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Efficient and low-scaling linear-response time-dependent density functional theory implementation for core-level spectroscopy of large and periodic systems


Augustin Bussy, Jürg Hutter

  • A new implementation of linear-response time-dependent density functional theory (LR-TDDFT) for core level near-edge absorption spectroscopy is discussed. The method is based on established LR-TDDFT approaches to X-ray absorption spectroscopy (XAS) with additional accurate approximations for increased efficiency. We validate our implementation by reproducing benchmark results at the K-edge and showing that spin–orbit coupling effects at the L2,3-edge are well described. We also demonstrate that the method is suitable for extended systems in periodic boundary conditions and measure a favorable sub-cubic scaling of the calculation cost with system size. We finally show that GPUs can be efficiently exploited and report speedups of up to a factor 2.

Latest version: v1
Publication date: Jul 29, 2021

Hidden bulk and surface effects in the spin polarization of the nodal-line semimetal ZrSiTe


G. Gatti, D. Gosálbez-Martínez, S. Roth, M. Fanciulli, M. Zacchigna, M. Kalläne, K. Rossnagel, C. Jozwiak, A. Bostwick, E. Rotenberg, A. Magrez, H. Berger, I. Vobornik, J. Fujii, O. V. Yazyev, M. Grioni, A. Crepaldi

  • In the present record we provide the data obtained in ARPES experiments and input/output files of Quantum ESPRESSO calculations used in the publication entitled as this record. The experimental data consist of the Fermi surface at kz=π/c, the experimental band dispersion along the MΓM, XΓX and XMX, spin-resolved ARPES spectra, and spin-resolved ARPES spectra of surface states. The theoretical data consist in the bulk and slab calculations to support the experimental data.

Latest version: v1
Publication date: Jul 29, 2021

Radial spin texture of the Weyl fermions in chiral tellurium


Gianmarco Gatti, Daniel Gosálbez-Martínez, Stepan S. Tsirkin, Mauro Fanciulli, Michele Puppin, Serhii Polishchuk, Simon Moser, Luc Testa, Edoardo Martino, Silvan Roth, Philippe Bugnon, Luca Moreschini, Aaron Bostwick, Chris Jozwiak, Eli Rotenberg, Giovanni Di Santo, Luca Petaccia, Ivana Vobornik, Jun Fujii, Joeson Wong, Deep Jariwala, Harry Atwater, Heinrik Rønnow, Majed Chergui, Oleg Yazyev, Marco Grioni, Alberto Crepaldi

  • Trigonal tellurium, a small-gap semiconductor with pronounced magneto-electric and magneto-optical responses, is among the simplest realizations of a chiral crystal. We have studied by spin- and angle-resolved photoelectron spectroscopy its unconventional electronic structure and unique spin texture. We identify Kramers–Weyl, composite, and accordionlike Weyl fermions, so far only predicted by theory, and show that the spin polarization is parallel to the wave vector along the lines in k space connecting high-symmetry points. Our results clarify the symmetries that enforce such spin texture in a chiral crystal, thus bringing new insight in the formation of a spin vectorial field more complex than the previously proposed hedgehog configuration. Our findings thus pave the way to a classification scheme for these exotic spin textures and their search in chiral crystals. This records refers to the experimental data shown in the referenced article, saved as txt files along with a metadata descriptor file.

Latest version: v1
Publication date: Jul 28, 2021

Light-induced renormalization of the Dirac quasiparticles in the nodal-line semimetal ZrSiSe


Gianmarco Gatti, Alberto Crepaldi, Michele Puppin, Nicolas Tancogne-Dejean, Lede Xian, Umberto De Giovannini, Silvan Roth, Serhii Polishchuk, Philippe Bugnon, Arnaud Magrez, Helmuth Berger, Fabio Frassetto, Luca Poletto, Luca Moreschini, Simon Moser, Aaron Bostwick, Eli Rotenberg, Angel Rubio, Majed Chergui, Marco Grioni

  • In nodal-line semimetals, linearly dispersing states form Dirac loops in the reciprocal space with a high degree of electron-hole symmetry and a reduced density of states near the Fermi level. The result is reduced electronic screening and enhanced correlations between Dirac quasiparticles. Here we investigate the electronic structure of ZrSiSe, by combining time- and angle-resolved photoelectron spectroscopy with ab initio density functional theory (DFT) complemented by an extended Hubbard model (DFT+U+V) and by time-dependent DFT+U+V. We show that electronic correlations are reduced on an ultrashort timescale by optical excitation of high-energy electrons-hole pairs, which transiently screen the Coulomb interaction. Our findings demonstrate an all-optical method for engineering the band structure of a quantum material. This record contains the ARPES raw data in txt format used to create the figures in the referenced publication.

Latest version: v1
Publication date: Jul 28, 2021

Computational synthesis of substrates by crystal cleavage


Joshua Paul, Alice Galdi, Christopher Parzyck, Kyle Shen, Jared Maxson, Richard Hennig

  • In order to identify novel substrate materials, we developed a high-throughput bond breaking algorithm. This algorithm takes a three-dimensional crystal as input, systematically breaks bonds, and checks if the bonding network has been reduced to two periodic directions. We apply this algorithm to Materials Project database and identify 4,693 symmetrically unique cleaved surfaces across 2,133 crystals. We then characterize the thermodynamic stability of these cleaved surfaces using the DFT software VASP, characterizing 3,991 surfaces as potential substrates with energy comparable to the experimentally used substrates (0001) AlN, ZnO, and CdS. This repository contains the structure files, setting files, pseudopotential choices, bulk precursor structure and MaterialsProject ID, and thermodynamic data for the substrates considered in this work.

Latest version: v1
Publication date: Jul 28, 2021

First principles correction scheme for linear-response time-dependent density functional theory calculations of core electronic states


Augustin Bussy, Jürg Hutter

  • Linear-response time-dependent density functional theory (LR-TDDFT) for core level spectroscopy using standard local functionals suffers from self-interaction error and a lack of orbital relaxation upon creation of the core hole. As a result, LR-TDDFT calculated X-ray absorption near edge structure (XANES) spectra need to be shifted along the energy axis to match experimental data. We propose a correction scheme based on many body perturbation theory to calculate the shift from first principles. The ionization potential of the core donor state is first computed and then substituted for the corresponding Kohn--Sham orbital energy, thus emulating Koopmans' condition. Both self-interaction error and orbital relaxation are taken into account. The method exploits the localized nature of core states for efficiency and integrates seamlessly in our previous implementation of core level LR-TDDFT, yielding corrected spectra in a single calculation. We benchmark the correction scheme on ...

Latest version: v2
Publication date: Jul 28, 2021

Anti-symmetric Compton scattering in LiNiPO4: Towards a direct probe of the magneto-electric multipole moment


Sayantika Bhowal, Daniel O'Neill, Michael Fechner, Nicola A. Spaldin, Urs Staub, Jon Duffy, Stephen P. Collins

  • We present a combined theoretical and experimental investigation of the anti-symmetric Compton profile in LiNiPO4 as a possible probe for magneto-electric toroidal moments. Understanding as well as detecting such magneto-electric multipoles is an active area of research in condensed matter physics. Our calculations, based on density functional theory, indicate an anti-symmetric Compton profile in the direction of the ty toroidal moment in momentum space, with the computed anti-symmetric profile around four orders of magnitude smaller than the total profile. The difference signal that we measure is consistent with the computed profile, but of the same order of magnitude as the statistical errors and systematic uncertainties of the experiment. Our results motivate further theoretical work to understand the factors that influence the size of the anti-symmetric Compton profile, and to identify materials exhibiting larger effects.

Latest version: v1
Publication date: Jul 23, 2021

The importance of nuclear quantum effects for NMR crystallography


Edgar A. Engel, Venkat Kapil, Michele Ceriotti

  • The resolving power of solid-state nuclear magnetic resonance (NMR) crystallography depends heavily on the accuracy of the computational prediction of NMR chemical shieldings of candidate structures, which are usually taken to be local minima in the potential energy surface. To test the limits of this approximation, we perform a systematic study of the role of finite-temperature and quantum nuclear fluctuations on 1H, 13C, and 15N chemical shieldings in molecular crystals -- considering the paradigmatic examples of the different polymorphs of benzene, glycine, and succinic acid. We find the effect of quantum fluctuations to be comparable in size to the typical errors of predictions of chemical shieldings for static nuclei with respect to experimental measurements, and to improve the match between experiments and theoretical predictions, translating to more reliable assignment of the NMR spectra to the correct candidate structure. Thanks to the use of integrated machine-learning ...

Latest version: v1
Publication date: Jul 23, 2021

Revealing hidden magneto-electric multipoles using Compton scattering


Sayantika Bhowal, Nicola A. Spaldin

  • Magneto-electric multipoles, which are odd under both space-inversion 𝓘 and time-reversal 𝓣 symmetries, are fundamental in understanding and characterizing magneto-electric materials. However, the detection of these magneto-electric multipoles is often not straightforward as they remain "hidden" in conventional experiments in part since many magneto-electrics exhibit combined 𝓘𝓣 symmetry. In the present work, we show that the anti-symmetric Compton profile is a unique signature for all the magneto-electric multipoles, since the asymmetric magnetization density of the magneto-electric multipoles couples to space via spin-orbit coupling, resulting in an anti-symmetric Compton profile. We develop the key physics of the anti-symmetric Compton scattering using symmetry analysis and demonstrate it using explicit first-principles calculations for two well-known representative materials with magneto-electric multipoles, insulating LiNiPO₄ and metallic Mn₂Au. Our work emphasizes the ...

Latest version: v1
Publication date: Jul 23, 2021

In situ inorganic conductive network enables superior high-voltage operation of single-crystal Ni-rich cathode


Xinming Fan, Xing Ou, Wengao Zhao, Yun Liu, Bao Zhang, Jiafeng Zhang, Lianfeng Zou, Lukas Seidl, Yangzhong Li, Guorong Hu, Corsin Battaglia, Yong Yang

  • High nickel content in LiNixCoyMnzO2 (NCM, x ≥ 0.8, x + y + z = 1) layered cathode material allows high energy density in lithium-ion batteries (LIBs). However, Ni-rich NCM cathodes suffer from performance degradation, mechanical and structural instability upon prolonged cell cycling. Although the use of single-crystal Ni-rich NCM can mitigate these drawbacks, the ion-diffusion in large single-crystal particles hamper its rate capability. Herein, we report a strategy to construct an in situ Li1.4Y0.4Ti1.6(PO4)3 (LYTP) ion/electron conductive network which interconnects single-crystal LiNi0.88Co0.09Mn0.03O2 (SC-NCM88) particles. The LYTP network facilitates the lithium-ion transport between SC-NCM88 particles, mitigates mechanical instability and prevents detrimental crystalline phase transformation. When used in combination with a Li metal anode, the LYTP-containing SC-NCM88-based cathode enables a coin cell capacity of 130 mAh g-1 after 500 cycles at 5 C rate in the 2.75-4.4 V ...

Latest version: v1
Publication date: Jul 21, 2021

Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks


Daniel Schwalbe-Koda, Aik Rui Tan, Rafael Gómez-Bombarelli

  • Neural network (NN) force fields can predict potential energy surfaces with high accuracy and speed compared to electronic structure methods typically used to generate their training data. However, NN predictions are well-defined only for points close to the training domains, and may exhibit poor results during extrapolation. Uncertainty quantification methods can detect geometries for which predicted errors are high, but sampling regions of high uncertainty requires a thorough exploration of the phase space, often using expensive simulations. Our work uses automatic differentiation to sample atomistic configurations by balancing thermodynamic accessibility and uncertainty quantification without using molecular dynamics simulations. This dataset provides the atomistic data used to train the NN potentials for the ammonia, alanine dipeptide, and zeolite-molecule systems. For all materials, geometries, energies, and forces are provided. The ammonia and zeolite systems were computed ...

Latest version: v1
Publication date: Jul 20, 2021

Electronic structure of water from Koopmans-compliant functionals


James Moraes de Almeida, Ngoc Linh Nguyen, Nicola Colonna, Wei Chen, Caetano Rodrigues Miranda, Alfredo Pasquarello, Nicola Marzari

  • Obtaining a precise theoretical description of the spectral properties of liquid water poses challenges for both molecular dynamics (MD) and electronic structure methods. The lower computational cost of the Koopmans-compliant functionals with respect to Green’s function methods allows the simulations of many MD trajectories, with a description close to the state-of-art quasi-particle self-consistent GW plus vertex corrections method (QSGW + fxc). Thus, we explore water spectral properties when different MD approaches are used, ranging from classical MD to first-principles MD, and including nuclear quantum effects. We have observed that different MD approaches lead to up to 1 eV change in the average band gap; thus, we focused on the band gap dependence with the geometrical properties of a system to explain such spread. We have evaluated the changes in the band gap due to variations in the intramolecular O–H bond distance and HOH angle, as well as the intermolecular hydrogen bond ...

