AndreaBozzo/ceres-open-data-index huggingface dataset:
Unveiling the self-assembly process of gellan-chitosan complexes through a combination of atomistic simulations and experiments

Polyelectrolyte complexes (PECs), formed via the self-assembly of oppositely charged polysaccharides, are highly valued for their biocompatibility, biodegradability, and hydrophilicity, offering significant potential for biotechnological applications. However, the complex nature and lack of insight at a molecular level into polyelectrolytes conformation and aggregation often hinders the possibility of achieving an optimal control of PEC systems, limiting their practical applications. To address this problem, an in-depth investigation of PECs microscopic structural organization is required. In this work, for the first time, a hybrid approach that combines experimental techniques with atomistic molecular dynamics simulations is used to elucidate, at a molecular level, the mechanisms underlying the aggregation and structural organization of complexes formed by gellan and chitosan, i.e. PECs commonly used in food technology. This combined analysis reveals a two-step complexation process: gellan initially self-assembles into a double-helix structure, subsequently surrounded and stabilized by chitosan via electrostatic interactions. Furthermore, these results show that complexation preserves the individual conformation and intrinsic functionality of both polyelectrolytes, thereby ensuring the efficacy of the PECs in biotechnological applications.

Tags: chitosan, gellan, gels, polyelectrolyte-complexes, polysaccharides
Spectroscopic investigations of complex electronic interactions by elemental doping and material compositing of cobalt oxide for enhanced oxygen evolution reaction activity

Doping and compositing are two universal design strategies used to engineer the electronic state of a material and mitigate its disadvantages. These two strategies have been extensively applied to the design of efficient electrocatalysts for water splitting. Using cobalt oxide (CoO) as a model catalyst, we prove that the oxygen evolution reaction (OER) performance could be progressively improved, first by Fe-doping to form Fe-CoO solid solution, and further by the addition of CeO2 to produce a Fe-CoO/CeO2 composite. X-ray adsorption spectroscopy (XAS) reveals that distinct electronic interactions are induced by the processes of doping and compositing. Fe-doping of CoO can break down the structural symmetry in the pristine material, changing the electronic structure of both Co and O species at the surface and decreasing the flat-band potential (Vfb). In comparison, subsequent compositing of Fe-CoO with CeO2 induces negligible electronic changes in the as-synthesized Fe-CoO (as seen in ex-situ characterizations), but significantly modifies the oxidative transformations of both Co and Fe under OER conditions. Our spectroscopic investigations reveal that Fe-doping and CeO2 compositing play different roles in modifying the electronic properties of CoO in its pristine state and during OER catalysis, respectively, in return, providing useful guidance for the design of more efficient electrocatalysts using these two strategies.

Tags: compositing, doping, electronic-interaction, oxygen-evolution-reaction, x-ray-adsorption-spectroscopy
Atomic insights into the oxidative degradation mechanisms of sulfide solid electrolytes

This database contains phosphorus and sulfur K-edge X-ray absorption near-edge structure (XANES) of delithiated Lithium-Phosphorus-Sulfur compounds. The structures were generated by a computational delithiation procedure of β-Li3PS4 with density functional theory calculations, where we systematically enumerated distinct lithium/vacancy orderings in the super cells with the general composition Li12-xP4S16 (i.e., four Li3PS4 formula units and x from 0 to 12). The database contains a total of 2227 P K-edge and 8885 S K-edge XANES spectra of symmetrically inequivalent absorbing P and S sites. The XANES spectra were calculated using the excited electron and core hole method as implemented in The Vienna Ab initio Simulation Package (VASP) 6.2.1. Details of the structure generation procedure as well as the VASP simulations can be found in the associated manuscript (see reference below).

