The CECAM electronic structure library and the modular software development paradigm.

First-principles electronic structure calculations are now accessible to a very large community of users across many disciplines, thanks to many successful software packages, some of which are described in this special issue. The traditional coding paradigm for such packages is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, essentially from the compiler up, possibly with the exception of linear-algebra and message-passing libraries. This model has endured and been quite successful for decades. The successful evolution of the electronic structure methodology itself, however, has resulted in an increasing complexity and an ever longer list of features expected within all software packages, which implies a growing amount of replication between different packages, not only in the initial coding but, more importantly, every time a code needs to be re-engineered to adapt to the evolution of computer hardware architecture. The Electronic Structure Library (ESL) was initiated by CECAM (the European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure codes and redesign them as open-source libraries available to everybody. Such libraries include "heavy-duty" ones that have the potential for a high degree of parallelization and adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by, e.g., physicists and chemists when implementing new ideas. We envisage that this modular paradigm will improve overall coding efficiency and enable specialists (whether they be computer scientists or computational scientists) to use their skills more effectively and will lead to a more dynamic evolution of software in the community as well as lower barriers to entry for new developers. The model comes with new challenges, though. The building and compilation of a code based on many interdependent libraries (and their versions) is a much more complex task than that of a code delivered in a single self-contained package. Here, we describe the state of the ESL, the different libraries it now contains, the short- and mid-term plans for further libraries, and the way the new challenges are faced. The ESL is a community initiative into which several pre-existing codes and their developers have contributed with their software and efforts, from which several codes are already benefiting, and which remains open to the community.

Exsolution on perovskite oxides: morphology and anchorage of nanoparticles.

Perovskites are very promising materials for a wide range of applications (such as catalysis, solid oxide fuel cells…) due to beneficial general properties (e.g. stability at high temperatures) and tunability - doping both A- and B-site cations opens the path to a materials design approach that allows specific properties to be finely tuned towards applications. A major asset of perovskites is the ability to form nanoparticles on the surface under certain conditions in a process called "exsolution". Exsolution leads to the decoration of the material's surface with finely dispersed nanoparticles (which can be metallic or oxidic - depending on the experimental conditions) made from B-site cations of the perovskite lattice (here, doping comes into play, as B-site doping allows control over the constitution of the nanoparticles). In fact, the ability to undergo exsolution is one of the main reasons that perovskites are currently a hot topic of intensive research in catalysis and related fields. Exsolution on perovskites has been heavily researched in the last couple of years: various potential catalysts have been tested with different reactions, the oxide backbone materials and the exsolved nanoparticles have been investigated with a multitude of different methods, and the effect of different exsolution parameters on the resulting nanoparticles has been studied. Despite all this, to our knowledge no comprehensive effort was made so far to evaluate these studies with respect to the effect that the exsolution conditions have on anchorage and morphology of the nanoparticles. Therefore, this highlight aims to provide an overview of nanoparticles exsolved from oxide-based perovskites with a focus on the conditions leading to nanoparticle exsolution.

Ca-doped rare earth perovskite materials for tailored exsolution of metal nanoparticles.

Perovskite-type oxide materials (nominal composition ABO3) are a very versatile class of materials, and their properties are tuneable by varying and doping A- and B-site cations. When the B-site contains easily reducible cations (e.g. Fe, Co or Ni), these can exsolve under reducing conditions and form metallic nanoparticles on the surface. This process is very interesting as a novel route for the preparation of catalysts, since oxide surfaces decorated with finely dispersed catalytically active (often metallic) nanoparticles are a key requirement for excellent catalyst performance. Five doped perovskites, namely, La0.9Ca0.1FeO3-δ, La0.6Ca0.4FeO3-δ, Nd0.9Ca0.1FeO3-δ, Nd0.6Ca0.4FeO3-δ and Nd0.6Ca0.4Fe0.9Co0.1O3-δ, have been synthesized and characterized by experimental and theoretical methods with respect to their crystal structures, electronic properties, morphology and exsolution behaviour. All are capable of exsolving Fe and/or Co. Special emphasis has been placed on the influence of the A-site elemental composition on structure and exsolution capability. Using Nd instead of La increased structural distortions and, at the same time, hindered exsolution. Increasing the amount of Ca doping also increased distortions and additionally changed the Fe oxidation states, resulting in exsolution being shifted to higher temperatures as well. Using the easily reducible element Co as the B-site dopant significantly facilitated the exsolution process and led to much smaller and homogeneously distributed exsolved particles. Therefore, the Co-doped perovskite is a promising material for applications in catalysis, even more so as Co is catalytically a highly active element. The results show that fine-tuning of the perovskite composition will allow tailored exsolution of nanoparticles, which can be used for highly sophisticated catalyst design.

The interaction of the estrogen receptor with mononucleosomes.

To directly activate specific gene expression, the estrogen receptor (ER) must bind to estrogen receptor response elements (EREs) in the context of nucleosomes. In order to investigate the interaction of the ER with mononucleosomes, we developed a mononucleosome gel shift assay. A 164 bp high specific activity [(32)P]probe DNA (32 bp consensus ERE with flanking regions separated by 23 nucleotides from an artificial nucleosome positioning sequence) was prepared. Nuclear extracts from MCF-7 cells or recombinant human ERalpha were incubated with the labeled ERE +/- excess ERE. A retarded band was seen which was completely obliterated with excess ERE, confirming the specificity of binding. This probe was then used to make reconstituted mononucleosomes by sequential dilution of a high salt histone preparation. The nucleosomes were purified by sucrose density gradients and footprinting analysis was performed to demonstrate that the mononucleosomes were rotationally phased as seen by a periodic digestion pattern (10 bp) of the nucleosomes versus ERE. Nucleosomes were incubated with nuclear extracts containing ER or recombinant ERalpha. Dose dependence in the shift of the mononucleosomes with increasing concentrations of ER was observed. Specificity was demonstrated in experiments with excess ERE and anti-ER antibody. Footprinting analysis was also performed. We also determined that addition of high mobility group protein-2 (HMGB-2, a protein closely related to HMGB-1) with the ER increased the interaction of ER with mononucleosomes. These studies will allow us to address the interactions of ER with core histones containing a multiplicity of variants and modifications in nucleosomal structure.

Aryl hydrocarbon receptor-mediated posttranscriptional regulation of IL-1beta.

TCDD stimulated IL-1beta gene expression in differentiating human keratinocyte cell lines in a time- and dose-dependent manner. Increases in prointerleukin-1beta (pIL-1beta) protein and IL-1beta steady state mRNA levels were observed in both SCC-12F and HaCaT cells following TCDD treatment. When pretreated with alpha-naphthoflavone, an AhR antagonist, TCDD-mediated increases in IL-1beta gene expression were attenuated, demonstrating for the first time that the environmental toxin, TCDD, can stimulate cytokine (IL-1beta) gene expression in an AhR-dependent manner. Nuclear run-on experiments were performed in SCC-12 cells to determine if the AhR-dependent increases in IL-1beta expression were due to transcriptional activation of the IL-1beta gene. Results showed high constitutive levels of IL-1beta transcriptional activity, however, TCDD treatment, which stimulated IL-1beta steady state mRNA levels, failed to potentiate IL-1beta transcription. Taken together, these results demonstrate that AhR-mediated IL-1beta regulation is occurring posttranscriptionally.