Latest version: v2
Publication date: Jul 20, 2021

Reconstruction of Bloch wavefunctions of holes in a semiconductor


J. B. Costello, S. D. O'Hara, Q. Wu, D. C. Valovcin, L. N. Pfeiffer, K. W. West, M. S. Sherwin

  • 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 ...

Latest version: v1
Publication date: Jul 20, 2021

Invariance principles in the theory and computation of transport coefficients


Federico Grasselli, Stefano Baroni

  • In this work we elaborate on recently discovered invariance principles, according to which transport coefficients are, to a large extent, independent of the microscopic definition of the densities and currents of the conserved quantities being transported (energy, momentum, mass, charge). These invariance principles can be combined with new spectral analysis methods for the current time series to be fed into the Green-Kubo formula to obtain accurate estimates of transport coefficients from relatively short molecular dynamics simulations. In this record we collect the time series of the ab initio charge flux for a simulation of molten potassium chloride, together with the Jupyter Notebooks we employed to analyse the data and produce the figures in the related article.

Latest version: v1
Publication date: Jul 19, 2021

Coherent energy exchange between carriers and phonons in Peierls-distorted bismuth unveiled by broadband XUV pulses


Romain Géneaux, Iurii Timrov, Christopher Kaplan, Andrew Ross, Peter Kraus, Stephen Leone

  • In Peierls-distorted materials, photoexcitation leads to a strongly coupled transient response between structural and electronic degrees of freedom, always measured independently of each other. Here we use transient reflectivity in the extreme ultraviolet to quantify both responses in photoexcited bismuth in a single measurement. With the help of first-principles calculations based on density-functional theory (DFT) and time-dependent DFT, the real-space atomic motion and the temperature of both electrons and holes as a function of time are captured simultaneously, retrieving an anticorrelation between the A1g phonon dynamics and carrier temperature. The results reveal a coherent, bi-directional energy exchange between carriers and phonons, which is a dynamical counterpart of the static Peierls-Jones distortion, providing first-time validation of previous theoretical predictions.

Latest version: v1
Publication date: Jul 16, 2021

Effects of interlayer confinement and hydration on capacitive charge storage in birnessite


Shelby Boyd, Karthik Ganeshan, Wan-Yu Tsai, Tao Wu, Saeed Saeed, De-en Jiang, Nina Balke, Adri van Duin, Veronica Augustyn

  • Nanostructured birnessite (δ-MnO2) exhibits high specific capacitance and nearly ideal capacitive behavior in aqueous electrolytes, rendering it an important electrode material for low-cost, high power energy storage devices. The mechanism of electrochemical capacitance in birnessite has been described as both faradaic (involving redox) and non-faradaic (involving only electrostatic interactions). To clarify the capacitive mechanism, we characterized birnessite’s response to applied potential using ex situ X-ray diffraction, electrochemical quartz crystal microbalance, in situ Raman spectroscopy, and operando atomic force microscopy dilatometry to provide a holistic understanding of its structural, gravimetric, and mechanical response. These observations are supported by atomic-scale simulations using density functional theory for the cation-intercalated structure of birnessite and ReaxFF-based molecular dynamics, as well as ReaxFF-based grand canonical Monte Carlo simulations on ...

Latest version: v1
Publication date: Jul 16, 2021

Importance of intersite Hubbard interactions in β-MnO2: A first-principles DFT+U+V study


Ruchika Mahajan, Iurii Timrov, Nicola Marzari, Arti Kashyap

  • We present a first-principles investigation of the structural, electronic, and magnetic properties of pyrolusite (β-MnO2) using conventional and extended Hubbard-corrected density-functional theory (DFT+U and DFT+U+V). The onsite U and intersite V Hubbard parameters are computed using linear-response theory in the framework of density-functional perturbation theory. We show that while the inclusion of the onsite U is crucial to describe the localized nature of the Mn(3d) states, the intersite V is key to capture accurately the strong hybridization between neighboring Mn(3d) and O(2p) states. In this framework, we stabilize the simplified collinear antiferromagnetic (AFM) ordering (suggested by the Goodenough-Kanamori rule) that is commonly used as an approximation to the experimentally-observed noncollinear screw-type spiral magnetic ordering. A detailed investigation of the ferromagnetic and of other three collinear AFM spin configurations is also presented. The findings from ...

Latest version: v1
Publication date: Jul 16, 2021

Structure and energetics of dye-sensitized NiO interfaces in water from ab-initio MD and large-scale GW calculations


Alekos Segalina, Sébastien Lèbegue, Dario Rocca, Simone Piccinin, Mariachiara Pastore

  • The energy level alignment across solvated molecule/semiconductor interfaces is a crucial property for the correct functioning of dye-sensitized photo-electrodes, where, following the absorption of solar light, a cascade of interfacial hole/electron transfer processes has to efficiently take place. In light of the difficulty of performing X-ray photoelectron spectroscopy measurements at the molecule/solvent/metal-oxide interface, being able to accurately predict the level alignment by first-principles calculations on realistic structural models would represent an important step toward the optimization of the device. In this respect dye/NiO surfaces, employed in p-type dye-sensitized solar cells, are undoubtedly challenging for ab initio methods and, also for this reason, much less investigated than the n-type dye/TiO2 counterpart. Here we consider the C343-sensitized NiO surface in water and combine ab initio Molecular Dynamics (AIMD) simulations with GW (G0W0) calculations, ...

Latest version: v1
Publication date: Jul 16, 2021

Machine learning for metallurgy: a neural network potential for Al-Cu-Mg


Daniel Marchand, W.A. Curtin

  • High-strength metal alloys achieve their performance via careful control of precipitates and solutes. The nucleation, growth, and kinetics of precipitation, and the resulting mechanical properties, are inherently atomic-scale phenomena, particularly during early-stage nucleation and growth. Atomistic modeling using interatomic potentials is a desirable tool for understanding the detailed phenomena involved in precipitation and strengthening, which requires length and time scales far larger than those accessible by first-principles methods. Current interatomic potentials for alloys are not, however, sufficiently accurate for such studies. Here, a family of neural-network potentials (NNPs) for the Al-Cu-Mg system is presented as the first example of a machine-learning potential that can achieve near-first-principles accuracy for many different metallurgically-important aspects of this alloy. High fidelity predictions of intermetallic compounds, elastic constants, dilute ...

Latest version: v1
Publication date: Jul 14, 2021

The importance of reference frame for pressure at the liquid-vapour interface


Edward R. Smith

  • This repository has the input files and a guide to recreate the data from "The importance of reference frame for pressure at the liquid-vapour interface" (https://arxiv.org/abs/2107.00499). It requires the Flowmol code to be downloaded and built from https://github.com/edwardsmith999/flowmol (it should work with the latest version but the paper was generated from commit c4a52d434053d676c0281449b0fce7112116fd54 or the persistent version linked to DOI https://doi.org/10.5281/zenodo.4639546). The included README.txt file outlines how to do this. The input files are also included on the Github repository. The summarised data is also included as a Python pickle (summary.p) with scripts to produce all plots from the paper. This data, which shows the profile going through a liquid vapour interface, can be analysed in Python. The abstract for the article, which explains the importance of this data, is as follows: The local pressure tensor is non-unique, a fact which has generated ...

Latest version: v1
Publication date: Jul 14, 2021

A microscopic picture of paraelectric perovskites from structural prototypes


Michele Kotiuga, Samed Halilov, Boris Kozinsky, Marco Fornari, Nicola Marzari, Giovanni Pizzi

  • This work details how to determine structural prototypes for the cubic perovskite structure that are used to study the B-site displacements in the cubic, paraelectric phase. Car-Parrinello MD simulations of cubic barium titanate (BaTiO3) show the titanium displacements from the undistorted cubic structure. Using a systematic symmetry analysis we construct microscopic templates, i.e. representative structural models in the form of supercells that satisfy a desired point symmetry but are built from the combination of lower-symmetry primitive cells. Density functional theory calculations, using the microscopic templates as starting structures for a relaxation, are carried out to find structural prototypes of BaTiO3 with local polar distortions but with cubic point symmetry. The stability of these structures is studied as a function of volume and with respect to the zone-boundary phonons of pristine cubic BaTiO3. The stable distortions patterns for BaTiO3 are investigated for other titanates and for a handful of niobates and zirconates.

Latest version: v1
Publication date: Jul 12, 2021

Zeo-1: A computational data set of zeolite structures


Leonid Komissarov, Toon Verstraelen

  • Fast, empirical potentials are gaining increased popularity in the computational fields of materials science, physics and chemistry. With it, there is a rising demand for high-quality reference data for the training and validation of such models. In contrast to research that is mainly focused on small organic molecules, this work presents a data set of geometry-optimized bulk phase zeolite structures. Covering a majority of framework types from the Database of Zeolite Structures, this set includes over thirty thousand geometries. Calculated properties include system energies, nuclear gradients and stress tensors at each point, making the data suitable for model development, validation or referencing applications focused on periodic silica systems.

Latest version: v1
Publication date: Jul 07, 2021

Exploding and weeping ceramics


Hanlin Gu, Jascha Rohmer, Justin Jetter, Andriy Lotnyk, Lorenz Kienle, Eckhard Quandt, Richard D. James

  • The systematic tuning of the lattice parameters to achieve improved kinematic compatibility between phases is a broadly effective strategy for improving the reversibility, and lowering the hysteresis, of solid-solid phase transformations. Here, “kinematic compatibility” refers to the fitting together of the phases. We present an apparently paradoxical example in which tuning to near perfect compatibility in (Zr/Hf)O2-(YNb)O4 results in a high degree of irreversibility, as manifested in explosive or “weeping” behavior on cooling through the tetragonal-to-monoclinic phase transformation. In the case of weeping the polycrystal slowly and steadily falls apart at the grain boundaries. These effects occur without chemical change. Finally, tuning to satisfy a condition we term the equidistance condition results in reversible behavior with the lowest hysteresis in this system. We give evidence that all these observations are explained by a more careful analysis of compatibility of the ...

Latest version: v1
Publication date: Jul 05, 2021

Interplay between polarization, strain and defect-pairs in Fe-doped SrMnO3-δ


Chiara Ricca, Ulrich Aschauer

  • Defect chemistry, strain, and structural, magnetic and electronic degrees of freedom constitute a rich space for the design of functional properties in transition metal oxides. Here, we show that it is possible to engineer polarity and ferroelectricity in non-polar perovskite oxides via polar defect pairs formed by anion vacancies coupled to substitutional cations. We use a self-consistent site-dependent DFT+U approach that accounts for local structural and chemical changes upon defect creation and which is crucial to reconcile predictions with the available experimental data. Our results for Fe-doped oxygen-deficient SrMnO3 show that substitutional Fe and oxygen vacancies can promote polarity due to an o -center displacement of the defect charge resulting in a net electric dipole moment, which polarizes the lattice in the defect neighborhood. The formation of these defects and the resulting polarization can be tuned by epitaxial strain, resulting in enhanced polarization also for ...

Latest version: v1
Publication date: Jul 01, 2021

Building a consistent and reproducible database for adsorption evaluation in Covalent-Organic Frameworks


Daniele Ongari, Aliaksandr V. Yakutovich, Leopold Talirz, Berend Smit

  • We present a workflow that traces the path from the bulk structure of a crystalline material to assessing its performance in carbon capture from coal’s postcombustion flue gases. This workflow is applied to a database of 324 covalent−organic frameworks (COFs) reported in the literature, to characterize their CO2 adsorption properties using the following steps: (1) optimization of the crystal structure (atomic positions and unit cell) using density functional theory, (2) fitting atomic point charges based on the electron density, (3) characterizing the pore geometry of the structures before and after optimization, (4) computing carbon dioxide and nitrogen isotherms using grand canonical Monte Carlo simulations with an empirical interaction potential, and finally, (5) assessing the CO2 parasitic energy via process modeling. The full workflow has been encoded in the Automated Interactive Infrastructure and Database for Computational Science (AiiDA). Both the workflow and the ...

