NFFA-Europe Pilot - D16.2 - Report on the first data services

This document describes the initial set of data services available in NFFA Europe Pilot

NFFA-Europe Pilot - D16.3 - Identification of good practices for data provenance

Here we elaborate and implement FAIR-oriented procedures and recommendations to enforce data provenance in the NFFA scientific experiment’s workflow, from data creation to data usage. The set of procedures is developed by taking into account needs coming from various communities within NEP. Close attention is paid to identify and tailor existing electronic lab notebook (ELN) and laboratory information management system solutions for describing sample processing workflows and (semi-) automated metadata recording during the experiments as initial steps for implementing FAIR by design datasets

D16.1 - Design of the service platform

This deliverable presents the initial design of the infrastructure for the NFFA-Europe Pilot (NEP). The infrastructure is planned to consist of diverse elements for the Data and the Metadata Management, as well as different services (in the frontend, in the backend, and for Virtual Access) which will be gradually developed and integrated in a seamless way. We distinguish between the basic elements, which are essential parts of the infrastructure planned in the NEP proposal, and additional elements which were not initially planned but might improve the interconnections and facilitate the Research Users, in case they will be developed as output of the scouting activities of the Task 16.4 of the Joint Activity 6 (Work Package 16). The elements of the infrastructure will be connected to each other and will be accessed by users or by other services thanks to interfaces

1D selective confinement and diffusion of metal atoms on graphene

The role of moiré graphene superstructures in favoring confined adsorption of different metal atoms is an intriguing problem not yet completely solved. Graphene (G) grown on Ni(100) forms a striped moiré pattern of valleys, where G approaches the nickel substrate and interacts with it rather strongly, and ridges, where G stays far away from the substrate and acts almost free-standing. Combining density functional theory (DFT) calculations and scanning-tunneling microscopy (STM) measurements, we show that this peculiar moiré constitutes a regular nanostructured template on a 2D support, confining in 1D trails single metal atoms and few atoms clusters. DFT calculations show that the confinement is selective and highly dependent on the atomic species, with some species preferring to adsorb on ridges and the other showing preference for valleys. Co and Au adsorbates, for instance, have opposite behavior, as predicted by DFT and observed by STM. The origin of such disparate behavior is traced back to the electrostatic interaction between the charged adsorbate and the nickel surface. Moreover, the selectivity is not restricted to the adsorption process only, but persists as adsorbate starts its diffusion, resulting in unidirectional mass transport on a continuous 2D support. These findings hold great promise for exploiting tailored nanostructured templates in a wide range of potential applications involving mass transport along element-specific routes

Exceptionally Stable Cobalt Nanoclusters on Functionalized Graphene

To improve reactivity and achieve a higher material efficiency, catalysts are often used in the form of clusters with nanometer dimensions, down to single atoms. Since the corresponding properties are highly structure-dependent, a suitable support is thus required to ensure cluster stability during operating conditions. Herein, an efficient method to stabilize cobalt nanoclusters on graphene grown on nickel substrates, exploiting the anchoring effect of nickel atoms incorporated in the carbon network is presented. The anchored nanoclusters are studied by in situ variable temperature scanning tunneling microscopy at different temperatures and upon gas exposure. Cluster stability upon annealing up to 200 °C and upon CO exposure at least up to 1 × 10−6 mbar CO partial pressure is demonstrated. Moreover, the dimensions of the cobalt nanoclusters remain surprisingly small (<3 nm diameter) with a narrow size distribution. Density functional theory calculations demonstrate that the interplay between the low diffusion barrier on graphene on nickel and the strong anchoring effect of the nickel atoms leads to the increased stability and size selectivity of these clusters. This anchoring technique is expected to be applicable also to other cases, with clear advantages for transition metals that are usually difficult to stabilize

