cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24435/materialscloud:2019.0026/v1
title: Oxygen defects in amorphous Al2O3

description: The electronic properties of the oxygen vacancy and interstitial in amorphous Al2O3 are studied via ab initio molecular dynamics simulations and hybrid functional calculations. Our results indicate that these defects do not occur in amorphous Al2O3, due to structural rearrangements which assimilate the defect structure and cause a delocalization of the associated defect levels. The imbalance of oxygen leads to a nonstoichiometric compound in which the oxygen occurs in the form of O2– ions. Intrinsic oxygen defects are found to be unable to trap excess electrons. For low Fermi energies, the formation of peroxy linkages is found to be favored leading to the capture of holes. The relative +2/0 defect levels occur at 2.5 eV from the valence band.
DOI: 10.24435/materialscloud:da-pj
title: Applicability of tail-corrections in the molecular simulations of porous materials

description: Molecular simulations with periodic boundary conditions require to define a certain cutoff distance   beyond which pairwise dispersion interactions are neglected. For the simulation of homogeneous phases it is well-established to use tail-corrections, that can remedy this truncation of the potential. These corrections are built under the assumption that beyond  the cutoff the radial distribution function is equal to one. In this work we shed some light on the discussion whether or not tail corrections should be used in the  modelling of heterogeneous systems. We show that for the adsorption of gasses in a diverse set  nanoporous crystalline materials (zeolites, Covalent Organic Frameworks (COFs), and Metal Organic Frameworks (MOFs)), tail-corrections are an appropriate choice with which the results are much less sensitive to the details of the truncation.
DOI: 10.24435/materialscloud:2020.0002/v3
title: Regioselective 3-O-Substitution of Unprotected Thiodigalactosides: Direct Route to Galectin Inhibitors

description: Regioselective derivatization of oligosaccharides is a challenging issue in carbohydrate chemistry. A commonly required series of (de)protection steps substantially lowers synthetic yields and increases time demands. We present here a regioselective one-step introduction of benzylic substituents at 3-hydroxy moieties of beta-D-galactopyranosyl-(1<->1)-thio-beta-D-galactopyranoside (TDG) employing tin butyl oxide in fair isolated yields. These glycomimetics act as inhibitors of galectins - human lectins, which are biomedically attractive targets for therapeutic inhibition. The affinity of prepared glycomimetics to recombinant galectin-1 and galectin-3 was studied in ELISA-type assay and their inhibitory potential was also demonstrated on the surface of a model HEK293 cell line. The results of biological experiments were correlated with data from molecular modelling with both galectins. The present work reveals a facile and elegant synthetic route for the preparation of glycomimetics that exhibit differing selectivity and affinity to various galectins depending on the choice of 3-O-substitution.
In order to rationalize structure-activity relationships of tested ligands we carried out a series of molecular dynamics simulations and quantum chemical calculations. We present input and output files for quantum chemical geometry optimizations and calculations of interactions energies. These calculations were carried out in Gaussian 09 package. These results can be visualized using Molden, Molekel or other programs.
Molecular dynamics simulations were carried out using Gromacs 5.1.3 package. Initial structures of production simulations and trajectories (without water) are presented. The results can be visualized by VMD or other structure visualization packages with a support for trajectory input.
DOI: 10.24435/materialscloud:q9-7b
title: Oxygen defects in amorphous Al2O3

description: The electronic properties of the oxygen vacancy and interstitial in amorphous Al2O3 are studied via ab initio molecular dynamics simulations and hybrid functional calculations. Our results indicate that these defects do not occur in amorphous Al2O3, due to structural rearrangements which assimilate the defect structure and cause a delocalization of the associated defect levels. The imbalance of oxygen leads to a nonstoichiometric compound in which the oxygen occurs in the form of O2– ions. Intrinsic oxygen defects are found to be unable to trap excess electrons. For low Fermi energies, the formation of peroxy linkages is found to be favored leading to the capture of holes. The relative +2/0 defect levels occur at 2.5 eV from the valence band.
DOI: 10.24435/materialscloud:2019.0030/v1
title: MD trajectories of bulk water and of the water-vacuum interface

description: This entry provides MD trajectories for bulk water and the water-vacuum interface generated with ab initio molecular dynamics using rVV10 density functional at the temperature of 350 K. In the rVV10 functional, the parameter b is set to 9.3.
DOI: 10.24435/materialscloud:2b-zv
title: Regioselective 3-O-Substitution of Unprotected Thiodigalactosides: Direct Route to Galectin Inhibitors

