine-learned H-Fe potential, which enables rapid sampling with near density functional theory accuracy, with a statistical mechanical calculation of the trap occu- pancy using the technique of nested sampling. In contrast to the conventional assumption (based on Oriani theory) that at industrially relevant hydrogen concentrations and ambient conditions vacancy traps are are fully occupied, we find that vacancy traps are less than fully occupied under these conditions, necessitating a reevaluation of how we think about “mobile hydrogen” in iron and steel

Introducing k-point parallelism into VASP

For many years ab initio electronic structure calculations based upon density functional theory have been one of the main application areas in high performance computing (HPC). Typically, the Kohn–Sham equations are solved by minimisation of the total energy functional, using a plane wave basis set for valence electrons and pseudopotentials to obviate the representation of core states. One of the best known and widely used software for performing this type of calculation is the Vienna Ab initio Simulation Package, VASP, which currently offers a parallelisation strategy based on the distribution of bands and plane wave coefficients over the machine processors. We report here an improved parallelisation strategy that also distributes the k-point sampling workload over different processors, allowing much better scalability for massively parallel computers. As a result, some difficult problems requiring large k-point sampling become tractable in current computing facilities. We showcase three important applications: dielectric function of epitaxially strained indium oxide, solution energies of tetravalent dopants in metallic VO2, and hydrogen on graphene

Grand canonical approach to modeling hydrogen trapping at vacancies in alpha-Fe

Vacancies in iron are hydrogen traps, important in the understanding of hydrogen embrittlement of steel. We present a grand canonical approach to computing the trap occupancy as a function of both temperature and hydrogen concentration from practically zero to super-saturation. Our method couples a purpose-made machine-learned H-Fe potential, which enables rapid sampling with near density functional theory accuracy, with a statistical mechanical calculation of the trap occu- pancy using the technique of nested sampling. In contrast to the conventional assumption (based on Oriani theory) that at industrially relevant hydrogen concentrations and ambient conditions vacancy traps are are fully occupied, we find that vacancy traps are less than fully occupied under these conditions, necessitating a reevaluation of how we think about “mobile hydrogen” in iron and steel

A grand canonical approach for modelling hydrogen trapping at vacancies in alpha-Fe

Vacancies in iron are hydrogen traps, important in the understanding of hydrogen embrittlement of steel. We present a grand canonical approach to computing the trap occupancy as a function of both temperature and hydrogen concentration from practically zero to supersaturation. Our method couples a purpose-made machine-learned H-Fe potential, which enables rapid sampling with near-density-functional-theory accuracy, with a statistical mechanical calculation of the trap occupancy using the technique of nested sampling. In contrast to the conventional assumption (based on Oriani theory) that at industrially relevant hydrogen concentrations and ambient conditions vacancy traps are are fully occupied, we find that vacancy traps are less than fully occupied under these conditions, necessitating a reevaluation of how we think about “mobile hydrogen” in iron and steel

Measurements in an urban-type boundary layer.

Wind tunnel measurements of the boundary layer flow over a very rough surface comprising a staggered array of cubes are presented and discussed. Attention is concentrated on the near-wall region, including the canopy region below the tops of the roughness elements. Particle image velocimetry (PIV) and laser Doppler anemometry were used to identify the dominant features of the mean and turbulent flow and these are compared with the better-known features of the flow above the roughness. Spatial correlation data, extracted from the PIV images, are used to provide information about eddy structures and it is shown that these differ in some crucial respects from those typical of more classical boundary layers. The implications of the results are discussed in terms of their relevance to flows within the urban environment

Phylogenomics of strongylocentrotid sea urchins

BACKGROUND: Strongylocentrotid sea urchins have a long tradition as model organisms for studying many fundamental processes in biology including fertilization, embryology, development and genome regulation but the phylogenetic relationships of the group remain largely unresolved. Although the differing isolating mechanisms of vicariance and rapidly evolving gamete recognition proteins have been proposed, a stable and robust phylogeny is unavailable. RESULTS: We used a phylogenomic approach with mitochondrial and nuclear genes taking advantage of the whole-genome sequencing of nine species in the group to establish a stable (i.e. concordance in tree topology among multiple lies of evidence) and robust (i.e. high nodal support) phylogenetic hypothesis for the family Strongylocentrotidae. We generated eight draft mitochondrial genome assemblies and obtained 13 complete mitochondrial genes for each species. Consistent with previous studies, mitochondrial sequences failed to provide a reliable phylogeny. In contrast, we obtained a very well-supported phylogeny from 2301 nuclear genes without evidence of positive Darwinian selection both from the majority of most-likely gene trees and the concatenated fourfold degenerate sites: ((P. depressus, (M. nudus, M. franciscanus), (H. pulcherrimus, (S. purpuratus, (S. fragilis, (S. pallidus, (S. droebachiensis, S. intermedius)). This phylogeny was consistent with a single invasion of deep-water environments followed by a holarctic expansion by Strongylocentrotus. Divergence times for each species estimated with reference to the divergence times between the two major clades of the group suggest a correspondence in the timing with the opening of the Bering Strait and the invasion of the holarctic regions. CONCLUSIONS: Nuclear genome data contains phylogenetic signal informative for understanding the evolutionary history of this group. However, mitochondrial genome data does not. Vicariance can explain major patterns observed in the phylogeny. Other isolating mechanisms are appropriate to explore in this system to help explain divergence patterns not well supported by vicariance, such as the effects of rapidly evolving gamete recognition proteins on isolating populations. Our findings of a stable and robust phylogeny, with the increase in mitochondrial and nuclear comparative genomic data, provide a system in which we can enhance our understanding of molecular evolution and adaptation in this group of sea urchins