A Decade with VAMDC: Results and Ambitions

This paper presents an overview of the current status of the Virtual Atomic and Molecular Data Centre (VAMDC) e-infrastructure, including the current status of the VAMDC-connected (or to be connected) databases, updates on the latest technological development within the infrastructure and a presentation of some application tools that make use of the VAMDC e-infrastructure. We analyse the past 10 years of VAMDC development and operation, and assess their impact both on the field of atomic and molecular (A&M) physics itself and on heterogeneous data management in international cooperation. The highly sophisticated VAMDC infrastructure and the related databases developed over this long term make them a perfect resource of sustainable data for future applications in many fields of research. However, we also discuss the current limitations that prevent VAMDC from becoming the main publishing platform and the main source of A&M data for user communities, and present possible solutions under investigation by the consortium. Several user application examples are presented, illustrating the benefits of VAMDC in current research applications, which often need the A&M data from more than one database. Finally, we present our vision for the future of VAMDC

A decade with vamdc: Results and ambitions

This paper presents an overview of the current status of the Virtual Atomic and Molecular Data Centre (VAMDC) e-infrastructure, including the current status of the VAMDC-connected (or to be connected) databases, updates on the latest technological development within the infrastructure and a presentation of some application tools that make use of the VAMDC e-infrastructure. We analyse the past 10 years of VAMDC development and operation, and assess their impact both on the field of atomic and molecular (A&amp;M) physics itself and on heterogeneous data management in international cooperation. The highly sophisticated VAMDC infrastructure and the related databases developed over this long term make them a perfect resource of sustainable data for future applications in many fields of research. However, we also discuss the current limitations that prevent VAMDC from becoming the main publishing platform and the main source of A&amp;M data for user communities, and present possible solutions under investigation by the consortium. Several user application examples are presented, illustrating the benefits of VAMDC in current research applications, which often need the A&amp;M data from more than one database. Finally, we present our vision for the future of VAMDC.</jats:p

A LCT pegmatite spectral library of the aldeia spodumene deposit: contributes to mineral exploration

Several methodologies can be employed in the prospection of Lithium (Li) in hard-rock (pegmatites). Spectrometry analysis, a Remote Sensing (RS) technique, can be applied to understand the surface spectral response of a sample, both to identify the rock-forming or alteration minerals in its composition and to validate the data collected in situ (by sensors onboard satellites/drones, for example). This paper aims to make available for public use the information acquired on the spectral composition of rock samples from the Barroso pegmatite field in Portugal, within the scope of the INOVMINERAL4.0 project. As a result, a spectral library was created with 47 spectra, collected from 11 different samples. All data is made available in a universal format, thus contributing to open science, corroborating the validation of local spectral data, and stimulating the creation of other databases, in other locations.The authors acknowledge the support provided by Portuguese National Funds through the FCT – Fundação para a Ciência e a Tecnologia, I.P. (Portugal) projects UIDB/04683/2020 and UIDP/04683/2020 (Institute of Earth Sciences); through ANI and COMPETE 2020 as well as European funds through the European Regional Development Fund (ERDF) with POCI-01-0247-FEDER- 046083 INOVMINERAL project. The authors also thank Savannah Resources PLC for access to the Aldeia pegmatite and for providing the samples used in this study. Cátia Rodrigues de Almeida and Douglas Santos were financially supported by Portuguese national funds through FCT (Grant: PRT/BD/153518/2021, Grant: UI/BD/154412/2023, respectively).info:eu-repo/semantics/publishedVersio

The INOVMineral Projects Contribution to Mineral Exploration A WebGIS Integration and Visualization of Spectral and Geophysical Properties of the Aldeia LCT Pegmatite Spodumene Deposit

Due to the energetic transition at course, new geological exploration technologies are needed to discover mineral deposits containing critical materials such as lithium (Li). The vast majority of European Li deposits are related to LiCsTa (LCT) pegmatites. Literature review indicates that conventional exploration campaigns are dominated by geochemical surveys and related exploration tools. However, other exploration techniques must be evaluated namely remote sensing (RS) and geophysics. This work presents the results of the INOVMINERAL4.0 project obtained through alternative approaches to traditional geochemistry that were gathered and integrated into a webGIS application. The specific objectives were to: (i) assess the potential of high-resolution elevation data; (ii) evaluate geophysical methods, particularly radiometry; (iii) establish a methodology for spectral data acquisition and build a spectral library; (iv) compare obtained spectra with Landsat 9 data for pegmatite identification; and (v) implement a user-friendly webGIS for data integration and visualization. Radiometric data acquisition using geophysical techniques effectively discriminated pegmatites from host rocks. The developed spectral library provided valuable insights for space-based exploration. Landsat 9 data accurately identified known LCT pegmatite targets, compared to Landsat 8. The user-friendly webGIS facilitated data integration, visualization, and sharing, supporting potential users in similar exploration approaches.</jats:p

The INOVMineral Project's Contribution to Mineral Exploration-A WebGIS Integration and Visualization of Spectral and Geophysical Properties of the Aldeia LCT Pegmatite Spodumene Deposit

