cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24435/materialscloud:9p-dp
title: Ab initio electron-phonon interactions in correlated electron systems

description: Electron-phonon (e-ph) interactions are pervasive in condensed matter, governing phenomena such as transport, superconductivity, charge-density waves, polarons, and metal-insulator transitions. First-principles approaches enable accurate calculations of e-ph interactions in a wide range of solids. However, they remain an open challenge in correlated electron systems (CES), where density functional theory often fails to describe the ground state. Therefore reliable e-ph calculations remain out of reach for many transition metal oxides, high-temperature superconductors, Mott insulators, planetary materials, and multiferroics. Here we show first-principles calculations of e-ph interactions in CES, using the framework of Hubbard-corrected density functional theory (DFT+U) and its linear response extension (DFPT+U), which can describe the electronic structure and lattice dynamics of many CES. We showcase the accuracy of this approach for a prototypical Mott system, CoO, carrying out a detailed investigation of its e-ph interactions and electron spectral functions. While standard DFPT gives unphysically divergent and short-ranged e-ph interactions, DFPT+U is shown to remove the divergences and properly account for the long-range Fröhlich interaction, allowing us to model polaron effects in a Mott insulator. Our work establishes a broadly applicable and affordable approach for quantitative studies of e-ph interactions in CES, a novel theoretical tool to interpret experiments in this broad class of materials.
DOI: 10.24435/materialscloud:je-7c
title: Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling

description: Folding of villin miniprotein was studied by parallel tempering metadynamics driven by machine learning. To obtain a training set for machine learning, we generated a large series of structures of the protein by the de novo protein structure prediction package Rosetta. A neural network was trained to approximate the Rosetta score. Parallel tempering metadynamics driven by this approximated Rosetta score successfully predicted the native structure and the free energy surface of the studied system.
These files make it possible to rerun all simulations. The directory METAD contains input files for metadynamics (no folding events observed). The directory PT-METAD contains input files for parallel tempering metadynamics. All simulations were done using Gromacs 2016.4, Anncolvar 0.8, Plumed 2.4 and OpenMPI 4.0.0.
DOI: 10.24435/materialscloud:5k-rm
title: Collective all‐carbon magnetism in triangulene dimers

description: This record contain data to support the result we published in the work "Collective All‐Carbon Magnetism in Triangulene Dimers". Triangular zigzag nanographenes, such as triangulene and its π‐extended homologues, have received widespread attention as organic nanomagnets for molecular spintronics, and may serve as building blocks for high‐spin networks with long‐range magnetic order, which are of immense fundamental and technological relevance. In the publication we present the on‐surface synthesis and a proof‐of‐principle experimental study of magnetism in covalently bonded triangulene dimers. On‐surface reactions of rationally designed precursor molecules on Au(111) lead to the selective formation of triangulene dimers in which the triangulene units are either directly connected through their minority sublattice atoms, or are separated via a 1,4‐phenylene spacer.
DOI: 10.24435/materialscloud:pa-1z
title: Collective all‐carbon magnetism in triangulene dimers

description: This record contain data to support the result we published in the work "Collective All‐Carbon Magnetism in Triangulene Dimers". Triangular zigzag nanographenes, such as triangulene and its π‐extended homologues, have received widespread attention as organic nanomagnets for molecular spintronics, and may serve as building blocks for high‐spin networks with long‐range magnetic order, which are of immense fundamental and technological relevance. In the publication we present the on‐surface synthesis and a proof‐of‐principle experimental study of magnetism in covalently bonded triangulene dimers. On‐surface reactions of rationally designed precursor molecules on Au(111) lead to the selective formation of triangulene dimers in which the triangulene units are either directly connected through their minority sublattice atoms, or are separated via a 1,4‐phenylene spacer.
DOI: 10.24435/materialscloud:j9-0n
title: Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling

description: Folding of villin miniprotein was studied by parallel tempering metadynamics driven by machine learning. To obtain a training set for machine learning, we generated a large series of structures of the protein by the de novo protein structure prediction package Rosetta. A neural network was trained to approximate the Rosetta score. Parallel tempering metadynamics driven by this approximated Rosetta score successfully predicted the native structure and the free energy surface of the studied system.
These files make it possible to rerun all simulations. The directory METAD contains input files for metadynamics (no folding events observed). The directory PT-METAD contains input files for parallel tempering metadynamics. All simulations were done using Gromacs 2016.4, Anncolvar 0.8, Plumed 2.4 and OpenMPI 4.0.0.
DOI: 10.24435/materialscloud:xv-qv
title: Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling

description: Folding of villin miniprotein was studied by parallel tempering metadynamics driven by machine learning. To obtain a training set for machine learning, we generated a large series of structures of the protein by the de novo protein structure prediction package Rosetta. A neural network was trained to approximate the Rosetta score. Parallel tempering metadynamics driven by this approximated Rosetta score successfully predicted the native structure and the free energy surface of the studied system.
These files make it possible to rerun all simulations. The directory METAD contains input files for metadynamics (no folding events observed). The directory PT-METAD contains input files for parallel tempering metadynamics. All simulations were done using Gromacs 2016.4, Anncolvar 0.8, Plumed 2.4 and OpenMPI 4.0.0.
DOI: 10.24435/materialscloud:w0-sz
title: Electron energy loss spectroscopy of bulk gold with ultrasoft pseudopotentials and the Liouville-Lanczos method

description: The implementation of ultrasoft pseudopotentials into time-dependent density-functional perturbation theory is detailed for both the Sternheimer approach and the Liouville-Lanczos (LL) method, and equations are presented in the scalar relativistic approximation for periodic solids with finite momentum transfer q. The LL method is applied to calculations of the electron energy loss (EEL) spectrum of face-centered cubic bulk Au both at vanishing and finite q. Our study reveals the richness of the physics underlying the various contributions to the density fluctuation in gold. In particular, our calculations suggest the existence in gold of two quasiseparate 5d and 6s electron gasses, each one oscillating with its own frequency at, respectively, 5.1 eV and 10.2 eV. We find that the contribution near 2.2 eV comes from 5d to 6s interband transitions modified by the intraband contribution to the real part of the dielectric function, which we call a mixed excitation.
DOI: 10.24435/materialscloud:py-h3
title: Global free-energy landscapes as a smoothly joined collection of local maps

description: This repository contains the scripts that were used to run the calculations that present a new biasing technique, the Adaptive Topography of Landscape for Accelerated Sampling (ATLAS). The techinque is implemented in plumed-2.0 and the input file are included in the repository, as well as a few scripts to postprocess the calculations and reproduce the plots presented in the paper
DOI: 10.24435/materialscloud:tn-1b
title: Electron energy loss spectroscopy of bulk gold with ultrasoft pseudopotentials and the Liouville-Lanczos method

description: The implementation of ultrasoft pseudopotentials into time-dependent density-functional perturbation theory is detailed for both the Sternheimer approach and the Liouville-Lanczos (LL) method, and equations are presented in the scalar relativistic approximation for periodic solids with finite momentum transfer q. The LL method is applied to calculations of the electron energy loss (EEL) spectrum of face-centered cubic bulk Au both at vanishing and finite q. Our study reveals the richness of the physics underlying the various contributions to the density fluctuation in gold. In particular, our calculations suggest the existence in gold of two quasiseparate 5d and 6s electron gasses, each one oscillating with its own frequency at, respectively, 5.1 eV and 10.2 eV. We find that the contribution near 2.2 eV comes from 5d to 6s interband transitions modified by the intraband contribution to the real part of the dielectric function, which we call a mixed excitation.
DOI: 10.24435/materialscloud:q1-0p
title: Global free-energy landscapes as a smoothly joined collection of local maps