Latest version: v9
Publication date: Jun 30, 2021

Observation of a singular Weyl point surrounded by charged nodal walls in PtGa


Junzhang Ma, Quansheng Wu, Meng Song, Shengnan Zhang, E.B. Guedes, S.A. Ekahana, M. Krivenkov, Mengyu Yao, Shunye Gao, Wenhui Fan, Tian Qian, Hong Ding, N.C. Plumb, Milan Radovic, J. H. Dil, Yimin Xiong, K. Manna, C. Felser, Oleg Yazyev, Ming Shi

  • This record contains all the raw data in the paper Nature Communications volume 12, Article number: 3994 (2021). Constrained by the Nielsen-Ninomiya no-go theorem, in all so-far experimentally determined Weyl semimetals (WSMs) the Weyl points (WPs) always appear in pairs in the momentum space with no exception. As a consequence, Fermi arcs occur on surfaces which connect the projections of the WPs with opposite chiral charges. However, this situation can be circumvented in the case of unpaired WP, without relevant surface Fermi arc connecting its surface projection, appearing singularly, while its Berry curvature field is absorbed by nontrivial charged nodal walls. Here, combining angle-resolved photoemission spectroscopy with density functional theory calculations, we show experimentally that a singular Weyl point emerges in PtGa at the center of the Brillouin zone (BZ), which is surrounded by closed Weyl nodal walls located at the BZ boundaries and there is no Fermi arc ...

Latest version: v1
Publication date: Jun 30, 2021

High-throughput calculation of interlayer van der Waals force validated with experimental measurements


Kewei Tang, Weihong Qi, Yaru Wei, Guoliang Ru, Weimin Liu

  • Interlayer binding strength is an important property of two-dimensional (2D) materials in various occasions including exfoliation and heterostructure construction. Though there are already many calculations and experimental measurements for interlayer binding energy, few calculation references regarding the interlayer binding force can be found which is often the quantity been directly measured in experiments. Moreover, binding force rather than binding energy should be considered more closely related to whether a layered structure can be exfoliated or not under certain circumstances. To our best knowledge, there exists no such a database for 2D materials interlayer binding forces. In this work, with a descent algorithm designed to work with first-principles code, maximum interlayer binding force with the accuracy down to 1 meV/Å per atom is directly calculated for 230 common 2D materials using both the vdW-DF2 and optB88-vdW functionals. The results show significant inconsistency ...

Latest version: v1
Publication date: Jun 30, 2021

Band gaps of liquid water and hexagonal ice through advanced electronic-structure calculations


Thomas Bischoff, Igor Reshetnyak, Alfredo Pasquarello

  • The fundamental band gaps of liquid water and hexagonal ice are calculated through advanced electronic-structure methods. We compare specifically the performance of state-of-the-art GW calculations with nonempirical hybrid functionals. For the latter, we fix the free parameters either through the dielectric response of the material or through enforcing Koopmans' condition to localized states. The various approaches yield consistent band gaps, in good agreement with available experimental references. Furthermore, we discuss the critical aspects of each approach that underlie the band-gap predictions.

Latest version: v1
Publication date: Jun 28, 2021

Impact of quantum-chemical metrics on the machine learning prediction of electron density


Ksenia R. Briling, Alberto Fabrizio, Clemence Corminboeuf

  • Machine learning (ML) algorithms have undergone an explosive development impacting every aspect of computational chemistry. To obtain reliable predictions, one needs to maintain the proper balance between the black-box nature of ML frameworks and the physics of the target properties. One of the most appealing quantum-chemical properties for regression models is the electron density, and some of us recently proposed a transferable and scalable model based on the decomposition of the density onto an atom-centered basis set. The decomposition, as well as the training of the model, is at its core a minimization of some loss function, which can be arbitrarily chosen and may lead to results of different quality. Well-studied in the context of density fitting (DF), the impact of the metric on the performance of ML models has not been analyzed yet. In this work, we compare predictions obtained using the overlap and the Coulomb repulsion metrics for both the decomposition and training. As ...

Latest version: v1
Publication date: Jun 28, 2021

Modeling the Ga/As binary system across temperatures and compositions from first principles


Giulio Imbalzano, Michele Ceriotti

  • Materials composed of elements from the third and fifth columns of the periodic table display a very rich behavior, with the phase diagram usually containing a metallic liquid phase and a polar semiconducting solid. As a consequence, it is very hard to achieve transferable empirical models of interactions between the atoms that can reliably predict their behavior across the temperature and composition range that is relevant to the study of the synthesis and properties of III/V nanostructures and devices. We present a machine-learning potential trained on density functional theory reference data that provides a general-purpose model for the Ga/As system. We provide a series of stringent tests that showcase the accuracy of the potential, and its applicability across the whole binary phase space, computing with ab initio accuracy a large number of finite-temperature properties as well as the location of phase boundaries. We also show how a committee model can be used to reliably ...

Latest version: v1
Publication date: Jun 28, 2021

First-principles predictions of Hall and drift mobilities in semiconductors


Samuel Poncé, Francesco Macheda, Elena Roxana Margine, Nicola Marzari, Nicola Bonini, Feliciano Giustino

  • Carrier mobility is one of the defining properties of semiconductors. Significant progress on parameter-free calculations of carrier mobilities in real materials has been made during the past decade; however, the role of various approximations remains unclear and a unified methodology is lacking. Here, we present and analyse a comprehensive and efficient approach to compute the intrinsic, phonon-limited drift and Hall carrier mobilities of semiconductors, within the framework of the first-principles Boltzmann transport equation. The methodology exploits a novel approach for estimating quadrupole tensors and including them in the electron-phonon interactions, and capitalises on a rigorous and efficient procedure for numerical convergence. The accuracy reached in this work allows to assess common approximations, including the role of exchange and correlation functionals, spin-orbit coupling, pseudopotentials, Wannier interpolation, Brillouin-zone sampling, dipole and quadrupole ...

Latest version: v1
Publication date: Jun 25, 2021

Ferroelectricity promoted by cation/anion divacancies in SrMnO3


Chiara Ricca, Danielle Berkowitz, Ulrich Aschauer

  • We investigate the effect of polar Sr-O vacancy pairs on the electric polarization of SrMnO3 (SMO) thin films using density functional theory (DFT) calculations. This is motivated by indications that ferroelectricity in complex oxides can be engineered by epitaxial strain but also via the defect chemistry. Our results suggest that intrinsic doping by cation and anion divacancies can induce a local polarization in unstrained non-polar SMO thin films and that a ferroelectric state can be stabilized below the critical strain of the stoichiometric material. This polarity is promoted by the electric dipole associated with the defect pair and its coupling to the atomic relaxations upon defect formation that polarize a region around the defect. This suggests that polar defect pairs affect the strain-dependent ferroelectricity in semiconducting antiferromagnetic SMO. For metallic ferromagnetic SMO we find a much weaker coupling between the defect dipole and the polarization due to much ...

Latest version: v1
Publication date: Jun 24, 2021

Effect of density, phonon scattering and nanoporosity on the thermal conductivity of anisotropic cellulose nanocrystal foams


Varvara Apostolopoulou-Kalkavoura, Pierre Munier, Lukasz Dlugozima, Veit-Lorenz Heuthe, Lennart Bergström

  • Ice templated anisotropic foams based on cellulose nanocrystals (CNC) with densities ranging between 25 to 130 kg.m-3 were prepared from aqueous CNC dispersions. The thermal conductivities perpendicular to the columnar macropores direction increased in a non-monotonous way with the increasing CNC foam density while the thermal conductivity reached a minimum value for the CNC foam with the highest nanoporosity. Theoretical calculations including the solid and gas conduction within the foams as well as the thermal conductivity of water showed that phonon scattering at the solid-solid interfaces is responsible for reaching low thermal conductivity values. The foam wall nanoporosity, the particle alignment, the macropores orientation and the foam wall thickness seem to have a minimal effect on the thermal conductivity but can explain the deviations between the theoretical estimates and the experimental data. To this end the identification of the important influencing factors and the ...

Latest version: v2
Publication date: Jun 24, 2021

Chemistry of oxygen ionosorption on SnO2 surfaces


Kostiantyn Sopiha, Oleksandr Malyi, Clas Persson, Ping Wu

  • Ionosorbed oxygen is the key player in reactions on metal-oxide surfaces. This is particularly evident for chemiresistive gas sensors, which operate by modulating the conductivity of active materials through the formation/removal of surface O-related acceptors. Herein, we carried out a detailed study of various charged oxygen species on three naturally occurring surfaces of SnO2. We employed first-principles calculations and revealed that two types of surface acceptors can form spontaneously upon the adsorption of atmospheric oxygen: (i) superoxide O2 (in 1- charged state) on the (110) and the (101) surfaces and (ii) doubly ionized O (in 2- charged state) on the (100) facet, with the experimental evidence pointing to the latter as the source of sensing response. In this dataset, we present the optimized geometries (in CIF format) of different O and O_2 adsorption configurations in the most relevant charged states.

Latest version: v1
Publication date: Jun 22, 2021

Ultrasonic spray coating of polyethylenimine (ethoxylated) as electron injection and transport layer for organic light emitting diodes


Inge Verboven, Rachith Shanivarasanthe Nithyananda Kumar, Melissa Van Landeghem, Hilde Pellaers, Bart Ruttens, Jan D’Haen, Koen Vandewal, Wim Deferme

  • The lighting of the future is expected to be light weight, flexible, highly efficient, non-expensive and fabricated in an environmentally friendly way. Organic light emitting diodes meet all these requirements and can be fabricated using inexpensive and roll-to-roll compatible printing techniques. They however often use low work function, highly reactive metals, such as barium and calcium to facilitate electron injection, deposited using expensive and non-continuous vacuum techniques. Efficient and stable alternatives can be found in the aliphatic amines, polyethylenimine and polyethylenimine(ethoxylated), which shift the work function of aluminum favorably for electron injection. This work demonstrates ultrasonic spray coating of polyethylenimine and polyethylenimine(ethoxylated) as electron injection and transport layer for OLEDs, reducing the work function of the aluminum cathode by 0.355 eV allowing a luminous efficacy comparable to that of the OLEDs using calcium/aluminum ...

Latest version: v1
Publication date: Jun 21, 2021

Enhancing sub-bandgap external quantum efficiency by photomultiplication for narrowband organic near-infrared photodetectors


Jonas Kublitski, Axel Fischer, Shen Xing, Lukasz Baisinger, Eva Bittrich, Johannes Benduhn, Donato Spoltore, Koen Vandewal, Karl Leo

  • Detection of electromagnetic signals for applications such as health, product quality monitoring or astronomy requires highly responsive and wavelength selective devices. Photomultiplication-type organic detectors (PM-OPDs) have shown to achieve high quantum efficiencies mainly in the visible range. Much less research has been focused on realizing near-infrared narrowband PM-OPDs. Here, we demonstrate fully vacuum-processed narrow- and broadband PM‑OPDs. Our devices are based on enhanced hole injection leading to a maximum external quantum efficiency (EQE) of almost 2000% at -10 V for the broadband device. The photomultiplicative effect is also observed in the charge-transfer (CT) state absorption region. By making use of an optical cavity device architecture, we enhance CT absorption and demonstrate a wavelength tunable narrowband PM-OPD with EQEs superior to those of pin‑devices. The presented concept can further improve the performance of state-of-the-art OPDs based on the ...

Latest version: v1
Publication date: Jun 21, 2021

Basic density, lignin content and cleavage strength of Eucalyptus grandis wood


Bruno Soares, José Tarcísio Lima, Claudineia Assis

  • Information about the influence of basic density and lignin content on the propensity of wood to checks, simulated in a cleavage mechanical test, is scarce in the literature. Therefore, the objective of this research was to investigate the functional relationships between the cleavage strength and the basic density and lignin content of the wood. For this, two Eucalyptus grandis trees were felled at 22 years of age and specimens for the cleavage test were made. From these specimens, the basic density and lignin content were determined. The basal logs were sawn for making 45 specimens, 22 from the tree “A” and 23 from the tree “B”. The production of the specimens followed the suggestions of the ASTM D143 standard (ASTM 2014), being free from any defects that could mask the test results, without distinction of heartwood and sapwood or juvenile and mature wood. The mechanical test was carried out with aid of a universal testing machine EMIC, model DL 30000. The 45 specimens tested in ...

Latest version: v1
Publication date: Jun 20, 2021

Chemical stability of hydrogen boride nanosheets in water


Kurt Irvin Rojas, Nguyen Thanh Cuong, Hiroaki Nishino, Ryota Ishibiki, Shin-ichi Ito, Masahiro Miyauchi, Yoshitaka Fujimoto, Satoshi Tominaka, Susumu Okada, Hideo Hosono, Nelson Jr., Arboleda, Takahiro Kondo, Yoshitada Morikawa, Ikutaro Hamada

  • Hydrogen boride sheet is a recently fabricated boron-based two-dimensional nanosheet. For the interest of using it in electronic and catalytic applications, it is important that it has sufficient chemical stability for common substances. In this case, we investigate its chemical stability in water, a common substance in ambient condition and many applications. The study was done using experimental and first-principles method. This record contains the crystal structures, optimized via first-principles calculations that were used in discussing the various properties and interaction between water and hydrogen boride sheet. Additionally, input files used to calculate for the systems were included to aid in reproducing results of the study.