Tags: lithium-ion-batteries, lithium-phosphorus-sulfide, solid-electrolyte, vasp, x-ray-absorption-spectroscopy
High-throughput computation of ab initio Raman spectra for two-dimensional materials

Raman spectra play an important role in characterizing two-dimensional materials, as they provide a direct link between the atomic structure and the spectral features. In this work, we present an  automatic computational workflow for Raman spectra using all-electron density functional perturbation theory. Utilizing this workflow, we have successfully completed the Raman spectra calculation for 3504 different two-dimensional materials, with the resultant data saved in a data repository.

Tags: fhi-aims, raman-spectra, two-dimensional-material
Machine-learning accelerated identification of exfoliable two-dimensional materials

Two-dimensional (2D) materials have been a central focus of recent research because they host a variety of properties, making them attractive both for fundamental science and for applications. It is thus crucial to be able to identify accurately and efficiently if bulk three-dimensional (3D) materials are formed by layers held together by weak binding energy and, thus, can be potentially exfoliated into 2D materials. In this work, we develop a machine-learning (ML) approach that, combined with a fast preliminary geometrical screening, is able to efficiently identify potentially exfoliable materials. Starting from a combination of descriptors for crystal structures, we work out a subset of them that are crucial for accurate predictions. Our final ML model, based on a random forest classifier, has a very high recall of 98%. Using a SHapely Additive exPlanations (SHAP) analysis, we also provide an intuitive explanation of the five most important variables of the model. Finally, we compare the performance of our best ML model with a deep neural network architecture using the same descriptors.
To make our algorithms and models easily accessible, we publish an online tool on the Materials Cloud portal that only requires a bulk 3D crystal structure as input. Our tool thus provides a practical yet straightforward approach to assess whether any 3D compound can be exfoliated into 2D layers.

Tags: binding-energy, crystal-structure, exfoliation, online-tool, two-dimensional
AIRSS data for carbon at 10GPa and the C+N+H+O system at 1GPa

Ab initio random structure searching (AIRSS) has been performed for carbon at 10GPa, a pressure at which diamond is expected to be the thermodynamic ground state. A small (~10K structures) and larger (~100K structures) set are provided. To demonstrate a search in a ternary composition space ~100K AIRSS structures for the C+N+H+O system are provided. All structures are generated at random using the buildcell tool of the AIRSS suite, and relaxed to a nearby local minimum in the DFT-PBE total energy using the CASTEP code. Computational details are provided in the REM block of the .res structure files.

Tags: ab-initio-random-structure-searching, carbon, dft
Two-dimensional materials from high-throughput computational exfoliation of  experimentally known compounds

Two-dimensional (2D) materials have emerged as promising candidates for next-generation electronic and optoelectronic applications. Yet, only a few dozens of 2D materials have been successfully synthesized or exfoliated. Here, we search for novel 2D materials that can be easily exfoliated from their parent compounds. Starting from 108423 unique, experimentally known three-dimensional compounds we identify a subset of 5619 that appear layered according to robust geometric and bonding criteria. High-throughput calculations using van-der-Waals density-functional theory, validated against experimental structural data and calculated random-phase-approximation binding energies, allow to identify 1825 compounds that are either easily or potentially exfoliable. In particular, the subset of 1036 easily exfoliable cases provides novel structural prototypes and simple ternary compounds as well as a large portfolio of materials to search from for optimal properties. For a subset of 258 compounds we explore vibrational, electronic, magnetic, and topological properties, identifying 56 ferromagnetic and antiferromagnetic systems, including half-metals and half-semiconductors. This archive entry contains the database of 2D materials (structural parameters, band structures, binding energies, etc.) together with the provenance of all data and calculations as stored by AiiDA.