Due to the current energetic transition, new geological exploration technologies are needed to discover mineral deposits containing critical materials such as lithium (Li). The vast majority of European Li deposits are related to Li-Cs-Ta (LCT) pegmatites. A review of the literature indicates that conventional exploration campaigns are dominated by geochemical surveys and related exploration tools. However, other exploration techniques must be evaluated, namely, remote sensing (RS) and geophysics. This work presents the results of the INOVMINERAL4.0 project obtained through alternative approaches to traditional geochemistry that were gathered and integrated into a webGIS application. The specific objectives were to: (i) assess the potential of high-resolution elevation data; (ii) evaluate geophysical methods, particularly radiometry; (iii) establish a methodology for spectral data acquisition and build a spectral library; (iv) compare obtained spectra with Landsat 9 data for pegmatite identification; and (v) implement a user-friendly webGIS platform for data integration and visualization. Radiometric data acquisition using geophysical techniques effectively discriminated pegmatites from host rocks. The developed spectral library provides valuable insights for space-based exploration. Landsat 9 data accurately identified known LCT pegmatite targets compared with Landsat 8. The user-friendly webGIS platform facilitates data integration, visualization, and sharing, supporting potential users in similar exploration approaches

Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations

Expanding the Horizons of Manufacturing: Towards Wide Integration, Smart Systems and Tools

This research topic aims at enterprise-wide modeling and optimization (EWMO) through the development and application of integrated modeling, simulation and optimization methodologies, and computer-aided tools for reliable and sustainable improvement opportunities within the entire manufacturing network (raw materials, production plants, distribution, retailers, and customers) and its components. This integrated approach incorporates information from the local primary control and supervisory modules into the scheduling/planning formulation. That makes it possible to dynamically react to incidents that occur in the network components at the appropriate decision-making level, requiring fewer resources, emitting less waste, and allowing for better responsiveness in changing market requirements and operational variations, reducing cost, waste, energy consumption and environmental impact, and increasing the benefits. More recently, the exploitation of new technology integration, such as through semantic models in formal knowledge models, allows for the capture and utilization of domain knowledge, human knowledge, and expert knowledge toward comprehensive intelligent management. Otherwise, the development of advanced technologies and tools, such as cyber-physical systems, the Internet of Things, the Industrial Internet of Things, Artificial Intelligence, Big Data, Cloud Computing, Blockchain, etc., have captured the attention of manufacturing enterprises toward intelligent manufacturing systems

Advances in raw material industries for sustainable development goals

"""Advances in Raw Material Industries for Sustainable Development Goals"" presents the results of joint scientific research conducted in the context of the Russian-German Raw Materials Forum. Today Russia and Germany are exploring various forms of cooperation in the field of mining, geology, mineralogy, mechanical engineering and energy. Russia and Germany are equally interested in expanding cooperation and modernizing the economy in terms of sustainable development. The main theme of this article collection is connected with existing business ventures and ideas from both Russia and Germany. In this book the authors regard complex processes in mining industry from various points of view, including: - modern technologies in prospecting, exploration and development of mineral resources - progressive methods of natural and industrial mineral raw materials processing - energy technologies and digital technologies for sustainable development - cutting-edge technologies and innovations in the oil and gas industry. Working with young researchers, supporting their individual professional development and creating conditions for their mobility and scientific cooperation are essential parts of Russian-German Raw Materials Forum founded in Dresden 13 years ago. This collection represents both willingness of young researchers to be involved in large-scale international projects like Russian-German Raw Material Forum and the results of their long and thorough work in the promising areas of cooperation between Russia and Germany.

Values in Action: Simplicity, Completeness, and Carefulness in the Development of the Systematisations of Chemical Elements

This thesis demonstrates how three chemists – Dmitrii Ivanovich Mendeleev, Julius Lothar Meyer, and John Newlands – emphasised different values when developing their systematisations of the chemical elements in 1863-1875. While no chemist emphasised just one value in the course of establishing of their systematisations, I argue that Newlands elevated simplicity (“simple relation”), Mendeleev completeness (polnost’), and Meyer carefulness when systematising the elements. This thesis sets to show that values provide an illuminating framework to articulate the differences among the competing periodic systems, and give us a novel reading of the priority dispute concerning the discovery of the periodic system. By examining the role of values in the systematisation of the elements, this thesis seeks to give an example of an integrated history and philosophy of science (iHPS) approach to values. As integrating history and philosophy of science introduces some methodological challenges, I will start by arguing in favour the hermeneutic model to iHPS as articulated by Jutta Schickore (Ch.1). Chapters 2-5 are largely historical. Chapter 2 introduces historical background to the challenge of systematising the elements in the nineteenth century. I then demonstrate how Newlands (Ch.3), Meyer (Ch.4), and Mendeleev (Ch.5) emphasised different values in the course of developing their systematisations of the chemical elements. Chapters 6-8 are more philosophical. In chapter 6, I argue in favour of specific abstract characterisations of simplicity, completeness, and carefulness on the basis of the historical material presented in chapters 3-5. After arguing in favour of a specific understanding of values, I identify a distinct relationship between the chemists’ subsequent uses of the systems and their emphasis on specific values during the development of their systems. In particular, I argue that valuing of completeness contributed to Mendeleev’s use of the system for making predictions (Ch.7), whereas valuing of carefulness did much to support using Meyer’s system for error determination (Ch.8).Oskar Huttunen foundatio