Warming Up Density Functional Theory

Density functional theory (DFT) has become the most popular approach to electronic structure across disciplines, especially in material and chemical sciences. Last year, at least 30,000 papers used DFT to make useful predictions or give insight into an enormous diversity of scientific problems, ranging from battery development to solar cell efficiency and far beyond. The success of this field has been driven by usefully accurate approximations based on known exact conditions and careful testing and validation. In the last decade, applications of DFT in a new area, warm dense matter, have exploded. DFT is revolutionizing simulations of warm dense matter including applications in controlled fusion, planetary interiors, and other areas of high energy density physics. Over the past decade or so, molecular dynamics calculations driven by modern density functional theory have played a crucial role in bringing chemical realism to these applications, often (but not always) with excellent agreement with experiment. This chapter summarizes recent work from our group on density functional theory at non-zero temperatures, which we call thermal DFT. We explain the relevance of this work in the context of warm dense matter, and the importance of quantum chemistry to this regime. We illustrate many basic concepts on a simple model system, the asymmetric Hubbard dimer

Integrating Species Traits into Species Pools

Despite decades of research on the species‐pool concept and the recent explosion of interest in trait‐based frameworks in ecology and biogeography, surprisingly little is known about how spatial and temporal changes in species‐pool functional diversity (SPFD) influence biodiversity and the processes underlying community assembly. Current trait‐based frameworks focus primarily on community assembly from a static regional species pool, without considering how spatial or temporal variation in SPFD alters the relative importance of deterministic and stochastic assembly processes. Likewise, species‐pool concepts primarily focus on how the number of species in the species pool influences local biodiversity. However, species pools with similar richness can vary substantially in functional‐trait diversity, which can strongly influence community assembly and biodiversity responses to environmental change. Here, we integrate recent advances in community ecology, trait‐based ecology, and biogeography to provide a more comprehensive framework that explicitly considers how variation in SPFD, among regions and within regions through time, influences the relative importance of community assembly processes and patterns of biodiversity. First, we provide a brief overview of the primary ecological and evolutionary processes that create differences in SPFD among regions and within regions through time. We then illustrate how SPFD may influence fundamental processes of local community assembly (dispersal, ecological drift, niche selection). Higher SPFD may increase the relative importance of deterministic community assembly when greater functional diversity in the species pool increases niche selection across environmental gradients. In contrast, lower SPFD may increase the relative importance of stochastic community assembly when high functional redundancy in the species pool increases the influence of dispersal history or ecological drift. Next, we outline experimental and observational approaches for testing the influence of SPFD on assembly processes and biodiversity. Finally, we highlight applications of this framework for restoration and conservation. This species‐pool functional diversity framework has the potential to advance our understanding of how local‐ and regional‐scale processes jointly influence patterns of biodiversity across biogeographic regions, changes in biodiversity within regions over time, and restoration outcomes and conservation efforts in ecosystems altered by environmental change

Concepts and applications in functional diversity

The use of functional diversity analyses in ecology has grown exponentially over the past two decades, broadening our understanding of biological diversity and its change across space and time. Virtually all ecological sub-disciplines recognise the critical value of looking at species and communities from a functional perspective, and this has led to a proliferation of methods for estimating contrasting dimensions of functional diversity. Differences between these methods and their development generated terminological inconsistencies and confusion about the selection of the most appropriate approach for addressing any particular ecological question, hampering the potential for comparative studies, simulation exercises and meta-analyses. Two general mathematical frameworks for estimating functional diversity are prevailing: those based on dissimilarity matrices (e.g. Rao entropy, functional dendrograms) and those relying on multidimensional spaces, constructed as either convex hulls or probabilistic hypervolumes. We review these frameworks, discuss their strengths and weaknesses and provide an overview of the main R packages performing these calculations. In parallel, we propose a way for organising functional diversity metrics in a unified scheme to quantify the richness, divergence and regularity of species or individuals under each framework. This overview offers a roadmap for confidently approaching functional diversity analyses both theoretically and practically.Peer reviewe

Semantic standards for genomic analyses of the South and Mediterranean plants: the Generation Challenge Program use case