Tags: 2d, database, dft, electronic-bands, electronic-properties, high-throughput, magnetic-properties, marvel, monolayer, phonons, two-dimensional, vibrational-properties
Two-dimensional materials from high-throughput computational exfoliation of  experimentally known compounds (Data download)

Two-dimensional (2D) materials have emerged as promising candidates for next-generation electronic and optoelectronic applications. Yet, only a few dozens of 2D materials have been successfully synthesized or exfoliated. Here, we search for novel 2D materials that can be easily exfoliated from their parent compounds. Starting from 108423 unique, experimentally known three-dimensional compounds we identify a subset of 5619 that appear layered according to robust geometric and bonding criteria. High-throughput calculations using van-der-Waals density-functional theory, validated against experimental structural data and calculated random-phase-approximation binding energies, allow to identify 1825 compounds that are either easily or potentially exfoliable. In particular, the subset of 1036 easily exfoliable cases provides novel structural prototypes and simple ternary compounds as well as a large portfolio of materials to search from for optimal properties. For a subset of 258 compounds we explore vibrational, electronic, magnetic, and topological properties, identifying 56 ferromagnetic and antiferromagnetic systems, including half-metals and half-semiconductors. This archive entry contains the database of 2D materials (structural parameters, band structures, binding energies, etc.) together with the provenance of all data and calculations as stored by AiiDA.

Tags: 2d, database, dft, electronic-bands, electronic-properties, high-throughput, magnetic-properties, marvel, monolayer, phonons, two-dimensional, vibrational-properties
Unconventional transverse transport above and below the magnetic transition temperature in Weyl semimetal EuCd₂As₂

As exemplified by the growing interest in the quantum anomalous Hall effect, the research on topology as an organizing principle of quantum matter is greatly enriched from the interplay with magnetism. In this vein, we present a combined electrical and thermoelectrical transport study on the magnetic Weyl semimetal EuCd₂As₂. Unconventional contribution to the anomalous Hall and anomalous Nernst effects were observed both above and below the magnetic transition temperature of EuCd₂As₂, indicating the existence of significant Berry curvature. EuCd₂As₂ represents a rare case in which this unconventional transverse transport emerges both above and below the magnetic transition temperature in the same material. The transport properties evolve with temperature and field in the antiferromagnetic phase in a different manner than in the paramagnetic phase, suggesting different mechanisms to their origin. Our results indicate EuCd₂As₂ is a fertile playground for investigating the interplay between magnetism and topology, and potentially a plethora of topologically nontrivial phases rooted in this interplay. This record contains the raw data for this manuscript [Physical Review Letters 126, 076602 (2021)].

Tags: anomalous-hall-effect, anomalous-nernst-effect, experimental, magnetic-weyl-semimetal, marveldd6, topological-spin-texture
Accurate fourth-generation machine learning potentials by electrostatic embedding

In recent years, significant progress has been made in the development of machine learning potentials (MLPs) for atomistic simulations with applications in many fields from chemistry to materials science. While most current MLPs are based on environment-dependent atomic energies, the limitations of this locality approximation can be overcome, e.g., in fourth-generation MLPs, which incorporate long-range electrostatic interactions based on an equilibrated global charge distribution. Apart from the considered interactions,  the quality of MLPs crucially depends on the information available about the system, i.e., the descriptors. 
In this work we show that including — in addition to structural information — the electrostatic potential arising from the charge distribution in the atomic environments significantly improves the quality and transferability of the potentials. Moreover, the extended descriptor allows to overcome current limitations of two- and three-body based feature vectors regarding artificially degenerate atomic environments.
The capabilities of such an electrostatically embedded fourth-generation high-dimensional neural network potential (ee4G-HDNNP), which is further augmented by pairwise interactions, are demonstrated for NaCl as a benchmark system. Employing a data set containing only neutral and negatively charged NaCl clusters, even small energy differences between different cluster geometries can be resolved, and the potential shows an impressive transferability to positively charged clusters as well as the melt.

Tags: dft, electrostatics, machine-learning-potentials
Data-driven studies of magnetic two-dimensional materials

We use a data-driven approach to study the magnetic and thermodynamic properties of van der Waals (vdW) layered materials. We investigate monolayers of the form A2B2X6, based on the known material Cr2Ge2Te6, using density functional theory (DFT) calculations and determine their magnetic properties, such as magnetic order and magnetic moment. We also examine formation energies and use them as a proxy for chemical stability.