Latest version: v1
Publication date: Jun 19, 2021

Learning the exciton properties of azo-dyes


Alberto Fabrizio, Sergi Vela, Ksenia R. Briling, Clemence Corminboeuf

  • The ab initio determination of the character and properties of electronic excited states (ES) is the cornerstone of modern theoretical photochemistry. Yet, traditional ES methods become readily impractical when applied to fairly large molecules, or when used on thousands of different systems. In contrast, Machine Learning (ML) techniques have demonstrated their accuracy at retrieving ES properties of large molecular databases at a reduced computational cost. Especially for excited states applications, non-linear algorithms tend to be specialized and to target only individual properties. Learning fundamental quantum chemical objects potentially represents a more efficient, yet complex, alternative as a large number of molecular properties could be then extracted through post-processing. Herein, we report the general framework able to learn three fundamental objects of an ES: the hole and particle densities, as well as the transition density. We demonstrate the advantages of ...

Latest version: v1
Publication date: Jun 19, 2021

Koopmans spectral functionals: an open-source periodic-boundary implementation


Nicola Colonna, Riccardo De Gennaro, Edward Linscott, Nicola Marzari

  • Koopmans' spectral functionals aim to describe simultaneously ground state properties and charged excitations of atoms, molecules, nanostructures and periodic crystals. This is achieved augmenting standard density functionals with simple but physically motivated orbital-density-dependent corrections. These corrections act on a set of localized orbitals that, in periodic systems, resembles maximally localized Wannier function. At variance with a direct supercell implementation, we discuss here i) the complex but efficient formalism required for a periodic-boundary code using explicit Brillouin zone sampling, and ii) the calculation of the screened Koopmans' corrections with density-functional perturbation theory. The implementation in the Quantum ESPRESSO distribution and the application to prototypical insulating and semiconducting systems are presented and discussed.

Latest version: v1
Publication date: Jun 01, 2021

Property map collective variable as a useful tool for force field correction


Dalibor Trapl, Martin Krupička, Vladimir Višňovský, Jana Hozzová, Jaroslav Oľha, Aleš Křenek, Vojtěch Spiwok

  • 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.

Latest version: v1
Publication date: Jun 01, 2021

Reaction pathway for coke-free methane steam reforming on a Ni/CeO2 catalyst: Active sites and role of metal-support interactions


Agustín Salcedo, Pablo G. Lustemberg, Ning Rui, Robert M. Palomino, Zongyuan Liu, Slavomir Nemsak, Sanjaya D. Senanayake, José A. Rodriguez, M. Verónica Ganduglia-Pirovano, Beatriz Irigoyen

  • Methane steam reforming (MSR) plays a key role in the production of syngas and hydrogen from natural gas. The increasing interest in the use of hydrogen for fuel cell applications demands the development of catalysts with high activity at reduced operating temperatures. Ni-based catalysts are promising systems because of their high activity and low cost, but coke formation generally poses a severe problem. Studies of ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) indicate that CH4/H2O gas mixtures react with Ni/CeO2(111) surfaces to form OH, CHx and CHxO at 300 K. All these species are easy to form and desorb at temperatures below 700 K when the rate of the MSR process accelerates. Density functional theory (DFT) modeling of the reaction over ceria-supported small Ni nanoparticles predicts relatively low activation barriers between 0.3–0.7 eV for the complete dehydrogenation of methane to carbon and the barrierless activation of water at interfacial Ni sites. Hydroxyls ...

Latest version: v1
Publication date: Jun 01, 2021

Computational design of moiré assemblies aided by artificial intelligence


Georgios Tritsaris, Stephen Carr, Gabriel R. Schleder

  • Two-dimensional (2D) layered materials offer a materials platform with potential applications from energy to information processing devices. Although some single- and few-layer forms of materials such as graphene and transition metal dichalcogenides have been realized and thoroughly studied, the space of arbitrarily layered assemblies is still mostly unexplored. The main goal of this work is to demonstrate precise control of layered materials' electronic properties through careful choice of the constituent layers, their stacking, and relative orientation. Physics-based and AI-driven approaches for the automated planning, execution, and analysis of electronic structure calculations are applied to layered assemblies based on prototype one-dimensional (1D) materials and realistic 2D materials. We find it is possible to routinely generate moiré band structures in 1D with desired electronic characteristics such as a band gap of any value within a large range, even with few layers and ...

Latest version: v1
Publication date: Jun 01, 2021

Aluminum alloy compositions and properties extracted from a corpus of scientific manuscripts and US patents


Olivia P. Pfeiffer, Haihao Liu, Luca Montanelli, Marat I. Latypov, Fatih G. Sen, Vishwanath Hegadekatte, Elsa A. Olivetti, Eric R. Homer

  • Researchers continue to explore and develop aluminum alloys with new compositions and improved performance characteristics. An understanding of the current design space can help accelerate the discovery of new alloys. We present two datasets: 1) chemical composition, and 2) mechanical properties for predominantly wrought aluminum alloys. The first dataset contains 13,358 entries on aluminum alloy compositions extracted from academic literature and US patents using text processing techniques, in addition to 93 wrought aluminum alloys which are already registered with the Aluminum Association. The second dataset contains 1,268 entries on mechanical properties for aluminum alloys, where each entry is associated with a particular wrought series designation, extracted from tables in academic literature.

Latest version: v1
Publication date: Jun 01, 2021

Porous functionalized polymers enable generating and transporting hyperpolarized mixtures of metabolites


Théo El Darai, Samuel Cousin, Quentin Stern, Morgan Ceillier, James Kempf, Dmitry Eshchenko, Roberto Melzi, Marc Schnell, Laurent Gremillard, Aurélien Bornet, Jonas Milani, Basile Vuichoud, Olivier Cala, Damien Montarnal, Sami Jannin

  • Hyperpolarization by dissolution dynamic nuclear polarization (dDNP) has enabled promising applications in spectroscopy and imaging, but remains poorly widespread due to experimental complexity. Broad democratization of dDNP would require remote preparation and distribution of hyperpolarized samples from dedicated facilities. We describe here new hyperpolarizing polymers (HYPOPs) that can generate radical- and contaminant-free hyperpolarized samples within minutes with lifetimes exceeding hours in the solid state. HYPOPs feature tunable macroporous porosity, with porous volumes up to 80% and concentration of nitroxide radicals grafted in the bulk matrix up to 285 μmol g-1. Analytes can be efficiently impregnated as aqueous/alcoholic solutions and hyperpolarized up to P(13C) =25% within 8 min, through the combination of 1H spin diffusion and 1H →13C cross polarization. Solutions of 13C-analytes of biological interest hyperpolarized in HYPOPs display a very long solid-state 13C ...

Latest version: v1
Publication date: May 31, 2021

The nature of the active sites on Ni/CeO2 catalysts for methane conversions


Pablo G. Lustemberg, Zhongtian Mao, Agustín Salcedo, Beatriz Irigoyen, M. Verónica Ganduglia-Pirovano, Charles T. Campbell

  • Effective catalysts for the direct conversion of methane to methanol and for methane’s dry reforming to syngas are Holy Grails of catalysis research toward clean energy technologies. It has recently been discovered that Ni at low loadings on CeO2 is very reactive towards reactants CH4, H2O and CO2 and active for both of these reactions. Revealing the nature of the active sites in such systems is paramount to a rational design of improved catalysts. Here, using a combination of experimental measurements and density functional theory calculations, we show that the most active sites are cationic Ni atoms in clusters at step edges on the CeO2 surface, using the activation of CH4 as an example . We show that the size and morphology of the supported nanoparticles together with strong Ni−support bonding and charge transfer at the step edge are key to the high catalytic activity towards these methane conversions. We anticipate that this knowledge will inspire the development of more efficient catalysts for these reactions.

Latest version: v1
Publication date: May 21, 2021

Simulating solvation and acidity in complex mixtures with first-principles accuracy: the case of CH₃SO₃H and H₂O₂ in phenol


Kevin Rossi, Veronika Juraskova, Raphael Wischert, Laurent Garel, Clemence Corminboeuf, Michele Ceriotti

  • Set of inputs to perform the calculations reported in the paper. The i-pi input enables to perform molecular dynamics / metadynamics / REMD / PIMD simulations, with adequate thermostats. The DFTB and LAMMPS input respectively enable to calculate force and energies within the DFTB and Neural Network Forcefield frameworks. The CP2K input files enable to calculate force and energies at PBE and PBE0 level. The latter is used as the reference to train the neural network correction on top of DFTB. Brief description of the work: We present a generally-applicable computational framework for the efficient and accurate characterization of molecular structural patterns and acid properties in explicit solvent using H₂O₂ and CH₃SO₃H in phenol as an example. In order to address the challenges posed by the complexity of the problem, we resort to a set of data-driven methods and enhanced sampling algorithms. The synergistic application of these techniques makes the first-principle estimation of ...

Latest version: v4
Publication date: May 21, 2021

A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency


Gianluca Prandini, Antimo Marrazzo, Ivano E. Castelli, Nicolas Mounet, Elsa Passaro, Nicola Marzari

  • Despite the enormous success and popularity of density functional theory, systematic verification and validation studies are still very limited both in number and scope. Here, we propose a universal standard protocol to verify publicly available pseudopotential libraries, based on several independent criteria including verification against all-electron equations of state and plane-wave convergence tests for phonon frequencies, band structure, cohesive energy and pressure. Adopting these criteria we obtain two optimal pseudopotential sets, namely the Standard Solid State Pseudopotential (SSSP) efficiency and precision libraries, tailored for high-throughput materials screening and high-precision materials modelling. As of today, the SSSP precision library is the most accurate open-source pseudopotential library available. This archive entry contains the database of calculations (phonons, cohesive energy, equation of state, band structure, pressure, etc.) together with the ...

Latest version: v7
Publication date: May 21, 2021

Interplay between ferroelectricity and metallicity in BaTiO3


Veronica F. Michel, Tobias Esswein, Nicola A. Spaldin

  • We explore the interplay between ferroelectricity and metallicity, which are generally considered to be contra-indicated properties, in the prototypical ferroelectric barium titanate, BaTiO3. Using first-principles density functional theory, we calculate the effects of electron and hole doping, first by introducing a hypothetical background charge, and second through the introduction of explicit impurities (La, Nb and V for electron doping, and K, Al and Sc for hole doping). We find that, apart from a surprising increase in polarization at small hole concentrations, both charge-carrier types decrease the tendency towards ferroelectricity, with the strength of the polarization suppression, which is different for electrons and holes, determined by the detailed structure of the conduction and valence bands. Doping with impurity atoms increases the complexity and allows us to identify three factors that influence the ferroelectricity: structural effects arising largely from the size ...

Latest version: v1
Publication date: May 21, 2021

Common workflows for computing material properties using different quantum engines


Sebastiaan P. Huber, Emanuele Bosoni, Marnik Bercx, Jens Bröder, Augustin Degomme, Vladimir Dikan, Kristjan Eimre, Espen Flage-Larsen, Alberto Garcia, Luigi Genovese, Dominik Gresch, Conrad Johnston, Guido Petretto, Samuel Poncé, Gian-Marco Rignanese, Christopher J. Sewell, Berend Smit, Vasily Tseplyaev, Martin Uhrin, Daniel Wortmann, Aliaksandr V. Yakutovich, Austin Zadoks, Pezhman Zarabadi-Poor, Bonan Zhu, Nicola Marzari, Giovanni Pizzi

  • The prediction of material properties through electronic-structure simulations based on density-functional theory has become routinely common, thanks, in part, to the steady increase in the number and robustness of available simulation packages. This plurality of codes and methods aiming to solve similar problems is both a boon and a burden. While providing great opportunities for cross-verification, these packages adopt different methods, algorithms, and paradigms, making it challenging to choose, master, and efficiently use any one for a given task. Leveraging recent advances in managing reproducible scientific workflows, we demonstrate how developing common interfaces for workflows that automatically compute material properties can tackle the challenge mentioned above, greatly simplifying interoperability and cross-verification. We introduce design rules for reproducible and reusable code-agnostic workflow interfaces to compute well-defined material properties, which we ...