The Generation Challenge Programme (GCP) platform was developed to meet the challenges of data acquisition, computational resources, and software interoperability and integration across a globally distributed consortium of partners. This platform includes: (i) shared, public platform-independent domain models, ontology and data formats (ii) web service and registry technologies (iii) platform-specific middleware implementations of the domain model integrating a suite of public databases and software tools into a workbench to facilitate biodiversity analysis, including the comparative analysis of crop genomic data. The cornerstone of the GCP platform is the development of common standards for GCP data. Major concepts in the domain of crop research - for example, concepts like "germplasm" and "genotype" - can be expressed in terms of a general blue print of such concepts-as-entities and of their relationships to one another, within a so-called domain model. The GCP development team has specified such a domain model to drive development of a "model driven architecture" within which tools and data sources may be efficiently connected to one another. The GCP domain model is not a complete embodiment of semantics in GCP software systems since specifying such a complete model would not be practically feasible. Therefore, in addition to the GCP domain model, the GCP development team has also specified a formal framework to manage a GCP ontology that complements the semantics of the domain model. Several applications and integrating tools have been developed, such as a GCP web query and display application ("Zeus"), a GCP Ontology browser, and the stand-alone molecular breeding components MBDT (Molecular Breeding Design Tool) and MOSEL (Molecular Selection Tool). Our team was particularly involved in the development of GenDiversity, a query and analysis Web application combining genotyping data from diverse data sources, developed in support of diversity studies. Furthermore, GCP components can also be used by non GCP projects. Indeed, we present Orylink, a personalized integrated system for rice functional genomic analysis. The infrastructure of the platform is complex, and it still may discourage developers from using it. Therefore, we need to establish better training and documentation for users of the platform. (Résumé d'auteur

Hierarchical coexistence of universality and diversity controls robustness and multi-functionality in intermediate filament protein networks

Proteins constitute the elementary building blocks of a vast variety of biological materials such as cellular protein networks, spider silk or bone, where they create extremely robust, multi-functional materials by self-organization of structures over many length- and time scales, from nano to macro. Some of the structural features are commonly found in a many different tissues, that is, they are highly conserved. Examples of such universal building blocks include alpha-helices, beta-sheets or tropocollagen molecules. In contrast, other features are highly specific to tissue types, such as particular filament assemblies, beta-sheet nanocrystals in spider silk or tendon fascicles. These examples illustrate that the coexistence of universality and diversity – in the following referred to as the universality-diversity paradigm (UDP) – is an overarching feature in protein materials. This paradigm is a paradox: How can a structure be universal and diverse at the same time? In protein materials, the coexistence of universality and diversity is enabled by utilizing hierarchies, which serve as an additional dimension beyond the 3D or 4D physical space. This may be crucial to understand how their structure and properties are linked, and how these materials are capable of combining seemingly disparate properties such as strength and robustness. Here we illustrate how the UDP enables to unify universal building blocks and highly diversified patterns through formation of hierarchical structures that lead to multi-functional, robust yet highly adapted structures. We illustrate these concepts in an analysis of three types of intermediate filament proteins, including vimentin, lamin and keratin

AADLib, A Library of Reusable AADL Models

The SAE Architecture Analysis and Design Language is now a well-established language for the description of critical embedded systems, but also cyber-physical ones. A wide range of analysis tools is already available, either as part of the OSATE tool chain, or separate ones. A key missing elements of AADL is a set of reusable building blocks to help learning AADL concepts, but also experiment already existing tool chains on validated real-life examples. In this paper, we present AADLib, a library of reusable model elements. AADLib is build on two pillars: 1/ a set of ready-to- use examples so that practitioners can learn more about the AADL language itself, but also experiment with existing tools. Each example comes with a full description of available analysis and expected results. This helps reducing the learning curve of the language. 2/ a set of reusable model elements that cover typical building blocks of critical systems: processors, networks, devices with a high level of fidelity so that the cost to start a new project is reduced. AADLib is distributed under a Free/Open Source License to further disseminate the AADL language. As such, AADLib provides a convenient way to discover AADL concepts and tool chains, and learn about its features

EU and OECD benchmarking and peer review compared

Benchmarking and peer review are essential elements of the so-called EU open method of coordination (OMC) which has been contested in the literature for lack of effectiveness. In this paper we compare benchmarking and peer review procedures as used by the EU with those used by the OECD. Different types of benchmarking and peer review are distinguished and pitfalls for (international) benchmarking are discussed. We find that the OECD has a clear single objective for its benchmarking and peer review activities (i.e. horizontal policy transfers) whereas the EU suffers from a mix of objectives (a. horizontal policy learning; b. EU wide vertical policy coordination and c. multilateral monitoring and surveillance under the shadow of hierarchy). Whereas the OECD is able to skirt around most of the benchmarking pitfalls, this is not the case for the EU. It is argued that, rather than continue working with the panacea OMC benchmarking and peer review currently represents, EU benchmarking should take a number of more distinct shapes in order to improve effectiveness. Moreover, in some areas benchmarking and peer review are not sufficient coordination tools, and are at best additional to those means of coordination that include enforceable sanctions