Specification of an extensible and portable file format for electronic structure and crystallographic data

In order to allow different software applications, in constant evolution, to interact and exchange data, flexible file formats are needed. A file format specification for different types of content has been elaborated to allow communication of data for the software developed within the European Network of Excellence "NANOQUANTA", focusing on first-principles calculations of materials and nanosystems. It might be used by other software as well, and is described here in detail. The format relies on the NetCDF binary input/output library, already used in many different scientific communities, that provides flexibility as well as portability accross languages and platforms. Thanks to NetCDF, the content can be accessed by keywords, ensuring the file format is extensible and backward compatible

The CECAM Electronic Structure Library and the modular software development paradigm

First-principles electronic structure calculations are very widely used thanks to the many successful software packages available. Their traditional coding paradigm is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, from the compiler up, with the exception of linear-algebra and message-passing libraries. This model has been quite successful for decades. The rapid progress in methodology, however, has resulted in an ever increasing complexity of those programs, which implies a growing amount of replication in coding and in the recurrent re-engineering needed to adapt to evolving hardware architecture. The Electronic Structure Library (\esl) was initiated by CECAM (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 programs and redesign them as free, open-source libraries. They include ``heavy-duty'' ones with a high degree of parallelisation, and potential for 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 scientists when implementing new ideas. It is a community effort, undertaken by developers of various successful codes, now facing the challenges arising in the new model. This modular paradigm will improve overall coding efficiency and enable specialists (computer scientists or computational scientists) to use their skills more effectively. It will lead to a more sustainable and dynamic evolution of software as well as lower barriers to entry for new developers

Inhibition of the inositol kinase Itpkb augments calcium signaling in lymphocytes and reveals a novel strategy to treat autoimmune disease

Emerging approaches to treat immune disorders target positive regulatory kinases downstream of antigen receptors with small molecule inhibitors. Here we provide evidence for an alternative approach in which inhibition of the negative regulatory inositol kinase Itpkb in mature T lymphocytes results in enhanced intracellular calcium levels following antigen receptor activation leading to T cell death. Using Itpkb conditional knockout mice and LMW Itpkb inhibitors these studies reveal that Itpkb through its product IP4 inhibits the Orai1/Stim1 calcium channel on lymphocytes. Pharmacological inhibition or genetic deletion of Itpkb results in elevated intracellular Ca2+ and induction of FasL and Bim resulting in T cell apoptosis. Deletion of Itpkb or treatment with Itpkb inhibitors blocks T-cell dependent antibody responses in vivo and prevents T cell driven arthritis in rats. These data identify Itpkb as an essential mediator of T cell activation and suggest Itpkb inhibition as a novel approach to treat autoimmune disease

Best Practices for Scientific Computing

Scientists spend an increasing amount of time building and using software. However, most scientists are never taught how to do this efficiently. As a result, many are unaware of tools and practices that would allow them to write more reliable and maintainable code with less effort. We describe a set of best practices for scientific software development that have solid foundations in research and experience, and that improve scientists' productivity and the reliability of their software.Comment: 18 page

Sharing electronic structure and crystallographic data with ETSF_IO

We present a library of routines whose main goal is to read and write exchangeable files (NetCDF file format) storing electronic structure and crystallographic information. It is based on the specification agreed inside the European Theoretical Spectroscopy Facility (ETSF). Accordingly, this library is nicknamed ETSF_IO. The purpose of this article is to give both an overview of the ETSF_IO library and a closer look at its usage. ETSF_IO is designed to be robust and easy to use, close to Fortran read and write routines. To facilitate its adoption, a complete documentation of the input and output arguments of the routines is available in the package, as well as six tutorials explaining in detail various possible uses of the library routines

Wannier functions approach to van der Waals interactions in ABINIT

The method to calculate van der Waals interactions based on maximally localized Wannier functions (MLWFs), proposed by Silvestrelli [Phys. Rev. Lett. 100 (2008) 053002], has been implemented within the ab initio DFT program ABINIT. In addition to a brief review of the theoretical background behind this methodology, we present the details of the implementation, which will help users to assess van der Waals corrections in both molecular and periodic systems with a negligible additional computational cost. Some tests on argon dimer, argon FCC solid, benzene dimer and bilayer of graphene are presented. A discussion about the reliability of the method is also included

Bimodal supramolecular functionalization of carbon nanotubes triggered by covalent bond formation

Many applications of carbon nanotubes require their chemical functionalization. Both covalent and supramolecular approaches have been extensively investigated. A less trodden path is the combination of both covalent and noncovalent chemistries, where the formation of covalent bonds triggers a particularly stable noncovalent interaction with the nanotubes. We describe a series of naphthalene diimide (NDI) bisalkene molecules that, upon mixing with single-walled carbon nanotubes (SWNTs) and Grubbs' catalyst, undergo two different reaction pathways. On one hand, they ring-close around the SWNTs to form rotaxane-like mechanically interlocked derivatives of SWNTs (MINTs). Alternatively, they oligomerize and then wrap around the SWNTs. The balance of MINTs to oligomer-wrapped SWNTs depends on the affinity of the NDI molecules for the SWNTs and the kinetics of the metathesis reactions, which can be controlled by varying the solvent. Thorough characterization of the products (TGA, TEM, AFM, Raman, UV-vis-NIR, PLE, XPS and UPS) confirms their structure and shows that each type of functionalization affects the electronic properties of the SWNTs differently

The ETSF : an e-infrastructure to bridge simulation and experiment

The European Theoretical Spectroscopy Facility (ETSF) is a distributed knowledge network that gives researchers access to state-of-the-art computer simulations for electronic excited states in matter. Focusing on the fundamental knowledge of matter at the quantum-mechanical level, ETSF seeks to transfer this understanding to the future design of technologies in multiple areas

The mechanical bond on carbon nanotubes: diameter-selective functionalization and effects on physical properties

We describe the functionalization of SWNTs enriched in (6,5) chirality with electron donating macrocycles to yield rotaxane-type mechanically interlocked carbon nanotubes (MINTs). Investigations by means of electron microscopy and control experiments corroborated the interlocked nature of the MINTs. A comprehensive characterization of the MINTs through UV-vis-NIR, Raman, fluorescence, transient absorption spectroscopy, cyclic voltammetry, and chronoamperometry was carried out. Analyses of the spectroscopic data reveal that the MINT-forming reaction proceeds with diameter selectivity, favoring functionalization of (6,5) SWNTs rather than larger (7,6) SWNTs. In the ground state, we found a lack of significant charge-transfer interactions between the electron donor exTTF and the SWNTs. Upon photoexcitation, efficient charge-transfer between the electron donating exTTF macrocycles and SWNTs was demonstrated. As a complement, we established significantly different charge-transfer rate constants and diffusion coefficients for MINTs and the supramolecular models, which confirms the fundamentally different type of interactions between exTTF and SWNTs in the presence or absence of the mechanical bond. Molecular mechanics and DFT calculations support the experimental findings