Tags: machine-learning, magnetic-materials, two-dimensional-materials
Benchmarking the GW100 dataset with the Yambo code by means of G₀W₀ approximation

In this work we provide the results for IP and EA of all the 100 molecules of the set as computed within the Yambo code. In this way, we enlarge the GW100 benchmark considering the largely used Godby-Need Plasmon Pole Approximation (GNPPA), used in Yambo to describe the frequency dependence of the screening potential and not yet included in previous GW100 studies. Fully converged results on HOMO and LUMO are provided here for each molecule of the GW100 set, as extrapolated from Yambo calculations with different value of the involved parameters (plane wave cutoff for the microscopic dielectric matrix and empty state summations).

Tags: aiida, aiida-yambo, first-principles, g0w0, godby-need-plasmon-pole-approximation, gw, gw100, high-throughput, yambo, yambo-code
Deep learning the slow modes for rare events sampling

The development of enhanced sampling methods has greatly extended the scope of atomistic simulations, allowing long-time phenomena to be studied with accessible computational resources. Many such methods rely on the identification of an appropriate set of collective variables. These are meant to describe the system's modes that most slowly approach equilibrium. Once identified, the equilibration of these modes is accelerated by the enhanced sampling method of choice. An attractive way of determining the collective variables is to relate them to the eigenfunctions and eigenvalues of the transfer operator. Unfortunately, this requires knowing the long-term dynamics of the system beforehand, which is generally not available. However, we have recently shown that it is indeed possible to determine efficient collective variables starting from biased simulations. In this paper, we bring the power of machine learning and the efficiency of the recently developed on-the-fly probability enhanced sampling method to bear on this approach. The result is a powerful and robust algorithm that, given an initial enhanced sampling simulation performed with trial collective variables or generalized ensembles, extracts transfer operator eigenfunctions using a neural network ansatz and then accelerates them to promote sampling of rare events. To illustrate the generality of this approach we apply it to several systems, ranging from the conformational transition of a small molecule to the folding of a mini-protein and the study of materials crystallization.

Tags: collective-variables, enhanced-sampling, machine-learning, molecular-dynamics, protein-folding, silicon-crystallization
Two-dimensional materials from high-throughput computational exfoliation of  experimentally known compounds

Two-dimensional (2D) materials have emerged as promising candidates for next-generation electronic and optoelectronic applications. Yet, only a few dozens of 2D materials have been successfully synthesized or exfoliated. Here, we search for novel 2D materials that can be easily exfoliated from their parent compounds. Starting from 108423 unique, experimentally known three-dimensional compounds we identify a subset of 5619 that appear layered according to robust geometric and bonding criteria. High-throughput calculations using van-der-Waals density-functional theory, validated against experimental structural data and calculated random-phase-approximation binding energies, allow to identify 1825 compounds that are either easily or potentially exfoliable. In particular, the subset of 1036 easily exfoliable cases provides novel structural prototypes and simple ternary compounds as well as a large portfolio of materials to search from for optimal properties. For a subset of 258 compounds we explore vibrational, electronic, magnetic, and topological properties, identifying 56 ferromagnetic and antiferromagnetic systems, including half-metals and half-semiconductors. This archive entry contains the database of 2D materials (structural parameters, band structures, binding energies, phonons for the subset of the 258 easily exfoliable materials with less than 6 atoms, structures and binding energies for the remaining 1567 materials) together with the provenance of all data and calculations as stored by AiiDA.

Tags: 2d, database, dft, electronic-bands, electronic-properties, high-throughput, magnetic-properties, marvel, monolayer, phonons, two-dimensional, vibrational-properties
Two-dimensional materials from high-throughput computational exfoliation of experimentally known compounds

