All-electron APW+lo calculation of magnetic molecules with the SIRIUS domain-specific package.

We report APW+lo (augmented plane wave plus local orbital) density functional theory (DFT) calculations of large molecular systems using the domain specific SIRIUS multi-functional DFT package. The APW and FLAPW (full potential linearized APW) task and data parallelism options and the advanced eigen-system solver provided by SIRIUS can be exploited for performance gains in ground state Kohn-Sham calculations on large systems. This approach is distinct from our prior use of SIRIUS as a library backend to another APW+lo or FLAPW code.

Lessons learned from urgent computing in Europe: Tackling the COVID-19 pandemic.

PRACE (Partnership for Advanced Computing in Europe), an international not-for-profit association that brings together the five largest European supercomputing centers and involves 26 European countries, has allocated more than half a billion core hours to computer simulations to fight the COVID-19 pandemic. Alongside experiments, these simulations are a pillar of research to assess the risks of different scenarios and investigate mitigation strategies. While the world deals with the subsequent waves of the pandemic, we present a reflection on the use of urgent supercomputing for global societal challenges and crisis management.

The digital revolution of Earth-system science.

Computational science is crucial for delivering reliable weather and climate predictions. However, despite decades of high-performance computing experience, there is serious concern about the sustainability of this application in the post-Moore/Dennard era. Here, we discuss the present limitations in the field and propose the design of a novel infrastructure that is scalable and more adaptable to future, yet unknown computing architectures.

Materials Cloud, a platform for open computational science.

Materials Cloud is a platform designed to enable open and seamless sharing of resources for computational science, driven by applications in materials modelling. It hosts (1) archival and dissemination services for raw and curated data, together with their provenance graph, (2) modelling services and virtual machines, (3) tools for data analytics, and pre-/post-processing, and (4) educational materials. Data is citable and archived persistently, providing a comprehensive embodiment of entire simulation pipelines (calculations performed, codes used, data generated) in the form of graphs that allow retracing and reproducing any computed result.

Surface reconstructions and related local properties of a BiFeO thin film.

Coupling between lattice and order parameters, such as polarization in ferroelectrics and/or polarity in polar structures, has a strong impact on surface relaxation and reconstruction. However, up to now, surface structures that involve the termination of both matrix polarization and polar atomic planes have received little attention, particularly on the atomic scale. Here, we study surface structures on a BiFeO thin film using atomic-resolution scanning transmission electron microscopy and spectroscopy.

Thermodynamic and Biophysical Analysis of the Membrane-Association of a Histidine-Rich Peptide with Efficient Antimicrobial and Transfection Activities.

LAH4-L1 is a synthetic amphipathic peptide with antimicrobial activity. The sequence of the 23 amino acid peptide was inspired by naturally occurring frog peptides such as PGLa and magainin. LAH4-L1 also facilitates the transport of nucleic acids through the cell membrane.

Thermal unfolding of apolipoprotein A-1. Evaluation of methods and models.

Human apolipoprotein A-1 (Apo A-1) was used as a model protein to compare experimental methods and theoretical models for protein unfolding. Thermal unfolding was investigated in aqueous buffer, in β-octylglucoside solution, and with phospholipid bilayer vesicles. The α-helix content of Apo A-1 increased from 50% in aqueous buffer to 75% in the presence of lipid vesicles, but remained constant in solutions of β-octyl glucoside.

All-electron GW quasiparticle band structures of group 14 nitride compounds.

We have investigated the group 14 nitrides (M3N4) in the spinel phase (γ-M3N4 with M = C, Si, Ge, and Sn) and β phase (β-M3N4 with M = Si, Ge, and Sn) using density functional theory with the local density approximation and the GW approximation. The Kohn-Sham energies of these systems have been first calculated within the framework of full-potential linearized augmented plane waves (LAPW) and then corrected using single-shot G0W0 calculations, which we have implemented in the modified version of the Elk full-potential LAPW code. Direct band gaps at the Γ point have been found for spinel-type nitrides γ-M3N4 with M = Si, Ge, and Sn.

Perturbation calculation of thermodynamic density of states.

The density of states g (ε) is frequently used to calculate the temperature-dependent properties of a thermodynamic system. Here a derivation is given for calculating the warped density of states g*(ε) resulting from the addition of a perturbation. The method is validated for a classical Heisenberg model of bcc Fe and the errors in the free energy are shown to be second order in the perturbation.

Dynamic cluster quantum Monte Carlo simulations of a two-dimensional Hubbard model with stripelike charge-density-wave modulations: interplay between inhomogeneities and the superconducting state.

Using dynamic cluster quantum Monte Carlo simulations, we study the superconducting behavior of a 1/8 doped two-dimensional Hubbard model with imposed unidirectional stripelike charge-density-wave modulation. We find a significant increase of the pairing correlations and critical temperature relative to the homogeneous system when the modulation length scale is sufficiently large. With a separable form of the irreducible particle-particle vertex, we show that optimized superconductivity is obtained for a moderate modulation strength due to a delicate balance between the modulation enhanced pairing interaction, and a concomitant suppression of the bare particle-particle excitations by a modulation reduction of the quasiparticle weight.

Calcium enhances the proteolytic activity of BACE1: An in vitro biophysical and biochemical characterization of the BACE1-calcium interaction.