description: This repository contains the scripts that were used to run the calculations that present a new biasing technique, the Adaptive Topography of Landscape for Accelerated Sampling (ATLAS). The techinque is implemented in plumed-2.0 and the input file are included in the repository, as well as a few scripts to postprocess the calculations and reproduce the plots presented in the paper
DOI: 10.24435/materialscloud:1h-bf
title: Finite-size corrections of defect energy levels involving ionic polarization

description: We develop a scheme for finite-size corrections of vertical transition energies and single-particle energy levels involving defect states with built-in ionic polarization in supercell calculations.The method accounts on an equal footing for the screening of the electrons and of the ionic polarization charge arising from the lattice distortions. We demonstrate the accuracy of our corrections for various defects in MgO and in water by comparing with the dilute limit achieved through the scaling of the system size. The general validity of our formulation is also confirmed through a sum rule that connects vertical transition energies with formation energies of structurally relaxed defects.
DOI: 10.24435/materialscloud:9p-g7
title: Finite-size corrections of defect energy levels involving ionic polarization

description: We develop a scheme for finite-size corrections of vertical transition energies and single-particle energy levels involving defect states with built-in ionic polarization in supercell calculations.The method accounts on an equal footing for the screening of the electrons and of the ionic polarization charge arising from the lattice distortions. We demonstrate the accuracy of our corrections for various defects in MgO and in water by comparing with the dilute limit achieved through the scaling of the system size. The general validity of our formulation is also confirmed through a sum rule that connects vertical transition energies with formation energies of structurally relaxed defects.
DOI: 10.24435/materialscloud:2v-4c
title: Local polarization in oxygen-deficient LaMnO3 induced by charge localization in the Jahn-Teller distorted structure

description: The functional properties of transition metal perovskite oxides are known to result from a complex interplay of magnetism, polarization, strain, and stoichiometry. Here, we show that for materials with a cooperative Jahn-Teller distortion, such as LaMnO3 (LMO), the orbital order can also couple to the defect chemistry and induce novel material properties. At low temperatures, LMO exhibits a strong Jahn-Teller distortion that splits the eg orbitals of the high-spin Mn3+ ions and leads to alternating long, short, and intermediate Mn-O bonds. Our DFT+U calculations show that, as a result of this orbital order, the charge localization in LMO upon oxygen vacancy formation differs from other manganites, like SrMnO3, where the two extra electrons reduce the two Mn sites adjacent to the vacancy. In LMO, relaxations around the defect depend on which type of Mn-O bond is broken, affecting the d-orbital energies and leading to asymmetric and hence polar excess electron localization with respect to the vacancy. Moreover, we show that the Mn-O bond lengths, the orbital order and consequently the charge localization and polarity are tunable via strain.
DOI: 10.24435/materialscloud:m0-t8
title: Reconstruction of Bloch wavefunctions of holes in a semiconductor

description: A central goal of condensed matter physics is to understand the rich and diverse electronic and optical properties that emerge as wavelike electrons move through the periodically-arranged atoms in crystalline materials. However, more than 90 years after Bloch derived the functional forms of electronic waves in crystals (now known as Bloch wavefunctions) rapid scattering processes have so far prevented their direct experimental reconstruction. In high-order sideband generation (HSG), electrons and holes generated in semiconductors by a near-infrared (NIR) laser are accelerated to high kinetic energy by a strong terahertz field, and recollide to emit NIR sidebands before they are scattered. Here we reconstruct the Bloch wavefunctions of two types of holes in gallium arsenide wavelengths much longer than the spacing between atoms by experimentally measuring sideband polarizations and introducing an elegant theory that ties those polarizations to quantum interference between different recollision pathways. These Bloch wavefunctions are compactly visualized on the surface of a sphere. Because HSG can, in principle, be observed from any direct-gap semiconductor or insulator, we expect the method introduced in this Article can be used to reconstruct low-energy Bloch wavefunctions in a large class of bulk and nanostructured crystalline materials, and thus enable important new insights into the origin and engineering of electronic and optical properties of condensed matter. This record contains the data and analysis scripts used for these experiments.
DOI: 10.24435/materialscloud:3n-e8
title: Analysis of minerals as electrode materials for Ca-based rechargeable batteries