Latest version: v1
Publication date: May 11, 2021

Global free-energy landscapes as a smoothly joined collection of local maps


Federico Giberti, Gareth Tribello, Michele Ceriotti

  • 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

Latest version: v1
Publication date: May 08, 2021

Carrier lifetimes and polaronic mass enhancement in the hybrid halide perovskite CH₃NH₃PbI₃ from multiphonon Fröhlich coupling


Martin Schlipf, Samuel Poncé, Feliciano Giustino

  • We elucidate the nature of the electron-phonon interaction in the archetypal hybrid perovskite CH₃NH₃PbI₃ using ab initio many-body calculations and an exactly solvable model. We demonstrate that electrons and holes near the band edges primarily interact with three distinct groups of longitudinal-optical vibrations, in order of importance: the stretching of the Pb-I bond, the bending of the Pb-I-Pb bonds, and the libration of the organic cations. These polar phonons induce ultrafast intraband carrier relaxation over timescales of 6–30 fs and yield polaron effective masses 28% heavier than the bare band masses. These findings allow us to rationalize previous experimental observations and provide a key to understanding carrier dynamics in halide perovskites.

Latest version: v1
Publication date: May 07, 2021

Plasmon energy changes in FeMo14C15B6Erx (x=0-2) bulk metallic glass during in-situ heating


Sengo Kobayashi, James Howe, Mitsuhiro Murayama

  • Variations of volume plasmon energy of both ribbon and bulk FeMo14C15B6Erx (x=0-2) metallic glasses were measured as a function of the temperature in an analytical transmission electron microscope using valence electron energy loss spectroscopy (VEELS). The plasmon energy was found to decrease with increasing temperature, due not only to thermal expansion but also to chemical reordering in the glasses. The chemical reordering stimulates a specific solute cluster formation; M23(C, B)6 solute clusters began to form above about 200°C in both ribbon and bulk FeMo14C15B6Erx (x=0, 0.5, 1) metallic glasses. The formation of the M23(C, B)6 solute clusters was only found above 400°C in the ribbon FeMo14C15B6Er2 metallic glass, indicating inhibition of the M23(C, B)6 solute clusters occurred owing to the formation of Er-(C, B) complexes/clusters. The Er-(C, B) complexes/clusters were formed in the cooling process of the sample fabrication. In contrast to the ribbon sample, the formation of ...

Latest version: v1
Publication date: May 06, 2021

On-the-fly assessment of diffusion barriers of disordered transition metal oxyfluorides using local descriptors


Jin Hyun Chang, Peter Bjørn Jørgensen, Simon Loftager, Arghya Bhowmik, Juan María García Lastra, Tejs Vegge

  • The dataset contains the result of 48 Nudged Elastic Band calculations of Li(2-x)VO2F diffusion barriers in the format of Atomic Simulation Environment (ASE) trajectories. The NEB was performed with VASP, using projector augmented-wave (PAW) method to describe electron-ion interaction. The disordered rock salt cells were created using a 3 x 4 x 4 supercell containing 96 atoms (in case of no vacancies). PBE is used as XC functional while a rotationally invariant Hubbard U correction was applied to the d orbital of V with a U value of 3.25 eV. See more details in the paper.

Latest version: v1
Publication date: May 03, 2021

Finding new crystalline compounds using chemical similarity


Hai-Chen Wang, Silvana Botti, Miguel A. L. Marques

  • We proposed an efficient high-throughput scheme for the discovery of new stable crystalline phases. Our approach was based on the transmutation of known compounds, through the substitution of atoms in the crystal structure with chemically similar ones. The concept of similarity is defined quantitatively using a measure of chemical replaceability, extracted by data mining experimental databases. In this way we build more than 250k possible crystal phases, with almost 20k that are on the convex hull of stability. This dataset contains the optimized structure and the energy of these 250k materials calculated with the PBE approximation, in a format that is convenient for data-mining or for machine-learning applications.

Latest version: v1
Publication date: May 03, 2021

Designing crystallization to tune the performance of phase-change memory: rules of hierarchical melt and coordinate bond


Jin Zhao, Wen-Xiong Song, Tianjiao Xin, Zhitang Song

  • While alloy design has practically shown an efficient strategy to mediate two seemingly conflicted performances of writing speed and data retention in phase-change memory, the detailed kinetic pathway of alloy-tuned crystallization is still unclear. Here, we propose hierarchical melt and coordinate bond strategies to solve them, where the former stabilizes a medium-range crystal-like region and the latter provides a rule to stabilize amorphous. The Er0.52Sb2Te3 compound we designed achieves writing speed of 3.2 ns and ten-year data retention of 161 °C. We provide a direct atomic-level evidence that two neighbor Er atoms stabilize a medium-range crystal-like region, acting as a precursor to accelerate crystallization; meanwhile, the essential reason of stabilization originates from the formation of coordinate bonds by sharing lone-pair electrons of chalcogenide atoms with the empty 5d orbitals of Er atoms. The two rules pave the way for the development of storage-class memory with ...

Latest version: v1
Publication date: Apr 29, 2021

Band gap engineering in blended organic semiconductor films based on dielectric interactions


Katrin Ortstein, Sebastian Hutsch, Mike Hambsch, Kristofer Tvingstedt, Berthold Wegner, Johannes Benduhn, Jonas Kublitski, Martin Schwarze, Sebastian Schellhammer, Felix Talnack, Astrid Vogt, Peter Bäuerle, Norbert Koch, Stefan C. B. Mannsfeld, Hans Kleemann, Frank Ortmann, Karl Leo

  • Blending organic molecules to tune their energy levels is currently investigated as an approach to engineer the bulk and interfacial optoelectronic properties of organic semiconductors. It has been proven that the ionization energy (IE) and electron affinity (EA) can be equally shifted in the same direction by electrostatic effects controlled by blending similar halogenated derivatives with different energetics. Here, we show that the energy gap of organic semiconductors can be tuned by blending as well. We use oligothiophenes with different numbers of thiophene rings as example and investigate their structure and electronic properties. Photoelectron spectroscopy and inverse photoelectron spectroscopy show tunability of the single-particle gap, with the optical gaps showing similar, but smaller effects. Theoretical analysis shows that this tuning is mainly caused by a change in the dielectric constant with blend ratio. Further studies will explore the practical impact of this ...

Latest version: v1
Publication date: Apr 28, 2021

Prediction of yield strength in refractory body-centered-cubic High Entropy Alloys


Francesco Maresca, Chanho Lee, Rui Feng, Yi Chou, Tamas Ungar, Michael Widom, Jonathan Poplawsky, Yi-Chia Chou, Peter Liaw, William Curtin

  • Energy efficiency is motivating the search for new high-temperature metals. Some new body-centered-cubic random multicomponent "high entropy alloys (HEAs)" based on refractory elements (Cr-Mo-Nb-Ta-V-W-Hf-Ti-Zr) possess exceptional strengths at high temperatures but the physical origins of this outstanding behavior are not known. Here, by using a recent mechanistic theory, we have computed the high-temperature (T=1300K) yield strength based on solute strengthening of over 10 million alloys within the whole Al-Cr-Mo-Nb-Ta-V-W-Hf-Ti-Zr alloy family. Also the yield strength/density has been computed. This database enables the efficient search of new alloys with exceptional high-temperature strength.

Latest version: v1
Publication date: Apr 28, 2021

On-surface activation of benzylic C-H bonds for the synthesis of pentagon-fused graphene nanoribbons


Xiushang Xu, Marco Di Giovannantonio, José I. Urgel, Carlo A. Pignedoli, Pascal Ruffieux, Klaus Müllen, Roman Fasel, Akimitsu Narita

  • In the record we provide the inputs and outputs for the calculations that support our recent results in the synthesis of pentagon-fused graphene nanoribbons (GNRs). GNRs have potential for applications in electronic devices. A key issue, thereby, is the fine-tuning of their electronic characteristics, which can be achieved through subtle structural modifications. These are not limited to the conventional armchair, zigzag, and cove edges, but also possible through incorporation of non-hexagonal rings. On-surface synthesis enables the fabrication and visualization of GNRs with atomically precise chemical structures, but strategies for the incorporation of non-hexagonal rings have been underexplored. In the manuscript, we describe the on-surface synthesis of armchair-edged GNRs with incorporated five-membered rings through the C-H activation and cyclization of benzylic methyl groups. ortho-Tolyl-substituted dibromobianthryl was employed as the precursor monomer, and visualization of ...

Latest version: v1
Publication date: Apr 15, 2021

Rules of formation of H–C–N–O compounds at high pressure and the fates of planetary ices


Lewis J. Conway, Chris J. Pickard, Andreas Hermann

  • Results of an ab initio structure search on the H+C+N+O quaternary space at 500GPa. The solar system’s outer planets, and many of their moons, are dominated by matter from the H–C–N–O chemical space, based on solar system abundances of hydrogen and the planetary ices H2O, CH4 , and NH3 . In the planetary interiors, these ices will experience extreme pressure conditions, around 5 Mbar at the Neptune mantle–core boundary, and it is expected that they undergo phase transitions, decompose, and form entirely new compounds. While temperature will dictate the formation of compounds, ground- state density functional theory allows us to probe the chemical effects resulting from pressure alone. These structural developments in turn determine the planets’ interior structures, thermal evolution, and magnetic field generation, among others. Despite its importance, the H–C–N–O system has not been surveyed systematically to explore which compounds emerge at high-pressure conditions, and what ...

Latest version: v1
Publication date: Apr 12, 2021

Dictionary of 140k GDB and ZINC derived AMONs


Bing Huang, Anatole von Lilienfeld

  • We present all AMONs for GDB and Zinc data-bases using no more than 7 non-hydrogen atoms (AGZ7)---a calculated organic chemistry building-block dictionary based on the AMON approach [Huang and von Lilienfeld, Nature Chemistry (2020)]. AGZ7 records Cartesian coordinates of compositional and constitutional isomers, as well as properties for ∼140k small organic molecules obtained by systematically fragmenting all molecules of Zinc and the majority of GDB17 into smaller entities, saturating with hydrogens, and containing no more than 7 heavy atoms (excluding hydrogen atoms). AGZ7 cover the elements H, B, C, N, O, F, Si, P, S, Cl, Br, Sn and I and includes optimized geometries, total energy and its decomposition, Mulliken atomic charges, dipole moment vectors, quadrupole tensors, electronic spatial extent, eigenvalues of all occupied orbitals, LUMO, gap, isotropic polarizability, harmonic frequencies, reduced masses, force constants, IR intensity, normal coordinates, rotational ...

Latest version: v1
Publication date: Apr 11, 2021

A new dataset of 175k stable and metastable materials calculated with the PBEsol and SCAN functionals


Jonathan Schmidt, Hai-Chen Wang, Tiago F. T. Cerqueira, Silvana Botti, Miguel A. L. Marques

  • In the past decade we have witnessed the appearance of large databases of calculated material properties. These are most often obtained with the Perdew-Burke-Ernzerhof (PBE) functional of density-functional theory, a well established and reliable technique that is by now the standard in materials science. However, there have been recent theoretical developments that allow for an increased accuracy in the calculations. Here, we present a dataset of calculations for 175k solid-state materials obtained with two improved functionals: PBE for solids (that yields consistently better geometries than the PBE) and SCAN (probably the best all-around functional at the moment). Our results provide an accurate overview of the landscape of stable (and nearly stable) materials, and as such can be used for more reliable predictions of novel compounds. They can also be used for training machine learning models, or even for the comparison and benchmark of PBE, PBE for solids, and SCAN.

Latest version: v1
Publication date: Apr 09, 2021

Reinvestigating the surface and bulk electronic properties of Cd3As2


Silvan Roth, Hyungjun Lee, Andrea Sterzi, Michele Zacchigna, Antonio Politano, Raman Sankar, Fang-Cheng Chou, Giovanni Di Santo, Luca Petaccia, Oleg V. Yazyev, Alberto Crepaldi

  • This record contains the experimental results of our reinvestigation of the bulk and surface electronic properties of Cd3As2, a well-known material proposed to realize the 3D Dirac semimetal phase. By using polarization-based matrix element effects in photoemission, we reveal multiple bands crossing the Fermi level, characterized by different orbital character. Those states exhibit also largely different effective masses, and by combining alkali metal deposition and photon energy dependent ARPES, we report that the linearly dispersing band, which was previously interpreted as a bulk Dirac particle, is indeed a 2D surface Dirac state.

