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FAIR-by-design NFFA case study within Module 3 of the course "News and insights from Open Science, and how to exploit them in your scientific work" held for MSCA-ITN SMART-X, held on 11 July 2023. This presentation focus on the implementation of Open Science and FAIR principles in a Scanning tunneling microscopy (STM) laboratory at CNR-IOM.

The influence on the growth of cobalt (Co)-based nanostructures of a surface carbide (Ni2C) layer formed at the Ni(100) surface is revealed via complementary scanning tunneling microscopy (STM) measurements and first-principles calculations. On clean Ni(100) below 200 degrees C in the sub-monolayer regime, Co forms randomly distributed two-dimensional (2D) islands, while on Ni2C it grows in the direction perpendicular to the surface as well, thus forming two-atomic-layers high islands. We present a simple yet powerful model that explains the different Co growth modes for the two surfaces. A jagged step decoration, not visible on stepped Ni(100), is present on Ni2C. This contrasting behavior on Ni2C is explained by the sharp differences in the mobility of Co atoms for the two cases. By increasing the temperature, Co dissolution is activated with almost no remaining Co at 250 degrees C on Ni(100) and Co islands still visible on the Ni2C surface up to 300 degrees C. The higher thermal stability of Co above the Ni2C surface is rationalized by ab initio calculations, which also suggest the existence of a vacancy-assisted mechanism for Co dissolution in Ni(100). The methodology presented in this paper, combining systematically STM measurements with first-principles calculations and computational modelling, opens the way to controlled engineering of bimetallic surfaces with tailored properties.

Under near-ambient pressure conditions, carbon monoxide molecules intercalate underneath an epitaxial graphene monolayer grown on Ni(111), getting trapped into the confined region at the interface. On the basis of ab-initio density functional theory calculations, we provide here a full investigation of the intercalated CO pattern, highlighting the modifications induced on the graphene electronic structure. For a CO coverage as low as 0.14 monolayer (ML), the graphene layer is spatially decoupled from the metallic substrate, with a significant C 1s core level shift towards lower binding energies. The most relevant signature of the CO intercalation is a clear switching of the graphene doping state, which changes from n-type, when strongly interacting with the metal surface, to p-type. The shift of the Dirac cone linearly depends on the CO coverage, reaching about 0.9 eV for the saturation value of 0.57 ML. Theoretical predictions are compared with the results of scanning tunnelling microscopy, low-energy electron diffraction and photoemission spectroscopy experiments, which confirm the proposed scenario for the nearly saturated intercalated CO system. This result opens the way to the application of the graphene/Ni(111) interface as gas sensor to easily detect and quantify the presence of carbon monoxide.

In 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.

The document presents the NEP Data Management Plan (NEP-DMP), and describes the measures envisaged to efficiently manage the Research Data collected and generated during the project. The NEP-DMP is intended to be a living document in which information can be made available on a finer level of granularity through updates as the implementation of the project progresses and when significant changes occur. The document is therefore versioned in order to keep track of changes and improvements. The NEP-DMP describes the standards and methodologies for the collection and generation of Research Data that will be applied throughout the duration of the project, as well as the conditions for publishing such data. This document aims to facilitate the creation of common understanding and, where possible, common practices.

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 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 glossary2, 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. [1] https://purls.helmholtz-metadaten.de/disos/diso [2] https://jl-mdmc-helmholtz.de [3] https://www.w3.org/TR/2013/NOTE-prov-primer-20130430/, {"references":["DISO Repository : https://github.com/Materials-Data-Science-and-Informatics/dislocation-ontology/","MDMC-NEP Prov Repository : https://github.com/Materials-Data-Science-and-Informatics/MDMC-NEP-top-level-ontology"]}

Published version and Supporting Information. Abstract: Dynamic covalent chemistry is a powerful approach to design covalent organic frameworks, where high crystallinity is achieved through reversible bond formation. Here, we exploit near-ambient pressure X-ray photoelectron spectroscopy to elucidate the reversible formation of a two-dimensional boroxine framework. By in situ mapping the pressure–temperature parameter space, we identify the regions where the rates of the condensation and hydrolysis reactions become dominant, being the key to enable the thermodynamically controlled growth of crystalline frameworks.

