arXiv subjects

Yosuke Kanai

Publications and source records attributed to Yosuke Kanai.

At least 19 recordsLinked to original sources

arXiv2026

Performance of Tkatchenko-Scheffler Dispersion Method with Updated van der Waals Radii: Importance for Alkali-Containing Systems

The Tkatchenko-Scheffler (TS) pairwise method to calculate dispersion interactions is a widely used approach to incorporate missing long-range van der Waals contributions in semilocal and hybrid density functional calculations. Despite numerous refinements of the approach to include many-body terms, the original formulation still remains highly relevant as an efficient and robust method, especially for organic and/or insulating materials. In 2018, Fedorov et al. reported updated van der Waals radii to the seminal work published in 2009. The present work examines the accuracy of the TS method with updated van der Waals radii (abbreviated as TS_2018), coupled with the semilocal Perdew-Burke-Ernzerhof density functional, for structural predictions of semiconducting and insulating materials in comparison to the non-local many-body dispersion method and the original TS method (TS_2009). Special attention is paid to materials containing alkali elements, for which the TS_2009 method exhibits a large overbinding, associated with potentially large errors in predicted atomic structures. We also consider a more narrow reformulation (TS_alkali) where only the the alkali atoms are corrected, so the method remains otherwise compatible with TS_2009. The binding energy curves of five alkali dimers are used to assess the TS_2009 and the TS_2018 methods in comparison to the random phase approximation. Using 45 inorganic solid compounds with available experimental reference data, as well as three widely studied, Cs-containing halide perovskites, CsPb$X_3$ ($X$ = Cl, Br, I), we then examine the performance of the TS_2018 and TS_alkali approaches compared to TS_2009 and the beyond-pairwise, nonlocal many-body dispersion method; the latter found to give good results as well.

cond-mat.mtrl-sci↗

arXiv2026

All-electron Dynamical Bethe-Salpeter Equation for Extended Systems with Atom-centered Orbital Basis

Solving Bethe-Salpeter equation (BSE) for the two-particle Green's function is the most widely used approach for taking into account the particle-hole (exciton) interaction in electronic excitation in the context of the many-body theory based on Green's function. In BSE calculations, the static approximation to the screened Coulomb interaction kernel is commonly employed. However, when the excitonic character is significant as typically indicated by a large exciton binding energy, dynamical screening effects become non-negligible, rendering the static approximation questionable. Because of the large computational cost due to the dense Brillouin zone integration necessary for convergence, solving the dynamical BSE for extended systems remains a significant challenge, especially when combined with GW calculation for the calculation of quasi-particle energies. In this work, we formulate the plane-wave based effective dielectric function method [Zhang, et al., Phys. Rev. B 107, 235205 (2023)] for the dynamical BSE calculation using atom-centered orbitals as basis functions. We implement this approach in our recently developed all-electron numerical atom-centered orbital (NAO) implementation of BSE@GW [Zhou, et. al. J. Chem. Theory Comput. 21, 291 (2025)] for extended systems. We validate our all-electron NAO-based implementation of the dynamical BSE method, and we then discuss its realistic application to molecular crystal of naphthalene by performing the dynamical BSE@G0W0 calculation.

physics.chem-ph↗

arXiv2026

Proton Quantum Effects in H$_3$S Electronic Structure: A Multicomponent DFT study via Nuclear-Electronic Orbital Method

We investigate the impact of the quantum effects of protons on the electronic structure of high-pressure H$_3$S, a benchmark hydrogen-rich superconductor with a critical temperature ($T_c$) exceeding 200 K. Using Nuclear-Electronic Orbital Density Functional Theory (NEO-DFT), we treat hydrogen nuclei quantum mechanically on the same footing as electrons within a first-principles framework. Our calculations reveal that nuclear quantum effects (NQEs) induce subtle modifications to the electronic band structure and density of states (DOS) near the Fermi energy, including features associated with van Hove singularities. However, the resulting changes in the DOS would increase $T_c$ by only a few percent. On the other hand, calculations of the phonon dispersion with the NEO-DFT method show large changes in the hydrogen-dominated phonons that arise from a stiffening of the S-H bonds due to NQEs. These findings imply that the experimentally observed reduction in $T_c$ upon deuteration arises predominantly from changes in the phonon properties, while NQEs-induced modifications to the electronic structure itself are minimal.

physics.comp-ph↗

arXiv2026

Proton Quantum Effects on Electronic Excitation in Hydrogen-bonded Organic Solid: A First-Principles Green's Function Theory Study