description: Regioselective derivatization of oligosaccharides is a challenging issue in carbohydrate chemistry. A commonly required series of (de)protection steps substantially lowers synthetic yields and increases time demands. We present here a regioselective one-step introduction of benzylic substituents at 3-hydroxy moieties of beta-D-galactopyranosyl-(1<->1)-thio-beta-D-galactopyranoside (TDG) employing tin butyl oxide in fair isolated yields. These glycomimetics act as inhibitors of galectins - human lectins, which are biomedically attractive targets for therapeutic inhibition. The affinity of prepared glycomimetics to recombinant galectin-1 and galectin-3 was studied in ELISA-type assay and their inhibitory potential was also demonstrated on the surface of a model HEK293 cell line. The results of biological experiments were correlated with data from molecular modelling with both galectins. The present work reveals a facile and elegant synthetic route for the preparation of glycomimetics that exhibit differing selectivity and affinity to various galectins depending on the choice of 3-O-substitution.
In order to rationalize structure-activity relationships of tested ligands we carried out a series of molecular dynamics simulations and quantum chemical calculations. We present input and output files for quantum chemical geometry optimizations and calculations of interactions energies. These calculations were carried out in Gaussian 09 package. These results can be visualized using Molden, Molekel or other programs.
Molecular dynamics simulations were carried out using Gromacs 5.1.3 package. Initial structures of production simulations and trajectories (without water) are presented. The results can be visualized by VMD or other structure visualization packages with a support for trajectory input.
DOI: 10.24435/materialscloud:d4-gb
title: MD trajectories of bulk water and of the water-vacuum interface

description: This entry provides MD trajectories for bulk water and the water-vacuum interface generated with ab initio molecular dynamics using rVV10 density functional at the temperature of 350 K. In the rVV10 functional, the parameter b is set to 9.3.
DOI: 10.24435/materialscloud:2020.0027/v1
title: AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance

description: The ever-growing availability of computing power and sustained development of advanced computational methods have contributed much to recent scientific progress.
These developments present new challenges driven by the sheer amount of calculations and data to manage. Next-generation exascale supercomputers will harden these challenges, such that automated and scalable solutions become crucial. In recent years, we have been developing AiiDA (http://www.aiida.net), a robust open-source high-throughput infrastructure addressing the challenges arising from the needs of automated workflow management and data provenance recording. Here, we introduce developments and capabilities required to reach sustained performance, with AiiDA supporting throughputs of tens of thousands processes/hour, while automatically preserving and storing the full data provenance in a relational database making it queryable and traversable, thus enabling high-performance data analytics. AiiDA's workflow language provides advanced automation, error handling features and a flexible plugin model to allow interfacing with any simulation software. The associated plugin registry enables seamless sharing of extensions, empowering a vibrant user community dedicated to making simulations more robust, user-friendly and reproducible.

This archive record contains the data to reproduce the figures on engine performance in the section "Event versus polling-based engine" of the paper entitled "AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance". It also includes instructions to reproduce the actual data from scratch using AiiDA v1.1.1 and AiiDA v0.12.5.
DOI: 10.24435/materialscloud:st-ht
title: AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance

description: The ever-growing availability of computing power and sustained development of advanced computational methods have contributed much to recent scientific progress.
These developments present new challenges driven by the sheer amount of calculations and data to manage. Next-generation exascale supercomputers will harden these challenges, such that automated and scalable solutions become crucial. In recent years, we have been developing AiiDA (http://www.aiida.net), a robust open-source high-throughput infrastructure addressing the challenges arising from the needs of automated workflow management and data provenance recording. Here, we introduce developments and capabilities required to reach sustained performance, with AiiDA supporting throughputs of tens of thousands processes/hour, while automatically preserving and storing the full data provenance in a relational database making it queryable and traversable, thus enabling high-performance data analytics. AiiDA's workflow language provides advanced automation, error handling features and a flexible plugin model to allow interfacing with any simulation software. The associated plugin registry enables seamless sharing of extensions, empowering a vibrant user community dedicated to making simulations more robust, user-friendly and reproducible.

This archive record contains the data to reproduce the figures on engine performance in the section "Event versus polling-based engine" of the paper entitled "AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance". It also includes instructions to reproduce the actual data from scratch using AiiDA v1.1.1 and AiiDA v0.12.5.
DOI: 10.24435/materialscloud:2020.0017/v1
title: On-the-Fly Active Learning of Interpretable Bayesian Force Fields for Atomistic Rare Events