description: Rechargeable lithium-ion batteries dominate the consumer electronics and electric vehicle markets. However, concerns on Li availability have prompted the development of alternative high energy density electrochemical energy storage systems. Rechargeable batteries based on a Ca metal anode can exhibit advantages in terms of energy density, safety and cost. The development of rechargeable Ca metal batteries requires the identification of suitable high specific energy cathode materials. This work focuses on Ca-bearing minerals because they represent stable and abundant compounds. Suitable minerals should contain a transition metal able of being reversibly reduced and oxidized, which points to several major classes of silicates and carbonates: olivine (CaFeSiO4; kirschsteinite), pyroxene (CaFe/MnSi2O6; hedenbergite and johannsenite, respectively), garnet (Ca3Fe/Cr2Si3O12; andradite and uvarovite, respectively), amphibole (Ca2Fe5Si8O22(OH)2; ferroactinolite) and double carbonates (CaMn(CO3)2; kutnahorite and CaFe(CO3)2; ankerite). This work discusses their electrode characteristics based on crystal chemistry analysis and density functional theory (DFT) calculations. The results indicate that upon Ca deintercalation, compounds such as pyroxene, garnet and double carbonate minerals could display high theoretical energy densities (ranging from 780 to 1500 Wh/kg) with moderate structural modifications. As a downside, DFT calculations indicate a hampered Ca mobility in their crystal structures. The overall analysis then disregards olivine, garnet, pyroxene, amphibole and double carbonates as structural types for future Ca-cathode materials design.
DOI: 10.24435/materialscloud:y2-7c
title: Reconstruction of Bloch wavefunctions of holes in a semiconductor

description: A central goal of condensed matter physics is to understand the rich and diverse electronic and optical properties that emerge as wavelike electrons move through the periodically-arranged atoms in crystalline materials. However, more than 90 years after Bloch derived the functional forms of electronic waves in crystals (now known as Bloch wavefunctions) rapid scattering processes have so far prevented their direct experimental reconstruction. In high-order sideband generation (HSG), electrons and holes generated in semiconductors by a near-infrared (NIR) laser are accelerated to high kinetic energy by a strong terahertz field, and recollide to emit NIR sidebands before they are scattered. Here we reconstruct the Bloch wavefunctions of two types of holes in gallium arsenide wavelengths much longer than the spacing between atoms by experimentally measuring sideband polarizations and introducing an elegant theory that ties those polarizations to quantum interference between different recollision pathways. These Bloch wavefunctions are compactly visualized on the surface of a sphere. Because HSG can, in principle, be observed from any direct-gap semiconductor or insulator, we expect the method introduced in this Article can be used to reconstruct low-energy Bloch wavefunctions in a large class of bulk and nanostructured crystalline materials, and thus enable important new insights into the origin and engineering of electronic and optical properties of condensed matter. This record contains the data and analysis scripts used for these experiments.
DOI: 10.24435/materialscloud:a1-4c
title: Analysis of minerals as electrode materials for Ca-based rechargeable batteries

description: Rechargeable lithium-ion batteries dominate the consumer electronics and electric vehicle markets. However, concerns on Li availability have prompted the development of alternative high energy density electrochemical energy storage systems. Rechargeable batteries based on a Ca metal anode can exhibit advantages in terms of energy density, safety and cost. The development of rechargeable Ca metal batteries requires the identification of suitable high specific energy cathode materials. This work focuses on Ca-bearing minerals because they represent stable and abundant compounds. Suitable minerals should contain a transition metal able of being reversibly reduced and oxidized, which points to several major classes of silicates and carbonates: olivine (CaFeSiO4; kirschsteinite), pyroxene (CaFe/MnSi2O6; hedenbergite and johannsenite, respectively), garnet (Ca3Fe/Cr2Si3O12; andradite and uvarovite, respectively), amphibole (Ca2Fe5Si8O22(OH)2; ferroactinolite) and double carbonates (CaMn(CO3)2; kutnahorite and CaFe(CO3)2; ankerite). This work discusses their electrode characteristics based on crystal chemistry analysis and density functional theory (DFT) calculations. The results indicate that upon Ca deintercalation, compounds such as pyroxene, garnet and double carbonate minerals could display high theoretical energy densities (ranging from 780 to 1500 Wh/kg) with moderate structural modifications. As a downside, DFT calculations indicate a hampered Ca mobility in their crystal structures. The overall analysis then disregards olivine, garnet, pyroxene, amphibole and double carbonates as structural types for future Ca-cathode materials design.
DOI: 10.24435/materialscloud:m9-9d
title: Local polarization in oxygen-deficient LaMnO3 induced by charge localization in the Jahn-Teller distorted structure

