Efficient simulations with electronic open boundaries

We present a reformulation of the Hairy Probe method for introducing electronic open boundaries that is appropriate for steady state calculations involving non-orthogonal atomic basis sets. As a check on the correctness of the method we investigate a perfect atomic wire of Cu atoms, and a perfect non-orthogonal chain of H atoms. For both atom chains we find that the conductance has a value of exactly one quantum unit, and that this is rather insensitive to the strength of coupling of the probes to the system, provided values of the coupling are of the same order as the mean inter-level spacing of the system without probes. For the Cu atom chain we find in addition that away from the regions with probes attached, the potential in the wire is uniform, while within them it follows a predicted exponential variation with position. We then apply the method to an initial investigation of the suitability of graphene as a contact material for molecular electronics. We perform calculations on a carbon nanoribbon to determine the correct coupling strength of the probes to the graphene, and obtain a conductance of about two quantum units corresponding to two bands crossing the Fermi surface. We then compute the current through a benzene molecule attached to two graphene contacts and find only a very weak current because of the disruption of the π-conjugation by the covalent bond between the benzene and the graphene. In all cases we find that very strong or weak probe couplings suppress the current

Multiscale modelling for fusion and fission materials: the M4F project

The M4F project brings together the fusion and fission materials communities working on the prediction of radiation damage production and evolution and its effects on the mechanical behaviour of irradiated ferritic/martensitic (F/M) steels. It is a multidisciplinary project in which several different experimental and computational materials science tools are integrated to understand and model the complex phenomena associated with the formation and evolution of irradiation induced defects and their effects on the macroscopic behaviour of the target materials. In particular the project focuses on two specific aspects: (1) To develop physical understanding and predictive models of the origin and consequences of localised deformation under irradiation in F/M steels; (2) To develop good practices and possibly advance towards the definition of protocols for the use of ion irradiation as a tool to evaluate radiation effects on materials. Nineteen modelling codes across different scales are being used and developed and an experimental validation programme based on the examination of materials irradiated with neutrons and ions is being carried out. The project enters now its 4th year and is close to delivering high-quality results. This paper overviews the work performed so far within the project, highlighting its impact for fission and fusion materials science.This work has received funding from the Euratom research and training programme 2014-2018 under grant agreement No. 755039 (M4F project)

Gaussian polarizable-ion tight binding

To interpret ultrafast dynamics experiments on large molecules, computer simulation is required due to the complex response to the laser field. We present a method capable of efficiently computing the static electronic response of large systems to external electric fields. This is achieved by extending the density-functional tight binding method to include larger basis sets and by multipole expansion of the charge density into electrostatically interacting Gaussian distributions. Polarizabilities for a range of hydrocarbon molecules are computed for a multipole expansion up to quadrupole order, giving excellent agreement with experimental values, with average errors similar to those from density functional theory, but at a small fraction of the cost. We apply the model in conjunction with the polarizable-point-dipoles model to estimate the internal fields in amorphous poly(3-hexylthiophene-2,5-diyl)

Efficient local-orbitals based method for Ultrafast Dynamics

Computer simulations are invaluable for the study of ultrafast phenomena, as they allow us to directly access the electron dynamics. We present an efficient method for simulating the evolution of electrons in molecules under the influence of time-dependent electric fields, based on the Gaussian tight binding model. This model improves upon standard self-charge-consistent tight binding by the inclusion of polarizable orbitals and a self-consistent description of charge multipoles. Using the examples of bithiophene, terthiophene, and tetrathiophene, we show that this model produces electrostatic, electrodynamic, and explicitly time-dependent properties in strong agreement with density-functional theory, but at a small fraction of the cost

Atomistic-to-continuum description of edge dislocation core: Unification of the Peierls-Nabarro model with linear elasticity

International audienceConventional linear elasticity theory predicts the strain fields of a dislocation core to diverge, whereas it is known from atomistic simulations that core strains should remain finite. We present an analytical solution to a generalized, variational Peierls-Nabarro model of edge dislocation displacement fields that features a finite core width and correct isotropic elastic behavior at large distances away from the core. We derive an analytical expression for the dislocation core radius, representing the convergence radius of the linear elasticity far-field expansion. The strain fields are in qualitative agreement with atomistic simulations of 12[111](10¯1) edge dislocations in bcc tungsten and iron. The treatment is based on the multistring Frenkel-Kontorova model that we reformulate as a generalized Peierls-Nabarro model using the principle of least action

Born to sense: biophysical analyses of the oxygen sensing prolyl hydroxylase from the simplest animal Trichoplax adhaerens

Background: In humans and other animals, the chronic hypoxic response is mediated by hypoxia inducible transcription factors (HIFs) which regulate the expression of genes that counteract the effects of limiting oxygen. Prolyl hydroxylases (PHDs) act as hypoxia sensors for the HIF system in organisms ranging from humans to the simplest animal Trichoplax adhaerens. Methods: We report structural and biochemical studies on the T. adhaerens HIF prolyl hydroxylase (TaPHD) that inform about the evolution of hypoxia sensing in animals. Results: High resolution crystal structures (≤1.3 Å) of TaPHD, with and without its HIFα substrate, reveal remarkable conservation of key active site elements between T. adhaerens and human PHDs, which also manifest in kinetic comparisons. Conclusion: Conserved structural features of TaPHD and human PHDs include those apparently enabling the slow binding/reaction of oxygen with the active site Fe(II), the formation of a stable 2-oxoglutarate complex, and a stereoelectronically promoted change in conformation of the hydroxylated proline-residue. Comparison of substrate selectivity between the human PHDs and TaPHD provides insights into the selectivity determinants of HIF binding by the PHDs, and into the evolution of the multiple HIFs and PHDs present in higher animals.</p