Two-dimensional (2D) materials have emerged as promising candidates for next-generation electronic and optoelectronic applications. Yet, only a few dozens of 2D materials have been successfully synthesized or exfoliated. Here, we search for novel 2D materials that can be easily exfoliated from their parent compounds. Starting from 108423 unique, experimentally known three-dimensional compounds we identify a subset of 5619 that appear layered according to robust geometric and bonding criteria. High-throughput calculations using van-der-Waals density-functional theory, validated against experimental structural data and calculated random-phase-approximation binding energies, allow to identify 1825 compounds that are either easily or potentially exfoliable. In particular, the subset of 1036 easily exfoliable cases provides novel structural prototypes and simple ternary compounds as well as a large portfolio of materials to search from for optimal properties. For a subset of 258 compounds we explore vibrational, electronic, magnetic, and topological properties, identifying 56 ferromagnetic and antiferromagnetic systems, including half-metals and half-semiconductors. This archive entry contains the database of 2D materials (structural parameters, band structures, binding energies, phonons for the subset of the 258 easily exfoliable materials with less than 6 atoms, structures and binding energies for the remaining 1567 materials) together with the provenance of all data and calculations as stored by AiiDA.

Tags: 2d, database, dft, electronic-bands, electronic-properties, high-throughput, magnetic-properties, marvel, monolayer, phonons, two-dimensional, vibrational-properties
Expectation consistency for calibration of neural networks (code)

Despite their incredible performance, it is well reported that deep neural networks tend to be overoptimistic about their prediction confidence. Finding effective and efficient calibration methods for neural networks is therefore an important endeavour towards better uncertainty quantification in deep learning. In this manuscript, we introduce a novel calibration technique named expectation consistency (EC), consisting of a post-training rescaling of the last layer weights by enforcing that the average validation confidence coincides with the average proportion of correct labels. First, we show that the EC method achieves similar calibration performance to temperature scaling (TS) across different neural network architectures and data sets, all while requiring similar validation samples and computational resources. However, we argue that EC provides a principled method grounded on a Bayesian optimality principle known as the Nishimori identity. Next, we provide an asymptotic characterization of both TS and EC in a synthetic setting and show that their performance crucially depends on the target function. In particular, we discuss examples where EC significantly outperforms TS.
This record provides the code for the paper "Expectation consistency for calibration of neural networks".

Tags: marvelp2, neural-networks, temperature-scaling, uncertainty-quantification
Enhanced photodegradation of dimethoxybenzene isomers in/on ice compared to in aqueous solution

Photochemical reactions of contaminants in snow and ice can be important sources and sinks for various organic and inorganic compounds. Snow contaminants can be found in the bulk ice matrix, in internal liquid-like regions (LLRs), or in quasi-liquid layers (QLLs) at the air-ice interface, where they can readily exchange with the firn air. Some studies have reported that direct photochemical reactions occur faster in LLRs and QLLs than in aqueous solution, while others have found similar rates. Here, we measure the photodegradation rate constants of the three dimethoxybenzene isomers under varying experimental conditions, including in aqueous solution, in LLRs, and at the air-ice interface of nature-identical snow. Relative to aqueous solution, we find modest photodegradation enhancements (3- and 6-fold) in LLRs for two of the isomers, and larger enhancements (15- to 30-fold) at the air-ice interface for all three isomers. We use computational modeling to assess the impact of light absorbance changes on photodegradation rate enhancements at the interface. We find small (2–5 nm) bathochromic (red) absorbance shifts at the interface relative to in solution, which increases light absorption, but this factor only accounts for less than 50 % of the measured rate constant enhancements. The major factor responsible for photodegradation rate enhancements at the air-ice interface appears to be more efficient photodecay: estimated dimethoxybenzene quantum yields are 6- to 24-fold larger at the interface compared to in aqueous solution and account for the majority (51–96 %) of the observed enhancements. Using a hypothetical model compound with an assumed Gaussian-shaped absorbance peak, we find that a shift in the peak to higher or lower wavelengths can have a minor to substantial impact on photodecay rate constants, depending on the original location of the peak and the magnitude of the shift. Changes in other peak properties at the air-ice interface, such as peak width and height (i.e., molar absorptivity) can also impact rates of light absorption and direct photodecay.

Tags: absorption-spectra, dimethoxybenzene, ice