Latest version: v1
Publication date: Apr 09, 2021

Persistence of a surface state arc in the topologically trivial phase of MoTe2


Alberto Crepaldi, Gabriel Autès, Andrea Sterzi, Giulia Manzoni, Michele Zacchigna, Federico Cilento, Ivana Vobornik, Jun Fujii, Philippe Bugnon, Arnaud Magrez, Helmuth Berger, Fulvio Parmigiani, Oleg V. Yazyev, Marco Grioni

  • This record contains the experimental band structure of MoTe2. The material exhibits a structural phase transition at approximately 240 K, and in the low-temperature 1T’ phase is expected to realize the type-II Weyl semimetal phase. In our data we compare the band structure and the Fermi surface in the topological and in the trivial (1T’’) phase. We report the existence of large surface arc, which is persistent across the topological phase transition, and we conclude that its observation cannot be taken alone as a smoking gun of the Weyl semimetal phase. The study is completed by a spin-resolved ARPES study of the bulk electronic properties in the low-temperature topological phase

Latest version: v1
Publication date: Apr 09, 2021

Enhanced ultrafast relaxation rate in the Weyl semimetal phase of MoTe2 measured by time- and angle-resolved photoelectron spectroscopy


Alberto Crepaldi, Gabriel Autès, Gianmarco Gatti, Silvan Roth, Andrea Sterzi, Giulia Manzoni, Michele Zacchigna, Cephice Cacho, Richard T. Chapman, Emma Springate, Elaine A. Seddon, Philippe Bugnon, Arnaud Magrez, Helmuth Berger, Ivana Vobornik, Matthias Kalläne, Arndt Quer, Kai Rossnagel, Fulvio Parmigiani, Oleg V. Yazyev, Marco Grioni

  • This record contains the results of the first experimental investigation of the change in the electron dynamics across the topological phase transition from the type-II Weyl semimetal phase of MoTe2 to the trivial phase. By using the capability of time-resolved ARPES to access the unoccupied density of states, we succeed in transiently populating the Weyl points, which are otherwise above the Fermi level and out of the reach of conventional ARPES. We observe a bottleneck in the electron dynamics when the Weyl points annihilate and gaps are opened in the high-temperature trivial phase. This interpretation is supported by the observation that, in the “sister” compound WTe2 the dynamics is not affected by the change in temperature, and it is always much slower, thus reflecting the larger energy separation between the valence and conduction band.

Latest version: v1
Publication date: Apr 09, 2021

SmB6 electron-phonon coupling constant from time- and angle-resolved photoelectron spectroscopy


Andrea Sterzi, Alberto Crepaldi, Federico Cilento, Giulia Manzoni, Emmanouil Frantzeskakis, Michele Zacchigna, Erik van Heumen, Yingkai Huang, Mark S. Golden, Fulvio Parmigiani

  • This record contains the experimental results of the first ultrafast spectroscopic investigation of the electronic properties of SmB6, proposed to realize a Kondo topological insulator. We employ a multi-temperature model to extract the electron-phonon coupling constant in the range 0.13-0.04, within the assumption of a strong coupling to the optical phonon modes in the range 10-19 meV.

Latest version: v1
Publication date: Apr 09, 2021

Using metadynamics to build neural network potentials for reactive events: the case of urea decomposition in water


Manyi Yang, Luigi Bonati, Daniela Polino, Michele Parrinello

  • The study of chemical reactions in aqueous media is very important for its implications in several fields of science, from biology to industrial processes. However, modeling these reactions is difficult when water directly participates in the reaction, since it requires a fully quantum mechanical description of the system. Ab-initio molecular dynamics is the ideal candidate to shed light on these processes. However, its scope is limited by a high computational cost. A popular alternative is to perform molecular dynamics simulations powered by machine learning potentials, trained on an extensive set of quantum mechanical calculations. Doing so reliably for reactive processes is difficult because it requires including very many intermediate and transition state configurations. In this study we used an active learning procedure accelerated by enhanced sampling to harvest such structures and to build a neural-network potential to study the urea decomposition process in water. This ...

Latest version: v1
Publication date: Apr 08, 2021

Accurate and scalable multi-element graph neural network force field and molecular dynamics with direct force architecture


Cheol Woo Park, Mordechai Kornbluth, Jonathan Vandermause, Chris Wolverton, Boris Kozinsky, Jonathan Mailoa

  • Data includes the the ab initio molecular dynamic simulation of Li7P3S11 that was used to measure the performance of the GNNFF. The data is divided into training and testing sets. Brief descirption of the work: Recently, machine learning (ML) has been used to address the computational cost that has been limiting ab initio molecular dynamics (AIMD). Here, we present GNNFF, a graph neural network framework to directly predict atomic forces from automatically extracted features of the local atomic environment that are translationally-invariant, but rotationally-covariant to the coordinate of the atoms. We demonstrate that GNNFF not only achieves high performance in terms of force prediction accuracy and computational speed on various materials systems, but also accurately predicts the forces of a large MD system after being trained on forces obtained from a smaller system. Finally, we use our framework to perform an MD simulation of Li7P3S11, a superionic conductor, and show that ...

Latest version: v1
Publication date: Apr 06, 2021

Time-resolved ARPES at LACUS: band structure and ultrafast electron dynamics of solids


Alberto Crepaldi, Silvan Roth, Gianmarco Gatti, Christopher A. Arrell, José Ojeda, Frank van Mourik, Philippe Bugnon, Arnaud Magrez, Helmuth Berger, Majed Chergui, Marco Grioni

  • This record contains the first experimental results obtained at the time-resolved ARPES endstation developed at the Lausanne Centre for Ultrafast Science. The use of VUV photons, generated by means of high-harmonic generation in gas, allows us to explore the out-of-equilibrium electron dynamics over the entire Brillouin zone of solids. In this work we give evidence of this capability by accessing the linearly dispersing surface state of the nodal-line Dirac semimetal ZrSiTe.

Latest version: v1
Publication date: Apr 02, 2021

Enlisting potential cathode materials for rechargeable Ca batteries.


M. Elena Arroyo-de Dompablo, Jose Luis Casals

  • The development of rechargeable batteries based on a Ca metal anode demands the identification of suitable cathode materials. This work investigates the potential application of a variety of compounds, which are selected from the In-organic Crystal Structural Database (ICSD) considering 3d-transition metal oxysulphides, pyrophosphates, silicates, nitrides, and phosphates with a maximum of four different chemical elements in their composition. Cathode perfor-mance of CaFeSO, CaCoSO, CaNiN, Ca3MnN3, Ca2Fe(Si2O7), CaM(P2O7) (M = V, Cr, Mn, Fe, Co), CaV2(P2O7)2, Ca(VO)2(PO4)2 and α-VOPO4 is evaluated throughout the calculation of operation voltages, volume changes associated to the redox reaction and mobility of Ca2+ ions. Some materials exhibit attractive specific capacities and intercalation voltages combined with energy barriers for Ca migration around 1 eV (CaFeSO, Ca2FeSi2O7 and CaV2(P2O7)2). Based on the DFT results, αI-VOPO4 is identified as a potential Ca-cathode with a ...

Latest version: v1
Publication date: Apr 01, 2021

Semi-local and hybrid functional DFT data for thermalised snapshots of polymorphs of benzene, succinic acid, and glycine


Edgar A. Engel, Venkat Kapil

  • Structure prediction for molecular crystals is a longstanding challenge, as often minuscule free energy differences between polymorphs are sensitively affected by the description of electronic structure, the statistical mechanics of the nuclei and the cell, and thermal expansion. The importance of these effects has been individually established, but rigorous free energy calculations, which simultaneously account for all terms, have not been computationally viable. Here we reproduce the experimental stabilities of polymorphs of prototypical compounds -- benzene, glycine, and succinic acid -- by computing rigorous first-principles Gibbs free energies, at a fraction of the cost of conventional methods. This is achieved by a bottom-up approach, which involves generating machine-learning potentials to calculate surrogate free energies and subsequently calculating true first-principles free energies using inexpensive free energy perturbations. Accounting for all relevant physical ...

Latest version: v1
Publication date: Mar 26, 2021

Detecting electron-phonon coupling during photoinduced phase transition


Takeshi Suzuki, Yasushi Shinohara, Yangfan Lu, Mari Watanabe, Jiadi Xu, Kenichi L. Ishikawa, Hide Takagi, Minoru Nohara, Naoyuki Katayama, Hiroshi Sawa, Masami Fujisawa, Teruto Kanai, Jiro Itatani, Takashi Mizokawa, Shik Shin, Kozo Okazaki

  • This record contains the data supporting our recent findings on electron-phonon coupling during photoinduced phase transition. We measure mode- and band-selective electron-phonon couplings during the photoinduced insulator-to-metal phase transition in Ta2NiSe5 (TNS) by frequency-domain angle-resolved photoemission spectroscopy (FDARPES). FDARPES gives us rich information about which band more couples which phonon mode by seeing frequency components of time-resolved angle-resolved photoemission spectra. The experiments indicate 2 THz and 3 THz phonon modes associated with the metallic and semiconducting phases. To get a more atomistic picture of the oscillation, we perform phonon-mode calculations relying on the density-functional theory (DFT). The computational scheme itself is very standard that density-functional-perturbation theory (DFPT) with semilocal or local exchange-correlation functionals. However, the required computational resources were rather ...

Latest version: v1
Publication date: Mar 26, 2021

Correlation between electronic and structural orders in 1T-TiSe2


Hiroki Ueda, Michael Porer, José Mardegan, Sergii Parchenko, Namrata Gurung, Federica Fabrizi, Mahesh Ramakrishnan, Larissa Boie, Martin Neugebauer, Bulat Burganov, Max Burian, Steven Johnson, Kai Rossnagel, Urs Staub

  • The correlation between electronic and crystal structures of 1T -TiSe2 in the charge-density wave (CDW) state is studied by x-ray diffraction in order to clarify basic properties in the CDW state, transport properties, and chirality. Three families of reflections are used to probe atomic displacements and the orbital asymmetry in Se. Two distinct onset temperatures are found: TCDW and a lower T∗ indicative for an onset of Se out-of-plane atomic displacements. T∗ coincides with a DC resistivity maximum and the onset of the proposed gyrotropic (chiral) electronic structure. However, no indication for chirality is found. The relation between the atomic displacements and the transport properties is discussed in terms of Ti 3d and Se 4p states that only weakly couple to the CDW order.

Latest version: v1
Publication date: Mar 26, 2021

Improved wetting model for the prediction of topography and dimensionality of superomniphobic surfaces


Nikolaos Lempesis, Aleš Janka, Oksana Gnatiuk, Stef J.L. van Eijndhoven, Rudolf J. Koopmans

  • 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 ...

Latest version: v1
Publication date: Mar 23, 2021

Simulating the ghost: quantum dynamics of the solvated electron


Jinggang Lan, Venkat Kapil, Piero Gasparotto, Michele Ceriotti, Marcella Iannuzzi, Vladimir Rybkin

  • The nature of the bulk hydrated electron has been a challenge for both experiment and theory due to its short lifetime and high reactivity, and the need for a high-level of electronic structure theory to achieve predictive accuracy. The lack of a classical atomistic structural formula makes it exceedingly difficult to model the solvated electron using conventional empirical force fields, which describe the system in terms of interactions between point particles associated with atomic nuclei. Here we overcome this problem using a machine-learning model, that is sufficiently flexible to describe the effect of the excess electron on the structure of the surrounding water, without including the electron in the model explicitly. The resulting potential is not only able to reproduce the stable cavity structure but also recovers the correct localization dynamics that follow the injection of an electron in neat water. The machine learning model achieves the accuracy of the ...

Latest version: v1
Publication date: Mar 18, 2021

Hidden order and multipolar exchange striction in a correlated f-electron system


Leonid V. Pourovskii, Sergii Khmelevskyi

  • The nature of order in low-temperature phases of some materials is not directly seen by experiment. Such "hidden orders" (HO) may inspire decades of research to identify the mechanism underlying those exotic states of matter. In insulators, HO phases originate in degenerate many-electron states on localized f or d shells that may harbor high-rank multipole moments. Coupled by inter-site exchange, those moments form a vast space of competing order parameters. Here, we show how the ground state order and magnetic excitations of a prototypical HO system, neptunium dioxide NpO2, can be fully described by a low-energy Hamiltonian derived by a many-body ab initio force theorem method. Superexchange interactions between the lowest crystal-field quadruplet of Np4+ ions induce a primary non-collinear order of time-odd rank-5 (triakontadipolar) moments with a secondary quadrupole order preserving the cubic symmetry of NpO2. Our study also reveals an unconventional multipolar ...