description: The functional properties of transition metal perovskite oxides are known to result from a complex interplay of magnetism, polarization, strain, and stoichiometry. Here, we show that for materials with a cooperative Jahn-Teller distortion, such as LaMnO3 (LMO), the orbital order can also couple to the defect chemistry and induce novel material properties. At low temperatures, LMO exhibits a strong Jahn-Teller distortion that splits the eg orbitals of the high-spin Mn3+ ions and leads to alternating long, short, and intermediate Mn-O bonds. Our DFT+U calculations show that, as a result of this orbital order, the charge localization in LMO upon oxygen vacancy formation differs from other manganites, like SrMnO3, where the two extra electrons reduce the two Mn sites adjacent to the vacancy. In LMO, relaxations around the defect depend on which type of Mn-O bond is broken, affecting the d-orbital energies and leading to asymmetric and hence polar excess electron localization with respect to the vacancy. Moreover, we show that the Mn-O bond lengths, the orbital order and consequently the charge localization and polarity are tunable via strain.
DOI: 10.24435/materialscloud:28-kh
title: Local polarization in oxygen-deficient LaMnO3 induced by charge localization in the Jahn-Teller distorted structure

description: The functional properties of transition metal perovskite oxides are known to result from a complex interplay of magnetism, polarization, strain, and stoichiometry. Here, we show that for materials with a cooperative Jahn-Teller distortion, such as LaMnO3 (LMO), the orbital order can also couple to the defect chemistry and induce novel material properties. At low temperatures, LMO exhibits a strong Jahn-Teller distortion that splits the eg orbitals of the high-spin Mn3+ ions and leads to alternating long, short, and intermediate Mn-O bonds. Our DFT+U calculations show that, as a result of this orbital order, the charge localization in LMO upon oxygen vacancy formation differs from other manganites, like SrMnO3, where the two extra electrons reduce the two Mn sites adjacent to the vacancy. In LMO, relaxations around the defect depend on which type of Mn-O bond is broken, affecting the d-orbital energies and leading to asymmetric and hence polar excess electron localization with respect to the vacancy. Moreover, we show that the Mn-O bond lengths, the orbital order and consequently the charge localization and polarity are tunable via strain.
DOI: 10.24435/materialscloud:z5-ec
title: Improved wetting model for the prediction of topography and dimensionality of superomniphobic surfaces

description: This code calculates the contact angle formed between a sessile drop of an arbitrarily defined liquid and a rough surface based on our improved Cassie-Baxter wetting model (https://doi.org/10.1088/2051-672X/ab9419). The topography of the surface needs to be predefined into the input file and may be any of the types: a) 2D pillars, b) fibers, c) sinusoids, d) 3D pillars. Although, theoretically, our model can be applied to topographies with arbitrarily large multiplicity, here the code was devised such that it considers up to three-level topographies hierarchically placed on top of one another. In the "Input" directory, three input files are given for single, two-level and three-level topographies, respectively. In multilevel topographies, the above-mentioned topography types may be combined at will. So, for example, we may have a three-level topography with sinusoidal pulses as the coarser level, fibers as the middle-level and 2D pillars as the finest level. Similarly, two-level and single-level topographies are also possible. The definitions of the multiplicity level and topography types proceed in the input file.