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

Siesta: Recent developments and applications

A review of the present status, recent enhancements, and applicability of the Siesta program is presented. Since its debut in the mid-1990s, Siesta?s flexibility, efficiency, and free distribution have given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of Siesta combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, and a real-space grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here, we describe the more recent implementations on top of that core scheme, which include full spin?orbit interaction, non-repeated and multiple-contact ballistic electron transport, density functional theory (DFT)+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, density-functional perturbation theory, efficient van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as wannier90 and the second-principles modeling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering Siesta runs, and various post-processing utilities. Siesta has also been engaged in the Electronic Structure Library effort from its inception, which has allowed the sharing of various low-level libraries, as well as data standards and support for them, particularly the PSeudopotential Markup Language definition and library for transferable pseudopotentials, and the interface to the ELectronic Structure Infrastructure library of solvers. Code sharing is made easier by the new open-source licensing model of the program. This review also presents examples of application of the capabilities of the code, as well as a view of on-going and future developments.SIESTA development was historically supported by different Spanish National Plan projects (Project Nos. MEC-DGES-PB95-0202, MCyT-BFM2000-1312, MEC-BFM2003-03372, FIS2006-12117, FIS2009-12721, FIS2012-37549, FIS2015-64886-P, and RTC-2016-5681-7), the latter one together with Simune Atomistics Ltd. We are thankful for financial support from the Spanish Ministry of Science, Innovation and Universities through Grant No. PGC2018-096955-

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

Placing the 'other' in our midst : immigrant Jews, gender and the British imperial imagination

This thesis traces cultural and socio-political responses to the alien Jew in Britain through the prism of genre, space and time. Beginning with the reports of persecution of Jews in Eastern Europe in the late nineteenth century, it examines how representations of these foreign Jews changed and developed as sympathy for their plight turned to anxiety at the prospect of their arrival in Britain. It shows how a Semitic discourse evolved alongside, and in response to, wider debates about the state of the self, nation and empire at the fin de siècle, arguing that the vocabulary and mentality of imperialism was a crucial tool for deciphering the nature of Jewish „difference‟. However, this thesis also enables fresh perspectives by considering the gender and spatial dynamics of Semitic representations in Britain during and beyond the period of mass immigration, from the end of the nineteenth century until the beginning of the twenty first. This extended view of the Jewish 'other', which follows the 'typical' Jewish migrant journey from the shtetl of Eastern Europe to the North London suburb of the present-day, considers how Jewish spatial and cultural practices have been interpreted and articulated by the British and the British-Jewish onlooker. The thesis' opening section, divided into three chapters, adopts an original approach to the aliens question by exploring how perspectives on the alien Jew were shaped and expressed within different mediums, or 'genres' at the fin de siècle. Through an assessment of newspapers, political debates, and fiction, this section offers a comparative analysis of how the particular dynamics and agendas of each of these genres operated to produce different textual and visual images of 'the Jew'. Building upon Bryan Cheyette's seminal work in relation to fiction, each of these chapters demonstrates not only the inherently ambivalent nature of Semitic representations but also reveal that, crucially, gender was an important moderator of Jewish „difference‟. This reading extends into the second section which, across four chapters, explores how gender functioned in conjunction with space to construct ideas in Britain about alien Jews as they traversed time and space from shtetl to suburb. Beginning with the point of departure, the opening chapter of the section reviews the long tradition of representing Eastern Europe by „the West‟, arguing that this tradition laid the foundation for a paradoxical view of the Jew in Eastern Europe as both territorialized and territorializing. This perceived struggle for spatial ownership amongst Jews also featured in narratives of the migrant journey – the topic of the second chapter. That perception generated the notion that migrating Jews were staging an alien invasion of Britain. Thus the prolonged fascination with London's Jewish 'ghetto' and its interior – 'alien' territory par excellence – provides the focus for the third chapter which, in turn, lays the foundation for the final chapter‟s exploration of the replacement of the urban with the suburban as the alien Jew's 'territory' of choice.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Gas sensing and thermal transport through carbon-nanotube-based nanodevices