Latest version: v1
Publication date: Mar 18, 2021

Data for ferromagnetic resonance simulation in a microtube


Vladimir Fel'k, Sergey Komogortsev

  • Ferromagnetic resonance fields in a microtube with the various ratio of the inner and outer diameter of the tube β were studied using micromagnetic simulation. For β < 0.15 the resonance field agrees with the prediction of the Kittel equation for an infinite ferromagnetic cylinder for both parallel and perpendicular orientation of the applied field to its axis. For β > 0.15 the resonance field increases from the resonance field of the infinite cylinder and approaches the level of the film magnetized along the plane. This behavior was at odds both with the prediction that can be made using analytically calculated demagnetizing factor in ferromagnetic tube, and with the prediction that use the empirical dependence of the demagnetizing field on β, established from the magnetization curves. For β > 0.15 and transverse applied field a number of resonance peaks were observed.

Latest version: v1
Publication date: Mar 17, 2021

Elucidating structure and function of Ni/La-doped-ceria catalysts for CO2 reduction by the reverse water gas shift reaction


Consuelo Alvarez-Galvan, Pablo Lustemberg, Jose A. Alonso, Freddy Oropeza, María Herranz, Jesus Cebollada, Martin Dapena, Jose M. Campos-Martin, Victor A. de la Peña-O’Shea, M. Veronica Ganduglia-Pirovano

  • Reducing and/or utilizing CO2 in the atmosphere is mandatory to decrease its negative effects as greenhouse gas. The reverse water gas shift reaction (rWGS) is one of the most promising routes for CO2 valorization. Here, we show that Ni/La-doped ceria catalysts, prepared by the solution combustion synthesis method, has an excellent catalytic performance per unit mass of catalyst. Structure-activity correlations obtained using a combination of different techniques such as X-ray and neutron diffraction, Raman spectroscopy, in-situ NAP-XPS, Electron Microscopy, and catalytic testing, point out to optimum values for the Ni loading and the La proportion. Density functional theory calculations of the elementary steps of the reaction on model Ni/ceria catalysts aid toward the microscopic understanding of the active sites nature. Metallic Ni activates H2 dissociation and a certain La doping maximizes Ce3+ sites, which supplies greater available oxygen to form H2O. These findings are ...

Latest version: v1
Publication date: Mar 17, 2021

Gaussian approximation potentials (GAP) for germanium telluride


Đorđe Dangić, Stephen Fahy, Ivana Savić

  • Quasiharmonic theory of atomic vibrations usually fails to describe materials that undergo structural phase transitions, which is the case with germanium telluride (GeTe) at high temperatures. To correctly model vibrational properties of GeTe at high temperatures, we use the temperature dependent effective potential (TDEP) method (Physical Review B 88, 144301 (2013)). Collecting data needed to fit TDEP models involves running ab-initio molecular dynamics (MD) simulations. These MD simulations can be very CPU time consuming. In order to speed up MD simulations, we fitted an interatomic potential using the Gaussian Approximation Potential (GAP) approach (Physical Review Letters 104, 136403 (2010)) to obtain interatomic forces during MD simulations. This dataset consists of the training set of density functional theory energies and forces of GeTe for GAP, and the training script used to generate the interatomic potential.

Latest version: v1
Publication date: Mar 16, 2021

Structure determination of an amorphous drug through large-scale NMR predictions


Manuel Cordova, Martins Balodis, Albert Hofstetter, Federico Paruzzo, Sten O. Nilsson Lill, Emma S. E. Eriksson, Pierrick Berruyer, Bruno Simões de Almeida, Michael J. Quayle, Stefan T. Norberg, Anna Svensk Ankarberg, Staffan Schantz, Lyndon Emsley

  • Knowledge of the structure of amorphous solids can direct, for example, the optimization of pharmaceutical formulations, but atomic-level structure determination in amorphous molecular solids has so far not been possible. Solid-state NMR is among the most popular methods to characterize amorphous materials, and Molecular Dynamics (MD) simulations can help describe the structure of disordered materials. However, directly relating MD to NMR experiments in molecular solids has been out of reach until now because of the large size of these simulations. Here, using a machine learning model of chemical shifts, we determine the atomic-level structure of the hydrated amorphous drug AZD5718 by combining dynamic nuclear polarization-enhanced solid-state NMR experiments with predicted chemical shifts for MD simulations of large systems. From these amorphous structures we then identify H-bonding motifs and relate them to local intermolecular complex formation energies.

Latest version: v1
Publication date: Mar 16, 2021

Reaction-based machine learning representations for predicting the enantioselectivity of organocatalysts


Simone Gallarati, Raimon Fabregat, Rubén Laplaza, Sinjini Bhattacharjee, Matthew Wodrich, Clemence Corminboeuf

  • Hundreds of catalytic methods are developed each year to meet the demand for high-purity chiral compounds. The computational design of enantioselective organocatalysts remains a significant challenge, as catalysts are typically discovered through experimental screening. Recent advances in combining quantum chemical computations and machine learning (ML) hold great potential to propel the next leap forward in asymmetric catalysis. Within the context of quantum chemical machine learning (QML, or atomistic ML), the ML representations used to encode the structure of molecules and evaluate their similarity cannot easily capture the subtle energy differences that govern enantioselectivity. Here, we present a general strategy for improving molecular representations within an atomistic machine learning model to predict the enantiomeric excess of asymmetric propargylation organocatalysts solely from the structure of catalytic cycle intermediates. Mean absolute errors as low as 0.25 kcal ...

Latest version: v1
Publication date: Mar 05, 2021

Importance of surface oxygen vacancies for ultrafast hot carrier relaxation and transport in Cu2O


Chiara Ricca, Ulrich Aschauer, Lisa Grad, Matthias Hengsberger, Jürg Osterwalder

  • Cu2O has appealing properties as an electrode for photo-electrochemical water splitting, yet its practical performance is severely limited by inefficient charge extraction at the interface. Using hybrid DFT calculations, we investigate carrier capture processes by oxygen vacancies (VO) in the experimentally observed (√3×√3)R30° reconstruction of the dominant (111) surface. Our results show that these VO are doubly ionized and that associated defects states strongly suppress electron transport. In particular, the excited electronic state of a singly charged VO plays a crucial role in the non-radiative electron capture process with a capture coefficient of about 10^-9 cm3/s and a lifetime of 0.04 ps, explaining the experimentally observed ultrafast carrier relaxation. These results highlight that engineering the surface VO chemistry will be a crucial step in optimizing Cu2O for photoelectrode applications.

Latest version: v1
Publication date: Mar 05, 2021

Asymmetric azide‐alkyne Huisgen cycloaddition on chiral metal surfaces


Samuel Stolz, Michael Bauer, Carlo A. Pignedoli, Nils Krane, Max Bommert, Elia Turco, Nicolo Bassi, Amogh Kinikar, Néstor Merino-Dìez, Roland Hany, Harald Brune, Oliver Gröning, Roland Widmer

  • The record contains the data supporting our recent findings on asymmetric azide-alkyne Huisgen cycloaddition on chiral metal surfaces: Achieving fundamental understanding of enantioselective heterogeneous synthesis is marred by the permanent presence of multitudinous arrangements of catalytically active sites in real catalysts. We address this issue by using structurally comparatively simple, well‐defined, and chiral intermetallic PdGa{111} surfaces as catalytic substrates. We demonstrate the impact of chirality transfer and ensemble effect for the thermally activated azide‐alkyne Huisgen cycloaddition between 3‐(4‐azidophenyl)propionic acid and 9‐ethynylphenanthrene on these threefold symmetric intermetallic surfaces under ultrahigh vacuum conditions. Specifically, we encounter a dominating ensemble effect for this reaction as on the Pd3‐terminated PdGa{111} surfaces no stable heterocoupled structures are created, while on the Pd1‐terminated PdGa{111} surfaces, the cycloaddition ...

Latest version: v1
Publication date: Mar 02, 2021

Reversible dehalogenation in on-surface aryl-aryl coupling


Samuel Stolz, Marco Di Giovannantonio, José I. Urgel, Qiang Sun, Amogh Kinikar, Gabriela Borin Barin, Max Bommert, Roman Fasel, Roland Widmer

  • The record contains the data to support the findings of our recent work on reversibility of the dehalogenation process in on-surface aryl-aryl coupling. In the emerging field of on‐surface synthesis, dehalogenative aryl–aryl coupling is unarguably the most prominent tool for the fabrication of covalently bonded carbon‐based nanomaterials. Despite its importance, the reaction kinetics are still poorly understood. Here we present a comprehensive temperature‐programmed x‐ray photoelectron spectroscopy investigation of reaction kinetics and energetics in the prototypical on‐surface dehalogenative polymerization of 4,4′′‐dibromo‐p‐terphenyl into poly(para‐phenylene) on two coinage metal surfaces, Cu(111) and Au(111). We find clear evidence for reversible dehalogenation on Au(111), which is inhibited on Cu(111) owing to the formation of organometallic intermediates. The incorporation of reversible dehalogenation in the reaction rate equations leads to excellent agreement with ...

Latest version: v1
Publication date: Mar 02, 2021

Extensive benchmarking of DFT+U calculations for predicting band gaps


Nicole Kirchner-Hall, Wayne Zhao, Yihuang Xiong, Iurii Timrov, Ismaila Dabo

  • Accurate computational predictions of band gaps are of practical importance to the modeling and development of semiconductor technologies, such as (opto)electronic devices and photoelectrochemical cells. Among available electronic-structure methods, density-functional theory (DFT) with the Hubbard U correction (DFT+U) applied to band edge states is a computationally tractable approach to improve the accuracy of band gap predictions beyond that of DFT calculations based on (semi)local functionals. At variance with DFT approximations, which are not intended to describe optical band gaps and other excited-state properties, DFT+U can be interpreted as an approximate spectral-potential method when U is determined by imposing the piecewise linearity of the total energy with respect to electronic occupations in the Hubbard manifold (thus removing self-interaction errors in this subspace), thereby providing a (heuristic) justification for using DFT+U to predict band gaps. However, it is ...

Latest version: v1
Publication date: Mar 02, 2021

Bias free multiobjective active learning for materials design and discovery


Kevin Maik Jablonka, Giriprasad Melpatti Jothiappan, Shefang Wang, Berend Smit, Brian Yoo

  • The design rules for materials are clear for applications with a single objective. For most applications, however, there are often multiple, sometimes competing objectives where there is no single best material, and the design rules change to finding the set of Pareto optimal materials. In this work, we introduce an active learning algorithm that directly uses the Pareto dominance relation to compute the set of Pareto optimal materials with desirable accuracy. We apply our algorithm to de novo polymer design with a prohibitively large search space. Using molecular simulations, we compute key descriptors for dispersant applications and reduce the number of materials that need to be evaluated to reconstruct the Pareto front with a desired confidence by over 98% compared to random search. This work showcases how simulation and machine learning techniques can be coupled to discover materials within a design space that would be intractable using conventional screening approaches.

Latest version: v1
Publication date: Feb 22, 2021

Machine learning for metallurgy: a neural network potential for Al-Mg-Si


Abhinav C. P. Jain, Daniel Marchand, Albert Glensk, Michele Ceriotti, W. A. Curtin

  • High-strength metal alloys achieve their performance via careful control of the nucleation, growth, and kinetics of precipitation. Alloy mechanical properties are then controlled by atomic scale phenomena such as shearing of the precipitates by dislocations. Atomistic modeling to understand the operative mechanisms requires length and time scales far larger than those accessible by first-principles methods. Here, a family of Behler-Parinello neural-network potentials (NNPs) for the Al-Mg-Si system is developed to enable quantitative studies of Al-6xxx alloys. The NNP is trained on metallurgically-important quantities computed by first principles density functional theory (DFT) leading to high fidelity predictions of intermetallic compounds, elastic constants, dilute solid-solution energetics, precipitate/matrix interfaces, Al stacking fault energies, antisite defect energies, and other quantities. A preliminary examination of early-stage clustering kinetics and energetics in ...

Latest version: v1
Publication date: Feb 09, 2021

Appraisal of calcium ferrites as cathodes for calcium rechargeable batteries: DFT, synthesis, characterization and electrochemistry of Ca4Fe9O17


M. Elena Arroyo-de Dompablo, José Luis Casals

  • Sustainability combined with high energy density prospects makes Fe-based oxides attractive as cathodes for calcium rechargeable batteries. This work presents a DFT evaluation of the CaFe2+nO4+n (0 < n < 3) family, for which both the average intercalation voltage and the theoretical specific capacity decrease with the increasing n value. The term n = 1/4, Ca4Fe9O17, meets the most appealing characteristics: a calculated average voltage of 4.16 V, a theoretical specific capacity of 230 mA h g−1 and the lowest energy barrier for Ca migration so far predicted for an existing oxide (0.72 eV). To overcome the previously reported synthesis difficulties, we employed a novel synthesis procedure in sealed quartz tubes followed by quenching in water. The XRD and SAED patterns of the prepared Ca4Fe9O17 powder reveal a certain degree of stacking defects along the c axis. Attempts to deinsert Ca ions from Ca4Fe9O17 by chemical means (NO2BF4 in ACN) and in electrochemical Ca cells were ...

