arXiv subjects

Rika Kobayashi

Publications and source records attributed to Rika Kobayashi.

10 recordsLinked to original sources

arXiv2025

Optimizing Data Extraction from Materials Science Literature: A Study of Tools Using Large Language Models

Large Language Models (LLMs) are increasingly utilized for large-scale extraction and organization of unstructured data owing to their exceptional Natural Language Processing (NLP) capabilities. Empowering materials design, vast amounts of data from experiments and simulations are scattered across numerous scientific publications, but high-quality experimental databases are scarce. This study considers the effectiveness and practicality of five representative AI tools (ChemDataExtractor, BERT-PSIE, ChatExtract, LangChain, and Kimi) to extract bandgaps from 200 randomly selected Materials Science publications in two presentations (arXiv and publisher versions), comparing the results to those obtained by human processing. Although the integrity of data extraction has not met expectations, encouraging results have been achieved in terms of precision and the ability to eliminate irrelevant papers from human consideration. Our analysis highlights both the strengths and limitations of these tools, offering insights into improving future data extraction techniques for enhanced scientific discovery and innovation. In conjunction with recent research, we provide guidance on feasible improvements for future data extraction methodologies, helping to bridge the gap between unstructured scientific data and structured, actionable databases.

cs.DL↗

arXiv2025

Reliable Density Functional Theory Predictions of Bandgaps for Materials

We consider methods for optimizing the bandgap calculation of 3D materials, considering 340 sample materials. Examined are the effects of the choice of the pseudopotential to describe core electrons, the plane-wave basis set cutoff energy, and the Brillouin zone integration. Cost-saving calculations in which the structure is optimized using reduced-quality Brillouin zone integrations and cutoff energies were found to lead to experimentally significant errors exceeding 0.1 eV in 18% of cases using the PBE functional and 21% of cases using PBE0. Such cost-savings approaches are therefore not recommended for general applications. Also, the current practice of using unoptimized grids to perform the Brillouin-zone integrations in bandgap calculations is found to be unreliable for 16% of materials using PBE and for 23% using PBE0. A k-space optimization scheme is introduced that interpolates extensive PBE results to determine a generally useful approach that when used in PBE0 calculations is found to be inadequate for only 1.6% of the materials studied.

cond-mat.mtrl-sci↗

arXiv2024

Analysis of Chiral Oxirane Molecules in Preparation for Next Generation Telescopes: A Review, New Analysis, & a Chiral Molecule Database

Human biology has a preference for left-handed chiral molecules and an outstanding question is if this is imposed through astrophysical origins. We aim to evaluate the known information about chiral molecules within astrophysical and astrochemical databases, evaluate chemical modeling accuracy, and use high-level CCSD(T) calculations to characterize propylene oxide and other oxirane variants. By comparing these computational values with past laboratory experiments, we find a 99.9% similarity. We also have put together a new database dedicated to chiral molecules and variants of chiral molecules to assist in answering this question.

astro-ph.IM↗

arXiv2023

Reliable density functional and G_0 W_0 approaches to the calculation of bandgaps in 2D materials

Optimizing density-functional theory (DFT) and G0W0 calculations present coupled problems as orbitals from DFT are needed as G0W0 starting points. Applied to 341 two-dimensional (2D) materials, we demonstrate that CAM-B3LYP provides minimal changes in bandgap (e.g., mean absolute deviation of 0.23 eV) when used to start G0W0 calculations, compared to traditional functionals such as PBE, PBE0, and HSE06 (1.07 eV, 1.48 eV, and 1.51 eV, respectively). CAM-B3LYP also delivers the smallest changes in orbital representation. These and other results indicate the suitability of CAM-B3LYP as a density-functional approach for modelling 2D materials, as well as for use in optimizing G0W0 calculations. Our findings parallel well established features of applications to molecules, as well as for spectroscopic applications involving 3D materials.

cond-mat.mtrl-sci↗

arXiv2022

Gather -- a better way to codehack online

A virtual hands-on computer laboratory has been designed within the Gather online meeting platform. Gather's features such as spatial audio, private spaces and interactable objects offer scope for great improvements over currently used platforms, especially for small-group based teaching. We describe our experience using this virtual computer laboratory for a recent 'Python for Beginners' workshop held as part of the Software Sustainability Institute's 2022 Research Software Camp.

cs.HC↗

arXiv2022

Accurate prediction of the properties of materials using the CAM-B3LYP Density Functional