Nuclear quantum effects of protons on electronic excitations in hydrogen-bonded organic materials remains underexplored. In theoretical studies, modeling excitons in these extended systems is particularly difficult because they tend to have a large exciton binding energy and sometimes exhibit charge transfer character. We demonstrate how first-principles Green's function theory combined with the nuclear-electronic orbital method enables us to examine the nature of excitons in a prototypical organic solid of eumelanin, for which the extensive hydrogen bonds have been proposed to facilitate the formation of delocalized excitons. We investigate how the quantization of protons impacts electronic excitations. We discuss the extent to which the resulting proton quantum effects can be described as being derived from structure and how they induce molecular-level anisotropy for the excitons in the organic solid.

cond-mat.mtrl-sci↗

arXiv2025

Robustness of Floquet topological phase at room temperature: a first-principles dynamics study

Nonadiabatic Thouless pumping of electrons is studied within the framework of topological Floquet engineering, particularly focused on how atomic lattice dynamics affect the emergent Floquet topological phase in trans-polyacetylene under the driving electric field. As similarly done in the earlier work [Zhou and Kanai, J. Phys. Chem. Lett., 12, 4496 (2021)], the real-time time-dependent density functional theory and Ehrenfest dynamics simulations were used to investigate the extent to which the number of pumped charges remains equal to the topological invariant, the winding number, when the temperature effect of ions and the dynamical coupling of electrons and ions are taken into account. Our theoretical work shows that the Floquet topological phase remains intact but the condition on the driving field necessary for observing the topological phase becomes more limiting.

cond-mat.mtrl-sci↗

arXiv2025

Molecular Control of Floquet Topological Phase in Non-adiabatic Thouless Pumping

Nonadiabatic Thouless pumping of electrons is studied in the framework of topological Floquet engineering, particularly focused on how changes to chemical moieties can control the emergence of the Floquet topological phase. We employ real-time time-dependent density functional theory to investigate the extent to which the topological invariant, the winding number, is impacted by molecular-level changes to trans-polyacetylene. In particular, several substitutions to trans-polyacetylene are studied to examine different effects on the electronic structure including mesomeric effect, inductive effect, and electron conjugation effect. Maximally-localized Wannier functions are employed to relate the winding number to the valence bond description by expressing the topological pumping as the transport dynamics of the localized Wannier functions. By further exploiting the gauge invariance of the quantum dynamics in terms of the minimal particle-hole excitations, the topological pumping of electrons can be also represented as a cyclic transition among the bonding and antibonding orbitals. Having connected the topological invariant to chemically intuitive concepts, we show the molecular-level control on the emergence of the Floquet topological phase, presenting us with a great opportunity for the intuitive engineering of molecular systems for such an exotic topological phase.

physics.chem-ph↗

arXiv2025

Roadmap on Advancements of the FHI-aims Software Package

Electronic-structure theory is the foundation of the description of materials including multiscale modeling of their properties and functions. Obviously, without sufficient accuracy at the base, reliable predictions are unlikely at any level that follows. The software package FHI-aims has proven to be a game changer for accurate free-energy calculations because of its scalability, numerical precision, and its efficient handling of density functional theory (DFT) with hybrid functionals and van der Waals interactions. It treats molecules, clusters, and extended systems (solids and liquids) on an equal footing. Besides DFT, FHI-aims also includes quantum-chemistry methods, descriptions for excited states and vibrations, and calculations of various types of transport. Recent advancements address the integration of FHI-aims into an increasing number of workflows and various artificial intelligence (AI) methods. This Roadmap describes the state-of-the-art of FHI-aims and advancements that are currently ongoing or planned.

cond-mat.mtrl-sci↗

arXiv2024

Machine-Learning Electron Dynamics with Moment Propagation Theory: Application to Optical Absorption Spectrum Computation using Real-Time TDDFT

We present an application of our new theoretical formulation of quantum dynamics, moment propagation theory (MPT) (Boyer et al., J. Chem. Phys. 160, 064113 (2024)), for employing machine-learning techniques to simulate the quantum dynamics of electrons. In particular, we use real-time time-dependent density functional theory (RT-TDDFT) simulation in the gauge of the maximally localized Wannier functions (MLWFs) for training the MPT equation of motion. Spatially-localized time-dependent MLWFs provide a concise representation that is particularly convenient for the MPT expressed in terms of increasing orders of moments. The equation of motion for these moments can be integrated in time while the analytical expressions are quite involved. In this work, machine-learning techniques were used to train the the second-order time derivatives of the moments using first-principles data from the RT-TDDFT simulation, and this MPT enabled us to perform electron dynamics efficiently. The application to computing optical absorption spectrum for various systems was demonstrated as a proof-of-principles example of this approach. In addition to isolated molecules (water, benzene, and ethene), condensed matter systems (liquid water and crystalline silicon) were studied, and we also explored how the principle of the nearsightedness of electrons can be employed in this context.

physics.chem-ph↗

arXiv2024

Lagrangian Formulation of Nuclear-Electronic Orbital Ehrenfest Dynamics with Real-time TDDFT for Extended Periodic Systems

