Structure of naturally hydrated ferrihydrite revealed through neutron diffraction and first-principles modeling

Ferrihydrite, with a ‘‘two-line’’ x-ray diffraction pattern (2L-Fh), is the most amorphous of the iron oxides and is ubiquitous in both terrestrial and aquatic environments. It also plays a central role in the regulation and metabolism of iron in bacteria, algae, higher plants, and animals, including humans. In this study, we present a single-phase model for ferrihydrite that unifies existing analytical data while adhering to fundamental chemical principles. The primary particle is small (20–50 Å) and has a dynamic and variably hydrated surface, which negates long-range order; collectively, these features have hampered complete characterization and frustrated our understanding of the mineral's reactivity and chemical/biochemical function. Near and intermediate range neutron diffraction (NIMROD) and first-principles density functional theory (DFT) were employed in this study to generate and interpret high-resolution data of naturally hydrated, synthetic 2L-Fh at standard temperature. The structural optimization overcomes transgressions of coordination chemistry inherent within previously proposed structures, to produce a robust and unambiguous single-phase model

DL_MG : A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution

The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential—a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with nonlinear dependencies, and diverse boundary conditions. The analytic solutions generally used to solve the Poisson equation in vacuum (or with homogeneous permittivity) are not applicable in these circumstances, and numerical methods must be used. In this work, we present DL_MG, a flexible, scalable, and accurate solver library, developed specifically to tackle the challenges of solving the Poisson equation in modern large-scale electronic structure calculations on parallel computers. Our solver is based on the multigrid approach and uses an iterative high-order defect correction method to improve the accuracy of solutions. Using two chemically relevant model systems, we tested the accuracy and computational performance of DL_MG when solving the generalized Poisson and Poisson–Boltzmann equations, demonstrating excellent agreement with analytic solutions and efficient scaling to ∼10^9 unknowns and 100s of CPU cores. We also applied DL_MG in actual large-scale electronic structure calculations, using the ONETEP linear-scaling electronic structure package to study a 2615 atom protein–ligand complex with routinely available computational resources. In these calculations, the overall execution time with DL_MG was not significantly greater than the time required for calculations using a conventional FFT-based solver

Realisation of magnetically and atomically abrupt half-metal/semiconductor interface: Co2FeSi0.5Al0.5/Ge(111)

Halfmetal-semiconductor interfaces are crucial for hybrid spintronic devices. Atomically sharp interfaces with high spin polarisation are required for efficient spin injection. In this work we show that thin film of half-metallic full Heusler alloy Co2FeSi0.5Al0.5 with uniform thickness and B2 ordering can form structurally abrupt interface with Ge(111). Atomic resolution energy dispersive X-ray spectroscopy reveals that there is a small outdiffusion of Ge into specific atomic planes of the Co2FeSi0.5Al0.5 film, limited to a very narrow 1 nm interface region. First-principles calculations show that this selective outdiffusion along the Fe-Si/Al atomic planes does not change the magnetic moment of the film up to the very interface. Polarized neutron reflectivity, x-ray reflectivity and aberration-corrected electron microscopy confirm that this interface is both magnetically and structurally abrupt. Finally, using first-principles calculations we show that this experimentally realised interface structure, terminated by Co-Ge bonds, preserves the high spin polarization at the Co2FeSi0.5Al0.5/Ge interface, hence can be used as a model to study spin injection from half-metals into semiconductors