In the context of the EOSC-Pillar project, Work Package 6 (EOSC in action: Use cases and community-driven pilots) delivers use cases to analyse different tools and services used for the "FAIRification". Among them, Use Case 1 (Defining procedures and services to enforce data provenance for thematic communities and beyond) aims at elaborating cross-domain, FAIR-oriented procedures and recommendations to enforce data provenance in two scientific domains: Materials Science/Nanoscience and Climate Science. Learn more about use case 1

Transition metal atoms are commonly used in catalysis and photo-catalysis, but their potential reactivity reduces with aggregation and alloying. We investigate in particular whether Cobalt adatoms float on Ni surfaces or dissolve into the metal. Density functional theory calculations have been performed in order to evaluate the stability of different Cobalt adsorption configurations on Nickel surfaces, mainly at (100) terraces and steps, and the relevant energy barriers for diffusion on terraces and across steps, segregation and dissolution into the substrate. The simulations have been compared with variable temperature scanning tunneling microscopy and low energy electron diffraction. The results show that the Cobalt adatoms and small aggregates are unstable with respect to the formation of Co-Ni alloys, but the presence of a carbide monolayer on Ni surface improve their stability. © 2022 Societa Italiana di Fisica. All rights reserved. Communications: SIF Congress 2021

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., WP16 - Implementing FAIR data approach within NEP

Due to the increasing complexity of data analysis workflows, provenance management is a key component to support the re-use of scientific data. Alongside findability, accessibility and interoperability, the reusability of data constitutes a pillar of the FAIR principles and in this regard rich and reliable provenance is essential to ensure that. In the context of the EOSC-Pillar project, Work Package 6 (EOSC in action: Use cases and community-driven pilots) delivers use cases to analyze different tools and services used for the "FAIRification". Among them, our use case (UC1: Defining procedures and services to enforce data provenance for thematic communities and beyond) aims at elaborating cross-domain, FAIR-oriented procedures and recommendations to enforce data provenance by taking into account needs coming from two scientific domains: Materials Science/Nanoscience and Climate Science. In such a context, (W3C) PROV standard has been considered a recommended family of specifications for tracking processes and responsibilities as well as describing provenance structures within complex experiments and large workflows on scientific data. Starting from the W3C PROV data model and ontology, the PROV Core concepts have been applied in the form of adaptations and extensions on top of the existing scientific data services, to enhance provenance capabilities, thus addressing FAIR-oriented full provenance management.

The electronic properties of graphene can be modified by the local interaction with a selected metal substrate. To probe this effect, Scanning Tunneling Microscopy is widely employed, particularly by means of local measurement via lock-in amplifier of the differential conductance and of the field emission resonance. In this article we propose an alternative, reliable method of probing the graphene/substrate interaction that is readily available to any STM apparatus. By testing the tunneling current as function of the tip/sample distance on nanostructured graphene on Ni(100), we demonstrate that I(z) spectroscopy can be quantitatively compared with Density Functional Theory calculations and can be used to assess the nature of the interaction between graphene and substrate. This method can expand the capabilities of standard STM systems to study graphene/substrate complexes, complementing standard topographic probing with spectroscopic information.

High-quality nitrogen-doped graphene on nickel is prepared by exploiting both the catalytic properties of nickel and the solubility of nitrogen atoms into its bulk. Following the standard chemical vapor deposition procedure, a previously nitrogen-doped nickel substrate is exposed to carbon-containing precursors so that nitrogen atoms, segregating to the surface, remain trapped in the growing graphene network. Morphological and chemical characterization by scanning tunneling microscopy and X-ray photoelectron spectroscopy demonstrates that the process yields a flat, wide, continuous nitrogen-doped graphene layer. Experimental results are combined with a thorough density functional theory investigation of possible structural models, to obtain a clear description at the atomic scale of the various configurations of the nitrogen atoms observed in the graphene mesh. This growth method is potentially scalable and suitable for the production of high-performance nano-devices with well-defined nitrogen centers, to be exploited as metal-free carbon-based catalysts in several applicative fields such as electrochemistry, energy storage, gas storage/sensing or wastewater treatment., 21 pages, including 4 figures, plus SI

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The document presents the NEP Data Management Plan (NEP-DMP), and describes the measures envisaged to efficiently manage the Research Data collected and generated during the project. The NEP-DMP is intended to be a living document in which information can be made available on a finer level of granularity through updates as the implementation of the project progresses and when significant changes occur. The document is therefore versioned in order to keep track of changes and improvements. The NEP-DMP describes the standards and methodologies for the collection and generation of Research Data that will be applied throughout the duration of the project, as well as the conditions for publishing such data. This document aims to facilitate the creation of common understanding and, where possible, common practices.

In a continued quest to monitor subsecond surface dynamics on the atomic scale and to improve imaging resolution, a FAST module to accelerate existing scanning probe microscopy setups was previously presented. Hereby, the speedup is enabled by external electronics without modification of the actual instrument. The resulting one-dimensional (1D) data stream, recorded while the tip oscillates in a sinusoidal motion, has to be reconstructed into a layered rectangular matrix in order to visualize the movie. The Pythonbased pyfastspm package performs this conversion, while also correcting for sample tilt, noise frequencies, piezo creep, and thermal drift. Quick automatic conversion even of considerable batches of data is achieved by efficient algorithms that bundle time-expensive steps, such as interpolation based on Delaunay triangulation.

This document describes the initial set of data services available in NFFA Europe Pilot., WP16 - Implementing FAIR data approach within NEP