et al.Designing nanoscale devices, such as gas sensors and thermal dissipators, is challenging at multiple levels. Exploring their properties through combined experimental and theoretical collaborations is a valuable approach that expands the understanding of their peculiarities and allows for the optimization of the design process. In order to select the most relevant functional molecules for carbon-based gas sensors, and provide the best sensitivity and selectivity possible, we study the electronic transport properties of functionalized carbon nanotubes (CNTs), both through experiments and theoretical calculations. The measurements are carried out both in argon and synthetic air, using CO, NO, and H2S as test cases, with carboxyl-functionalized CNTs. The calculations, performed in the framework of density functional theory, consider both metallic and semi-conducting prototype CNTs, with respective chiralities (6,6) and (7,0), exploring a broader range of functional molecules and gases. The behavior of individual carboxyl-functionalized CNTs deduced from the multiscale results consistently reflect what happens at a larger scale and provides useful insights regarding the experimental results. CNTs are excellent thermal conductors as well and show much promise as heat dissipators in microelectronics. However, in practice, thermal properties of CNTs are affected due to the unavoidable presence of defects and interface with the environment. We investigated these limitations using a multiscale approach. Using molecular dynamics simulations, here we investigate the heat flow across the interface of a (10,10) CNT with various substances, including air and water. We also analyzed computationally the impact of CNT defects on its thermal transport properties using first principles calculations.We acknowledge financial support from the European Union through the FP7 project: “Thermal management with carbon nanotube architectures” (THEMA-CNT, contract number 228539), the European Research Council Advanced Grant DYNamo (ERC-2010-AdG - 267374) and European Commission projects CRONOS (Grant number 280879-2 CRONOS CP-FP7) and POCAONTAS (FP7-PEOPLE-2012-ITN. Project number 316633). We also received financial support from the Spanish Grants FIS2011-65702-C02-01 and PIB2010US-00652, as well as from the Ikerbasque foundation. Y.P. and A.R. acknowledge funding by the Spanish MEC (FIS2007-65702-C02-01), “Grupos Consolidados UPV/EHU del Gobierno Vasco” (IT-319-07 & IT578-13). Y.P. also acknowledges a contract funded by MICINN (PTA2008-0982-I) and ETORTEK-inanoGUNE (2009–2011).Peer Reviewe

Hyloidichnus trackways with digit and tail drag traces from the Permian of Gonfaron (Var, France): New insights on the locomotion of captorhinomorph eureptiles

This work received support from the CERCA programme (ICP) from the Generalitat de Catalunya.Newly discovered tetrapod footprints from the middle Permian Pelitic Formation of Gonfaron (Le Luc Basin, Var, France) are described in detail and assigned to the ichnogenus Hyloidichnus. These specimens are very well-preserved, with detailed trackways showing anatomical features, digit drag traces and continuous tail impressions. Together with other Hyloidichnus specimens from the same locality and from the University of Burgundy collections, they allow the identification of the possible trackmakers of Hyloidichnus: small Hyloidichnus footprints are correlated with captorhinomorphs with autopodia similar to Captorhinus whereas large Hyloidichnus footprints might be correlated with larger captorhinomorphs or other 'basal' (eventually stem-) moradisaurines. A detailed comparative analysis is proposed to better understand the locomotion style of the trackmakers. Starting from the reconstruction of the stance phase of Captorhinus, we document the swing phase of the fore- and hind-limbs of captorhinomorphs thanks to the continuous digit drag traces associated with Hyloidichnus. A link between gait and track preservation have been highlighted through the analysis of tail impressions and high-resolution 3D models. In all, this study increases our understanding of captorhinomorph locomotion and enhances the integration of both tracks and skeletal remains to highlight the biomechanics of Permian tetrapods