Domain level ontology design: DISO and MDMC-NEP Provenance

How can a computer understand the relations of data or objects from the real world? Ontologies are semantic artifacts that capture knowledge about their domain of interest in a machine-understandable form. The main goal of developing ontologies is to formalize concepts and their relations through which humans express meaning and to use them as a communication interface to machines. Thus, ontology development is an important step towards generating linked and FAIR data. Within HMC we support and co-develop domain and application-level ontologies. Here we present two developments: Dislocation Ontology (DISO) and Model and Data-Driven Materials Characterization Provenance (MDMC-PROV). DISO: An important class of materials is crystalline materials, e.g., metals and semiconductors, which nearly always contain defects, the “dislocations”. This type of defect determines many important material properties, e.g., strength and ductility. Over the past years, significant effort has been put into understanding dislocation behavior across different length scales via experimental characterization techniques and simulations. However, there is still a lack of common standards to formally describe and represent disclocations. Thus, in this work we develop the dislocation ontology (DISO), which is a domain ontology that defines the concepts and relationships related to linear defects in crystalline materials. DISO is published [1] through a persistent URL following W3C best practices for publishing Linked data. MDMC-Prov: The rapid development of science and technology in everyday large data generation does not match the data understanding. These days, understanding how experiments are performed and results are derived become more complex due to a lack of provenance documentation. Therefore, the provenance must be tracked, described, and managed over the research process. Thus, in this work, we report an application ontology that can capture provenance information in materials science experiments. The ontology is based on the MDMC glossary [2], which defines the common terms in the materials science experiments. From each term, we map to PROV-O [3]. These ensure the validity, reproducibility, and reusability of the data. [1] https://purls.helmholtz-metadaten.de/diso [2] https://jl-mdmc-helmholtz.de [3] https://www.w3.org/TR/2013/NOTE-prov-primer-20130430/ DISO:  An important class of materials is crystalline materials, e.g., metals and semiconductors, which nearly always contain defects, the “dislocations”. This type of defect determines many important material properties, e.g., strength and ductility. Over the past years, significant effort has been put into understanding dislocation behavior across different length scales via experimental characterization techniques and simulations. However, there is still a lack of common standards to formally describe and represent disclocations. Thus, in this work we develop the dislocation ontology (DISO), which is a domain ontology that defines the concepts and relationships related to linear defects in crystalline materials. DISO is published1 through a persistent URL following W3C best practices for publishing Linked data. MDMC-Prov: The rapid development of science and technology in everyday large data generation does not match the data understanding. These days, understanding how experiments are performed and results are derived become more complex due to a lack of provenance documentation. Therefore, the provenance must be tracked, described, and managed over the research process. Thus, in this work, we report an application ontology that can capture provenance information in materials science experiments. The ontology is based on the MDMC glossary, which defines the common terms in the materials science experiments. From each term, we map to PROV-O3. These ensure the validity, reproducibility, and reusability of the data

Towards the FAIRification of Scanning Tunneling Microscopy Images

ABSTRACTIn this paper, we describe the data management practices and services developed for making FAIR compliant a scientific archive of Scanning Tunneling Microscopy (STM) images. As a first step, we extracted the instrument metadata of each image of the dataset to create a structured database. We then enriched these metadata with information on the structure and composition of the surface by means of a pipeline that leverages human annotation, machine learning techniques, and instrument metadata filtering. To visually explore both images and metadata, as well as to improve the accessibility and usability of the dataset, we developed “STM explorer” as a web service integrated within the Trieste Advanced Data services (TriDAS) website. On top of these data services and tools, we propose an implementation of the W3C PROV standard to describe provenance metadata of STM images

Stabilizing edge fluorination in graphene nanoribbons

The on-surface synthesis of edge-functionalized graphene nanoribbons (GNRs) is challenged by the stability of the functional groups throughout the thermal reaction steps of the synthetic pathway. Edge fluorination is a particularly critical case in which the interaction with the catalytic substrate and intermediate products can induce the complete cleavage of the otherwise strong C-F bonds before the formation of the GNR. Here, we demonstrate how a rational design of the precursor can stabilize the functional group, enabling the synthesis of edge-fluorinated GNRs. The survival of the functionalization is demonstrated by tracking the structural and chemical transformations occurring at each reaction step with complementary X-ray photoelectron spectroscopy and scanning tunneling microscopy measurements. In contrast to previous attempts, we find that the C-F bond survives the cyclodehydrogenation of the intermediate polymers, leaving a thermal window where GNRs withhold more than 80% of the fluorine atoms. We attribute this enhanced stability of the C-F bond to the particular structure of our precursor, which prevents the cleavage of the C-F bond by avoiding interaction with the residual hydrogen originated in the cyclodehydrogenation. This structural protection of the linking bond could be implemented in the synthesis of other sp2-functionalized GNRs