Density functionals with asymptotic corrections to the long-range potential provide entry-level methods for calculations on molecules that can sustain charge transfer, but similar applications in Materials Science are rare. We describe an implementation of the CAM-B3LYP range-separated functional within the Vienna Ab-initio Simulation Package (VASP) framework, together with its analytical functional derivatives. Results obtained for eight representative materials: aluminum, diamond, graphene, silicon, NaCl, MgO, 2D h-BN and 3D h-BN, indicate that CAM-B3LYP predictions embody mean-absolute deviations (MAD) compared to HSE06 that are reduced by a factor of 6 for lattice parameters, 4 for quasiparticle band gaps, 3 for the lowest optical excitation energies, and 6 for exciton binding energies. Further, CAM-B3LYP appears competitive compared to ab initio G0W0 and Bethe-Salpeter equation (BSE) approaches. The CAM-B3LYP implementation in VASP was verified by comparison of optimized geometries and reaction energies for isolated molecules taken from the ACCDB database, evaluated in large periodic unit cells, to analogous results obtained using Gaussian basis sets. Using standard GW pseudopotentials and energy cutoffs for the plane-wave calculations and the aug-cc-pV5Z basis set for the atomic-basis ones, the MAD in energy for 1738 chemical reactions was 0.34 kcal mol-1, whilst for 480 unique bond lengths this was 0.0036 Å; these values reduced to 0.28 kcal mol-1 (largest error 0.94 kcal mol-1) and 0.0009 Å by increasing the plane-wave cuttoff energy to 850 eV.

cond-mat.mtrl-sci↗

arXiv2022

Density functionals with asymptotic-potential corrections are required for the simulation of spectroscopic properties of materials

Five effects of correction of the asymptotic potential error in density functionals are identified that significantly improve calculated properties of molecular excited states involving charge-transfer character. Newly developed materials-science computational methods are used to demonstrate how these effects manifest in materials spectroscopy. Connection is made considering chlorophyll-a as a paradigm for molecular spectroscopy, 22 iconic materials as paradigms for 3D materials spectroscopy, and the VN- defect in hexagonal boron nitride as an example of the spectroscopy of defects in 2D materials pertaining to nanophotonics. Defects can equally be thought of as being "molecular" and "materials" in nature and hence bridge the realms of molecular and materials spectroscopies. It is concluded that the density functional HSE06, currently considered as the standard for accurate calculations of materials spectroscopy, should be replaced, in most instances, by the computationally similar but asymptotically corrected CAM-B3LYP functional, with some specific functionals for materials use only providing further improvements.

cond-mat.mtrl-sci↗

arXiv2020

Convergence of defect energetics calculations

Determination of the chemical and spectroscopic natures of defects in materials such as hexagonal boron nitride (h-BN) remains a serious challenge for both experiment and theory. To establish basics needs for reliable calculations, we consider a model defect $V_N N_B$ in h-BN in which a boron-for-nitrogen substitution is accompanied by a nitrogen vacancy, examining its lowest-energy transition, (1)2B1 to (1)2A1. This provides a relatively simple test system as open-shell and charge-transfer effects, that are difficult to model and can dominate defect spectroscopy, are believed to be small. We establish calculation convergence with respect to sample size using both cluster and 2D-periodic models, convergence with respect to numerical issues such as use of plane-wave or Gaussian-basis-set expansions, and convergence with respect to the treatment of electron correlation. The results strongly suggest that poor performance of computational methods for defects of other natures arise through intrinsic methodological shortcomings.

cond-mat.mtrl-sci↗

arXiv2020

Possible nanophotonics applications of the $V_N N_B$ defect in hexagonal boron nitride

The $V_N N_B$ defect in hexagonal boron nitride (h-BN), comprising a nitrogen vacancy adjacent to a nitrogen-for-boron substitution, is modelled in regard to its possible usefulness in a nanophotonics device. The modelling is done on both a simple model compound and on a 2D periodic representation of the defect, considering its magnetic and spectroscopic properties. The electronic distribution in $V_N N_B$ excited states is very open-shell in nature, and to deal with this two new computational methods are developed: one allows standard density-functional theory (DFT) calculations to be employed to evaluate state energies, the other introduces techniques needed to apply the VASP computational package to these and many other problems involving excited states. Also of general use, results from DFT calculations are then calibrated against those from ab initio methods, seeking robust computational schemes. These innovations allow 45 electronic states of the defect in its neutral, +1 and -1 charged forms to be considered. The charged forms of the defect are predicted to display properties of potential interest to nanophotonics.

cond-mat.mtrl-sci↗

arXiv2018

Understanding and calibrating Density-Functional-Theory calculations describing the energy and spectroscopy of defect sites in hexagonal boron nitride

Defect states in 2D materials present many possible uses but both experimental and computational characterization of their spectroscopic properties is difficult. We provide and compare results from 13 DFT and ab initio computational methods for up to 25 excited states of a paradigm system, the VNCB defect in hexagonal boron nitride (h-BN). Studied include include: (i) potentially catastrophic effects for computational methods arising from the multi-reference nature of the closed-shell and open-shell states of the defect, which intrinsically involves broken chemical bonds, (ii) differing results from DFT and time-dependent DFT (TDDFT) calculations, (iii) comparison of cluster models to periodic-slab models of the defect, (iv) the starkly differing effects of nuclear relaxation on the various electronic states as broken bonds try to heal that control the widths of photoabsorption and photoemission spectra, (v) the effect of zero-point energy and entropy on free-energy differences, (vi) defect-localized and conduction/valence band transition natures, and (vii) strategies needed to ensure that the lowest-energy state of a defect can be computationally identified.

physics.comp-ph↗