DUNE-PRISM - a new method to measure neutrino oscillations

The Deep Underground Neutrino Experiment (DUNE) is a next-generation long baseline neutrino oscillation experiment designed to make precision measurements in a 1.2--2.4 MW neutrino beam, which is directed 1285~km from the Fermi National Accelerator Laboratory (Fermilab) to the Sandford Underground Research Facility (SURF) in South Dakota. Neutrinos are measured at two detector facilities: a near detector located at Fermilab close to where the beam is produced and a far detector at SURF. The neutrino beam can be configured to be composed primarily of either $\nu_{\mu}$ or $\bar{\nu}_{\mu}$. DUNE measures the disappearance of $\nu_{\mu}$ and $\bar{\nu}_{\mu}$ and the appearance $\nu_{e}$ and $\bar{\nu}_{e}$ in the neutrino beam. Measuring these neutrino flavour transitions provides DUNE with sensitivity to the neutrino mass ordering, $\delta_{CP}$, $\theta_{13}$, $\theta_{23}$ and the magnitude of $\Delta m^{2}_{32}$. The DUNE Precision Reaction Independent Spectrum Measurement (DUNE-PRISM) concept presents a novel way to perform a neutrino oscillation analysis, which has the potential to significantly reduce the impact of large systematic uncertainties in the neutrino interaction model. The PRISM method linearly combines measurements of off-axis neutrino interactions at the DUNE near detector to produce data-driven predictions of the oscillated neutrino event rate spectrum at the far detector. By building an oscillated far detector prediction directly from data, any unknown or poorly modelled neutrino interaction effects will be naturally incorporated into the measurement of the parameters of the neutrino oscillation model. This thesis presents the first complete neutrino oscillation analysis for DUNE using the PRISM method. Details of the methodology are fully explained and the prospects for further improvements to the techniques described are highlighted. The expected impact and relative importance of the neutrino flux, cross section and detector systematic uncertainties are described in detail. Finally, this thesis demonstrates that the PRISM method is capable of performing a measurement of the oscillation parameters that is robust against neutrino interaction modelling errors

The role of chemical structure on the magnetic and electronic properties of Co2FeAl0.5Si0.5/Si(111) interface

We show that Co2FeAl0.5Si0.5 film deposited on Si(111) has a single crystal structure and twin related epitaxial relationship with the substrate. Sub-nanometer electron energy loss spectroscopy shows that in a narrow interface region there is a mutual inter-diffusion dominated by Si and Co. Atomic resolution aberration-corrected scanning transmission electron microscopy reveals that the film has B2 ordering. The film lattice structure is unaltered even at the interface due to the substitu- tional nature of the intermixing. First-principles calculations performed using structural models based on the aberration corrected electron microscopy show that the increased Si incorporation in the film leads to a gradual decrease of the magnetic moment as well as significant spin-polarization reduction. These effects can have significant detrimental role on the spin injection from the Co2FeAl0.5Si0.5 film into the Si substrate, besides the structural integrity of this junction

Controlling the half-metallicity of Heusler/Si(1 1 1) interfaces by a monolayer of Si–Co–Si

By using first-principles calculations we show that the spin-polarization reverses its sign at atomically abrupt interfaces between the half-metallic Co₂ (Fe,Mn)(Al,Si) and Si(1 1 1). This unfavourable spin-electronic configuration at the Fermi-level can be completely removed by introducing a Si–Co–Si monolayer at the interface. In addition, this interfacial monolayer shifts the Fermi-level from the valence band edge close to the conduction band edge of Si. We show that such a layer is energetically favourable to exist at the interface. This was further confirmed by direct observations of CoSi₂ nano-islands at the interface, by employing atomic resolution scanning transmission electron microscopy

Furan in heat-treated foods: Formation, exposure, toxicity, and aspects of risk assessment

Furan is formed in a variety of heat-treated foods through thermal degradation of natural food constituents. Relatively high levels of furan contamination are found in ground roasted coffee, instant coffee, and processed baby foods. European exposure estimates suggest that mean dietary exposure to furan may be as high as 1.23 and 1.01 μg/kg bw/day for adults and 3- to 12-month-old infants, respectively. Furan is a potent hepatotoxin and hepatocarcinogen in rodents, causing hepatocellular adenomas and carcinomas in rats and mice, and high incidences of cholangiocarcinomas in rats at doses ≥2 mg/kg bw. There is therefore a relatively low margin of exposure between estimated human exposure and doses that cause a high tumor incidence in rodents. Since a genotoxic mode of action cannot be excluded for furan-induced tumor formation, the present exposures may indicate a risk to human health and need for mitigation. This review summarizes the current knowledge on mechanisms of furan formation in food, human dietary exposure to furan, and furan toxicity, and highlights the need to establish the risk resulting from the genotoxic and carcinogenic properties of furan at doses lower than 2 mg/kg bw. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Portable Acceleration of Materials Modeling Software:CASTEP, GPUs, and OpenACC

In this article, we present work to port the CASTEP first-principles materials modeling program to accelerators using open accelerator (OpenACC). We discuss the challenges and opportunities presented by graphical processing units (GPU) architectures in particular, and the approach taken in the CASTEP OpenACC port. Whilst the port is still under active development, early performance results show that significant speed-ups may be gained, particularly for materials simulations using so-called "nonlocal functionals,"where speed-ups can exceed a factor of ten