BACE1 is a novel type I transmembrane aspartyl protease that has been implicated in the pathogenesis of Alzheimer's disease. Cleavage of the amyloid precursor protein by the beta-secretase, BACE1, is the first step in the production of the Abeta peptide and is a prime target for therapeutic intervention. Using circular dichroism, we reveal that the secondary structure of BACE1 in a membrane environment is significantly different from what was determined from the previously resolved crystal structure, and, we provide the first evidence that show differences in stability between the active (pH 4.

Thermodynamics of melittin binding to lipid bilayers. Aggregation and pore formation.

Lipid membranes act as catalysts for protein folding. Both alpha-helical and beta-sheet structures can be induced by the interaction of peptides or proteins with lipid surfaces. Melittin, the main component of bee venom, is a particularly well-studied example for the membrane-induced random coil-to-alpha-helix transition.

Link between perpendicular coupling and exchange biasing in Fe(3)O(4)/CoOMultilayers.

In studying well-characterized, exchange-biased Fe(3)O(4)/CoO superlattices, we demonstrate a causal link between the exchange bias effect and the perpendicular coupling of the ferrimagnetic and antiferromagnetic spins. Neutron diffraction studies reveal that for thin CoO layers the onset temperature for exchange biasing T(B) matches the onset of locked-in, preferential perpendicular coupling of the spins, rather than the antiferromagnetic ordering temperature T(N). The results are explained by considering the role of anisotropic exchange first proposed by Dzyaloshinsky and Moriya and developing a model based purely on information on structural defects and exchange for these oxides.

Wang-Landau algorithm for continuous models and joint density of states.

We present a modified Wang-Landau algorithm for models with continuous degrees of freedom. We demonstrate this algorithm with the calculation of the joint density of states of ferromagnet Heisenberg models and a model polymer chain. The joint density of states contains more information than the density of states of a single variable-energy, but is also much more time consuming to calculate.

Systematic study of d-wave superconductivity in the 2D repulsive Hubbard model.

The cluster size dependence of superconductivity in the conventional two-dimensional Hubbard model, commonly believed to describe high-temperature superconductors, is systematically studied using the dynamical cluster approximation and quantum Monte Carlo simulations as a cluster solver. Because of the nonlocality of the d-wave superconducting order parameter, the results on small clusters show large size and geometry effects. In large enough clusters, the results are independent of the cluster size and display a finite temperature instability to d-wave superconductivity.

Spin waves in paramagnetic bcc iron: spin dynamics simulations.

Large scale computer simulations are used to elucidate a long-standing controversy regarding the existence, or otherwise, of spin waves in paramagnetic bcc iron. Spin dynamics simulations of the dynamic structure factor of a Heisenberg model of Fe with first principles interactions reveal that well defined peaks persist far above Curie temperature Tc. At large wave vectors these peaks can be ascribed to propagating spin waves; at small wave vectors the peaks correspond to overdamped spin waves.

Toward an atomistic model for predicting transcription-factor binding sites.

Identifying the specific DNA-binding sites of transcription-factor proteins is essential to understanding the regulation of gene expression in the cell. Bioinformatics approaches are fast compared to experiments, but require prior knowledge of multiple binding sites for each protein. Here, we present an atomistic force-field method to predict binding sites based only on the X-ray structure of a related bound complex.

Ferromagnetic stability in Fe nanodot assemblies on Cu(111) induced by indirect coupling through the substrate.

We report collective ferromagnetic behavior with high Curie temperatures (T(c)) in Fe dot assemblies supported by the Cu(111) surface. Our ability to tune the average size and spacing of the individual dots allows us to conclude that enhanced magnetic anisotropy cannot account for this high-T(c) ferromagnetic order. Because our Monte Carlo simulations have ruled out the dipolar interaction as the dominant factor in this system, we attribute the origin of the ferromagnetic order to indirect exchange coupling via the Cu(111) substrate.

Modulation of agrin function by alternative splicing and Ca2+ binding.

The aggregation of acetylcholine receptors on postsynaptic membranes is a key step in neuromuscular junction development. This process depends on alternatively spliced forms of the proteoglycan agrin with "B-inserts" of 8, 11, or 19 residues in the protein's globular C-terminal domain, G3. Structures of the neural B8 and B11 forms of agrin-G3 were determined by X-ray crystallography.

Collagen stabilization at atomic level: crystal structure of designed (GlyProPro)10foldon.

In a designed fusion protein the trimeric domain foldon from bacteriophage T4 fibritin was connected to the C terminus of the collagen model peptide (GlyProPro)(10) by a short Gly-Ser linker to facilitate formation of the three-stranded collagen triple helix. Crystal structure analysis at 2.6 A resolution revealed conformational changes within the interface of both domains compared with the structure of the isolated molecules.

Collagen triple helix formation can be nucleated at either end.

The directional dependence of folding rates for rod-like macromolecules such as parallel alpha-helical coiled-coils, DNA double-helices, and collagen triple helices is largely unexplored. This is mainly due to technical difficulties in measuring rates in different directions. Folding of collagens is nucleated by trimeric non-collagenous domains.

Homoassociation of VE-cadherin follows a mechanism common to "classical" cadherins.

Vascular endothelial cadherin (VE-cadherin/cadherin5) is specifically expressed in adherens junctions of endothelial cells and exerts important functions in cell-cell adhesion as well as signal transduction. To analyze the mechanism of VE-cadherin homoassociation, the ectodomains CAD1-5 were connected by linker sequences to the N terminus of the coiled-coil domain of cartilage matrix protein (CMP). The chimera VECADCMP were expressed in mammalian cells.