description: Machine learned force fields typically require manual construction of training sets consisting of thousands of first principles calculations, which can result in low training efficiency and unpredictable errors when applied to structures not represented in the training set of the model. This severely limits the practical application of these models in systems with dynamics governed by important rare events, such as chemical reactions and diffusion. We present an adaptive Bayesian inference method for automating the training of interpretable, low-dimensional, and multi-element interatomic force fields using structures drawn on the fly from molecular dynamics simulations. Within an active learning framework, the internal uncertainty of a Gaussian process regression model is used to decide whether to accept the model prediction or to perform a first principles calculation to augment the training set of the model. The method is applied to a range of single- and multi-element systems and shown to achieve a favorable balance of accuracy and computational efficiency, while requiring a minimal amount of ab initio training data. We provide a fully open-source implementation of our method, as well as a procedure to map trained models to computationally efficient tabulated force fields.
DOI: 10.24435/materialscloud:a1-ra
title: On-the-Fly Active Learning of Interpretable Bayesian Force Fields for Atomistic Rare Events

description: Machine learned force fields typically require manual construction of training sets consisting of thousands of first principles calculations, which can result in low training efficiency and unpredictable errors when applied to structures not represented in the training set of the model. This severely limits the practical application of these models in systems with dynamics governed by important rare events, such as chemical reactions and diffusion. We present an adaptive Bayesian inference method for automating the training of interpretable, low-dimensional, and multi-element interatomic force fields using structures drawn on the fly from molecular dynamics simulations. Within an active learning framework, the internal uncertainty of a Gaussian process regression model is used to decide whether to accept the model prediction or to perform a first principles calculation to augment the training set of the model. The method is applied to a range of single- and multi-element systems and shown to achieve a favorable balance of accuracy and computational efficiency, while requiring a minimal amount of ab initio training data. We provide a fully open-source implementation of our method, as well as a procedure to map trained models to computationally efficient tabulated force fields.
DOI: 10.24435/materialscloud:2019.0027/v1
title: Extrinsic Defects in Amorphous Oxides: Hydrogen, Carbon, and Nitrogen Impurities in Alumina

description: This entry provides the most stable defect configurations of hydrogen, carbon, and nitrogen impurities in alumina, which are identified through ab initio molecular dynamics in various charge states and structural relaxations with the PBE functional. The structural configurations related to carbon and nitrogen impurities are found to depend on the total charge set in the simulation cell.
DOI: 10.24435/materialscloud:g4-jw
title: All-polymer organic solar cells with nano-to-micron hierarchical morphology and large light receiving angle

description: Distributed photovoltaics in living environment harvest the sunlight in different incident angles throughout the day. The development of planer solar cells with large light-receiving angle can reduce the requirements in installation form factor and is therefore urgently required. Here, thin film organic photovoltaics with nano-sized phase separation integrated in micro-sized surface topology is demonstrated as an ideal solution to proposed applications. All-polymer solar cells, by means of a newly developed sequential processing, show large magnitude hierarchical morphology with facilitated exciton-to-carrier conversion. The nano fibrilar donor-acceptor network and micron-scale optical field trapping structure in combination contributes to an efficiency of 19.06% (certified 18.59%), which is the highest value to date for all-polymer solar cells. Furthermore, the micron-sized surface topology also contributes to a large light-receiving angle. A 30% improvement of power gain is achieved for the hierarchical morphology comparing to the flat-morphology devices. These inspiring results show that all-polymer solar cell with hierarchical features are particularly suitable for the commercial applications of distributed photovoltaics due to its low installation requirement.
DOI: 10.24435/materialscloud:nz-9r
title: Extrinsic Defects in Amorphous Oxides: Hydrogen, Carbon, and Nitrogen Impurities in Alumina

description: This entry provides the most stable defect configurations of hydrogen, carbon, and nitrogen impurities in alumina, which are identified through ab initio molecular dynamics in various charge states and structural relaxations with the PBE functional. The structural configurations related to carbon and nitrogen impurities are found to depend on the total charge set in the simulation cell.
DOI: 10.24435/materialscloud:g4-f5
title: All-polymer organic solar cells with nano-to-micron hierarchical morphology and large light receiving angle

description: Distributed photovoltaics in living environment harvest the sunlight in different incident angles throughout the day. The development of planer solar cells with large light-receiving angle can reduce the requirements in installation form factor and is therefore urgently required. Here, thin film organic photovoltaics with nano-sized phase separation integrated in micro-sized surface topology is demonstrated as an ideal solution to proposed applications. All-polymer solar cells, by means of a newly developed sequential processing, show large magnitude hierarchical morphology with facilitated exciton-to-carrier conversion. The nano fibrilar donor-acceptor network and micron-scale optical field trapping structure in combination contributes to an efficiency of 19.06% (certified 18.59%), which is the highest value to date for all-polymer solar cells. Furthermore, the micron-sized surface topology also contributes to a large light-receiving angle. A 30% improvement of power gain is achieved for the hierarchical morphology comparing to the flat-morphology devices. These inspiring results show that all-polymer solar cell with hierarchical features are particularly suitable for the commercial applications of distributed photovoltaics due to its low installation requirement.
DOI: 10.24435/materialscloud:yp-51
title: Property map collective variable as a useful tool for force field correction