Latest version: v1
Publication date: Feb 07, 2021

Efficient Kr/Xe separation from triangular g-C3N4 nanopores: density-functional theory calculations benchmarked with random phase approximation


Mohammad Tohidivahdat, Davide Campi, Nicola Colonna, Luis Francisco Villalobos, Nicola Marzari, Kumar Agrawal Varoon

  • Poly(triazine imide) or PTI is a promising material for molecular sieving membranes, thanks to its atom-thick ordered lattice with an extremely high density (1.6 × 10^14 pores/cm2) of triangular-shaped nanopores of ~0.34 nm diameter. Here, we investigate the application of PTI nanopores in the purification of Kr from Xe to reduce the storage volume of the mixture of 85Kr/Xe. Using van-der-Waals density-functional theory (vdW-DFT) calculations, benchmarked against the random phase approximation (RPA), we calculate the potential energy profiles for Kr and Xe across the nanopores. For each gas, starting from the RPA potential-energy profile, the force-field parameters to be used in the classical molecular dynamics framework are trained to calculate the Helmholtz free energy barrier as a function of temperature, and therefore, the corresponding entropic loss. Overall, due to the much higher activation energy from the adsorbed state in Xe (17.61 and 42.10 kJ/mole for Kr and Xe, ...

Latest version: v1
Publication date: Feb 07, 2021

Biomimetic high performance artificial muscle built on sacrificial coordination network and mechanical training process


Zhikai Tu, Weifeng Liu, Jin Wang, Jinhao Huang, Jinxing Li, Hongming Lou, Xueqing Qiu

  • Artificial muscle materials promise incredible applications in actuators, robotics and medical apparatus, yet the ability to mimic the full characteristics of skeletal muscles into synthetic materials remains a huge challenge. Herein, inspired by the dynamic sacrificial bonds in biomaterials and the self-strengthening of skeletal muscles by physical exercise, high performance artificial muscle material is prepared by rearrangement of sacrificial coordination bonds in the polyolefin elastomer via a repetitive mechanical training process. Biomass lignin is incorporated as a green reinforcer for the construction of interfacial coordination bonds. The prepared artificial muscle material exhibits high actuation strain (>40%), high actuation stress (1.5 MPa) which can lift more than 10000 times its own weight with 30% strain, characteristics of excellent self-strengthening by mechanical training, strain-adaptive stiffening, and heat/electric programmable actuation performance. In this ...

Latest version: v1
Publication date: Feb 07, 2021

DFT investigation of Ca mobility in reduced-perovskite and oxidized-marokite oxides


M. Elena Arroyo-de Dompablo, José Luis Casals

  • Progress in the development of rechargeable Ca-ion batteries demands the discovery of potential cathode materials. Transition metal oxides are interesting candidates due to their theoretical high energy densities, but with the drawback of a low Ca mobility. Previous computational/experimental investigations associate the electrochemical inactivity of various oxides (CaMO3-perovskite, CaMn2O4-post-spinel and CaV2O5) to high energy barriers for Ca migration. The introduction of oxygen and/or Ca vacancies in ternary transition metal oxides is a likely way to reshape the local topology and hence improve the Ca diffusivity. In this work, the energy barriers for Ca migration are calculated and discussed for (i) oxygen-deficient perovskites within the related Ca2Fe2O5-brownmillerite and Ca2Mn2O5 structures, and (ii) tunnel CaMn4O8, a derivative of the CaMn2O4-marokite with Ca vacancies.

Latest version: v1
Publication date: Feb 07, 2021

Radial spin texture of the Weyl fermions in chiral tellurium


G. Gatti, D. Gosálbez-Martínez, S. S. Tsirkin, M. Fanciulli, M. Puppin, S. Polishchuk, S. Moser, L. Testa, E. Martino, S. Roth, Ph. Bugnon, L. Moreschini, A. Bostwick, C. Jozwiak, E. Rotenberg, G. Di Santo, L. Petaccia, I. Vobornik, J. Fujii, J. Wong, D. Jariwala, H. A. Atwater, H. M. Rønnow, M. Chergui, O. V. Yazyev, M. Grioni, A. Crepaldi

  • In the present record we provide the theoretical calculations used in the article: G. Gatti et al., Radial Spin Texture of the Weyl Fermions in Chiral Tellurium, Phys. Rev. Lett. 125, 216402. It consist of a detailed analysis of the electronic structure and spin textures at different points of the Brillouin zone. We provide the band structure and spin expectation values along different high-symmetry lines, Fermi surface contour plots in the ΓMLA plane, and spin texture in small sphere around two points of the Brillouin zone. The data is provided as the output format of the Quantum Espresso package. We also include the pseudopotential used in these calculations.

Latest version: v1
Publication date: Jan 27, 2021

Structural involvement in the melting of the charge density wave in 1T-TiSe2


Max Burian, Michael Porer, Jose R.L. Mardegan, Vincent Esposito, Sergii Parchenko, Burganov Bulat, Namrata Gurung, Mahesh Ramakrishnan, Valerio Scagnoli, Hirkoi Ueda, Sonia Francoual, Federica Fabrizi, Yoshikazu Tanaka, Tadashi Togashi, Kai Rossnagel, Steven L. Johnson, Urs Staub

  • The simultaneous condensation of electronic and structural degrees of freedom gives rise to new states of matter, including superconductivity and charge-density-wave formation. When exciting such a condensed system, it is commonly assumed that the ultrafast laser pulse disturbs primarily the electronic order, which in turn destabilizes the atomic structure. Contrary to this conception, we show here that structural destabilization of few atoms causes macroscopic melting of the charge-density wave in 1T-TiSe2. In detail, we use ultrafast pump-probe non-resonant and resonant X-ray diffraction to track the periodic lattice distortion and the electronic charge density wave in 1T-TiSe2 upon optical excitation. We observe a fluence regime in which the periodic lattice deformation is strongly suppressed but the charge density wave related Se 4p orbital order remains mostly intact. Complete melting of both structural and electronic order occurs 4-5 times faster than expected from a purely ...

Latest version: v1
Publication date: Jan 27, 2021

Screening from eg states and antiferromagnetic correlations in d(1,2,3) perovskites: A GW+EDMFT investigation


Francesco Petocchi, Fredrik Nilsson, Ferdi Aryasetiawan, Philipp Werner

  • We perform a systematic ab initio study of the electronic structure of Sr(V,Mo,Mn)O3 perovskites, using the parameter-free GW+EDMFT method. This approach self-consistently calculates effective interaction parameters, taking into account screening effects due to nonlocal charge fluctuations. Comparing the results of a 3-band (t2g) description to those of a 5-band (t2g+eg) model, it is shown that the eg states have little effect on the low-energy properties and the plasmonic features for the first two compounds but play a more active role in SrMnO3. In the case of SrMnO3 paramagnetic GW+EDMFT yields a metallic low-temperature solution on the verge of a Mott transition, while antiferromagnetic GW+EDMFT produces an insulating solution with the correct gap size. We discuss the possible implications of this result for the nature of the insulating state above the Neel temperature, and the reliability of the GW+EDMFT scheme.

Latest version: v1
Publication date: Jan 27, 2021

Normal State of Nd_(1-x)Sr_xNiO2 from Self-Consistent GW+EDMFT


Francesco Petocchi, Viktor Christiansson, Fredrik Nilsson, Ferdi Aryasetiawan, Philipp Werner

  • Superconductivity with a remarkably high Tc has recently been observed in hole-doped NdNiO2, a material that shares similarities with the high-Tc cuprates. This discovery promises new insights into the mechanism of unconventional superconductivity, but at the modeling level, there are fundamental issues that need to be resolved. While it is generally agreed that the low-energy properties of cuprates can, to a large extent, be captured by a single-band model, there has been a controversy in the recent literature about the importance of a multiband description of the nickelates. Here, we use a multisite extension of the recently developed GW+EDMFT method, which is free of adjustable parameters, to self-consistently compute the interaction parameters and electronic structure of hole-doped NdNiO2. This full ab initio simulation demonstrates the importance of a multiorbital description, even for the undoped compound, and it produces results for the resistivity and Hall conductance in qualitative agreement with experiment.

Latest version: v1
Publication date: Jan 27, 2021

Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA


Hisashi Ishida, Hidetoshi Kono

  • Torsional stress has a significant impact on the structure and stability of the nucleosome. RNA polymerase imposes torsional stress on the DNA in chromatin and unwraps the DNA from the nucleosome to access the genetic information encoded in the DNA. To understand how the torsional stress affects the stability of the nucleosome, we examined the unwrapping of two half superhelical turns of nucleosomal DNA from either end of the DNA under torsional stress with all-atom molecular dynamics simulations. The free energies for unwrapping the DNA indicate that positive stress that overtwists DNA facilitates a large-scale asymmetric unwrapping of the DNA without a large extension of the DNA. During the unwrapping, one end of the DNA was dissociated from H3 and H2A-H2B while the other end of the DNA stably remained wrapped. The detailed analysis indicates that this asymmetric dissociation is facilitated by the geometry and bendability of the DNA under positive stress. The geometry ...

Latest version: v1
Publication date: Jan 27, 2021

Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling


Kateřina Tomášková, Dalibor Trapl, Vojtěch Spiwok

  • 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.

Latest version: v3
Publication date: Jan 26, 2021

Thermodynamics of order and randomness in dopant distributions inferred from atomically resolved images


Lukas Vlcek, Shize Yang, Yongji Gong, Pulickel Ajayan, Wu Zhou, Matthew Chisholm, Maxim Ziatdinov, Rama Vasudevan, Sergei Kalinin

  • Exploration of structure-property relationships as a function of dopant concentration is commonly based on mean field theories for solid solutions. However, such theories that work well for semiconductors tend to fail in materials with strong correlations, either in electronic behavior or chemical segregation. In these cases, the details of atomic arrangements are generally not explored and analyzed. The knowledge of the generative physics and chemistry of the material can obviate this problem, since defect configuration libraries as stochastic representation of atomic level structures can be generated, or parameters of mesoscopic thermodynamic models can be derived. To obtain such information for improved predictions, we use data from atomically resolved microscopic images that visualize complex structural correlations within the system and translate them into statistical mechanical models of structure formation. Given the significant uncertainties about the microscopic aspects ...

Latest version: v1
Publication date: Jan 26, 2021

Confinement effects and acid strength in Zeolites


Emanuele Grifoni, GiovanniMaria Piccini, Johannes Lercher, Vassiliki-Alexandra Glezakou, Roger Rousseau, Michele Parrinello

  • Chemical reactivity and sorption in zeolites are coupled to confinement and - to a lesser extent- to the acid strength of Brønsted acid sites (BAS). In presence of water the zeolite Brønsted acid sites eventually convert into hydronium ions. The gradual transition from zeolite Brønsted acid sites to hydronium ions conversion in zeolites of varying pore size is examined by ab initio molecular dynamics combined with enhanced sampling based on well-tempered metadynamics and a recently developed set of collective variables. While at low water content (1-2 water/BAS) the acidic protons prefer to be shared between zeolites and water, higher water contents (n>2) invariably lead to solvation of the protons within a localized water cluster adjacent to the BAS. At low water loadings the standard free energy of the formed complexes is dominated by enthalpy and is associated with the acid strength of the BAS and the space around the site. Conversely, the entropy increases linearly with the ...

Latest version: v1
Publication date: Jan 26, 2021

Towards constant potential modeling of CO-CO coupling at liquid water-Cu(100) interfaces


Henrik H. Kristoffersen, Karen Chan

  • We have studied electrochemical *CO-*CO coupling in explicit electrolyte with density functional theory, molecular dynamics, and metadynamics. We considered both the *CO-*CO coupling reaction and the charging process required to keep the potential constant. The charging process consists of transferring explicit cations from the electrolyte and electrons from the potentiostat to the interface. Under constant charge conditions (non-constant electrostatic potential), the *CO-*CO coupling reaction energies are relative insensitive to the charge state at the interface and the electrolyte composition and the reaction occurs with co-adsorption of water. Under constant potential conditions, the *CO-*CO coupling reaction is stabilized at lower potentials because of charging and the reaction is influenced by the electrolyte composition. Here we have collected the data from the eight AIMD metadynamics simulations conducted in the study. Each AIMD data tar.gz file contains the VASP input ...

Latest version: v1
Publication date: Jan 26, 2021

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