description: Molecular mechanics potentials for small molecules suffer inaccuracies. To apply corrections we used a concept called property map to calculate corrections. It was calculated as a sum of [correction_i exp(-lambda D(x, x_i))] divided by the sum of [exp(-lambda D(x, x_i))], where correction_i is the difference between the accurate and inaccurate potential for i-th landmark structure x_i, lambda is a chosen prefactor, D is a distance (e.g. RMSD or MSD) and x are atomic coordinates. The concept was tested on alanine dipeptide (all combinations of 7 force fields, one used as a model of accurate and one as inaccurate). Next it was applied on an anticancer drug Imatinib (General AMBER Force Field corrected to DFT).
Simulations were carried out in Gromacs 2016.4. Correction was Implemented using Plumed 2.4. DFT energies were calculated by ORCA 4.0 at the BP86/def2-TZVP level of theory.
DOI: 10.24435/materialscloud:nq-ht
title: The JuDiT database of impurities embedded into a topological insulator

description: We present JuDiT (Jülich Database of impurities embedded into a Topological insulator) which collects first principles calculation of impurities embedded into the prototypical topological insulator Sb2Te3. The density functional calculations of this work were performed with the JuKKR package [1], which allows to embed translational invariance breaking impurities into a crystalline host system based on the Korringa-Kohn-Rostoker Green function method, and were performed with the AiiDA-KKR package [2]. Our database collects, among others, predicted impurity properties like charge doping introduced by the defects, magnetic moments of the impurities and impurity density of states calculations. We include calculations for the intrinsic Fermi level in the middle of the bulk band gap as well as for shifted Fermi level into valence and conduction band which models different experimental conditions. The impurities were embedded into different layers throughout a 6 quintuple layer thick film which allows to investigate the effect of the topological surface state (localized at the surface) on impurity properties. The JuDiT database allows to uncover chemical trends in impurity properties and can help optimizing the next generation of topological materials.

[1] https://jukkr.fz-juelich.de and www.judft.de
[2] https://github.com/JuDFTteam/aiida-kkr
DOI: 10.24435/materialscloud:2020.0041/v1
title: Hund excitations and the efficiency of Mott solar cells

description: We study the dynamics of photoinduced charge carriers in semirealistic models of LaVO3 and YTiO3 polar heterostructures. It is shown that two types of impact ionization processes contribute to the carrier multiplication in these strongly correlated multiorbital systems: The first mechanism involves local spin state transitions, while the second mechanism involves the scattering of high-kinetic-energy carriers. Both processes act on the 10-fs timescale and play an important role in the harvesting of high-energy photons in solar cell applications. As a consequence, the optimal gap size for Mott solar cells is substantially smaller than for semiconductor devices.
DOI: 10.24435/materialscloud:3m-72
title: Hund excitations and the efficiency of Mott solar cells

description: We study the dynamics of photoinduced charge carriers in semirealistic models of LaVO3 and YTiO3 polar heterostructures. It is shown that two types of impact ionization processes contribute to the carrier multiplication in these strongly correlated multiorbital systems: The first mechanism involves local spin state transitions, while the second mechanism involves the scattering of high-kinetic-energy carriers. Both processes act on the 10-fs timescale and play an important role in the harvesting of high-energy photons in solar cell applications. As a consequence, the optimal gap size for Mott solar cells is substantially smaller than for semiconductor devices.
DOI: 10.24435/materialscloud:vb-mk
title: Non-Abelian reciprocal braiding of Weyl points and its manifestation in ZrTe

description: Weyl semimetals in three-dimensional crystals provide the paradigm example of topologically protected band nodes. It is usually taken for granted that a pair of colliding Weyl points annihilate whenever they carry opposite chiral charges. In stark contrast, here we report that Weyl points in systems symmetric under the composition of time-reversal with a π-rotation are characterized by a non-Abelian topological invariant. The topological charges of the Weyl points are transformed via braid phase factors which arise upon exchange inside symmetric planes of the reciprocal momentum space. We elucidate this process with an elementary two-dimensional tight-binding model implementable in cold-atoms setups and in photonic systems. In three dimensions, interplay of the non-Abelian topology with point-group symmetry is shown to enable topological phase transitions in which pairs of Weyl points may scatter or convert into nodal-line rings. By combining our theoretical arguments with first-principles calculations, we predict that Weyl points occurring near the Fermi level of zirconium telluride (ZrTe) carry non-trivial values of the non-Abelian charge, and that uniaxial compression strain drives a non-trivial conversion of the Weyl points into nodal lines.