We present a Lagrangian-based implementation of Ehrenfest dynamics with nuclear-electronic orbital (NEO) theory and real-time time-dependent density functional theory (RT-TDDFT) for extended periodic systems. In addition to a quantum dynamical treatment of electrons and selected protons, this approach allows for the classical movement of all other nuclei to be taken into account in simulations of condensed matter systems. Furthermore, we introduce a Lagrangian formulation for the traveling proton basis approach and propose new schemes to enhance its application for extended periodic systems. Validation and proof-of-principle applications are performed on electronically excited proton transfer in the o-hydroxybenzaldehyde molecule with explicit solvating water molecules. These simulations demonstrate the importance of solvation dynamics and a quantum treatment of transferring protons. This work broadens the applicability of the NEO Ehrenfest dynamics approach for studying complex heterogeneous systems in the condensed phase.

physics.chem-ph↗

arXiv2024

All-electron BSE@GW method with Numeric Atom-Centered Orbitals for Extended Systems

Green's function theory has emerged as a powerful many-body approach not only in condensed matter physics but also in quantum chemistry in recent years. We have developed a new all-electron implementation of the BSE@GW formalism using numeric atom-centered orbital basis sets (Liu et al., J. Chem. Phys. 152, 044105 (2020)). We present our recent developments in implementing this formalism for extended systems with periodic boundary conditions. We discuss its numerical implementation and various convergence tests pertaining to numerical atom-centered orbitals, auxiliary basis sets for the resolution-of-identity formalism, and Brillouin zone sampling. Proof-of-principle examples are presented to compare with other formalisms, illustrating the new all-electron BSE@GW method for extended systems.

physics.chem-ph↗

arXiv2024

Ion Type Dependence of DNA Electronic Excitation in Water under Proton, alpha-particle, and Carbon Ion Irradiation: A First-Principles Simulation Study

Understanding how the electronic excitation of DNA changes in response to different high-energy particles is central to advancing ion beam cancer therapy. While protons have been the predominant ion of choice in beam cancer therapy, heavier ions, particularly carbon ions, have drawn significant attention over the past decade. Carbon ions are expected to transfer larger amounts of energy accordingly to the linear response theory. However, the molecular-level details of the electronic excitation under heavier ion irradiation remain unknown. In this work, we use real-time time-dependent density functional theory simulations to examine the quantum-mechanical details of DNA electronic excitations in water under proton, alpha-particle, and carbon ion irradiation. Our results show that the energy transfer does indeed increase for the heavier ions, while the excitation remains highly conformal. However, the increase in the energy transfer rate, measured by electronic stopping power, does not match the prediction by the linear response model, even when accounting for the velocity-dependence of the irradiating ions charge. The simulations also reveal that while the number of holes generated on DNA increases for heavier ions, the increase is only partially responsible for the larger stopping power. Larger numbers of highly energetic holes formed from the heavier ions also contribute significantly to the increased electronic stopping power.

cond-mat.soft↗

arXiv2024

Theory of Moment Propagation for Quantum Dynamics in Single-Particle Description

We present a novel theoretical formulation for performing quantum dynamics in terms of moments within the single-particle description. By expressing the quantum dynamics in terms of increasing orders of moments, instead of single-particle wave functions as generally done in time-dependent density functional theory, we describe an approach for reducing the high computational cost of simulating the quantum dynamics. The equation of motion is given for the moments by deriving analytical expressions for the first-order and second-order time derivatives of the moments, and a numerical scheme is developed for performing quantum dynamics by expanding the moments in the Taylor series as done in classical molecular dynamics simulation. We propose a few numerical approaches using this theoretical formalism on a simple one-dimensional model system, for which an analytically exact solution can be derived. Application of the approaches to an anharmonic system is also discussed to illustrate their generality. We also discuss the use of an artificial neural network model to circumvent the numerical evaluation of the second-order time derivatives of the moments, as analogously done in the context of classical molecular dynamics simulations.

physics.chem-ph↗

arXiv2023

First-Principles Approach for Coupled Quantum Dynamics of Electrons and Protons in Heterogeneous Systems

The coupled quantum dynamics of electrons and protons is ubiquitous in many dynamical processes involving light-matter interaction, such as solar energy conversion in chemical systems and photosynthesis. A first-principles description of such nuclear-electronic quantum dynamics requires not only the time-dependent treatment of nonequilibrium electron dynamics but also that of quantum protons. Quantum mechanical correlation between electrons and protons adds further complexity to such coupled dynamics. Here we extend real-time nuclear-electronic orbital time-dependent density functional theory (RT-NEO-TDDFT) to periodic systems and perform first-principles simulations of coupled quantum dynamics of electrons and protons in complex heterogeneous systems. The process studied is electronically excited state intramolecular proton transfer of o-hydroxybenzaldehyde in water and at a silicon (111) semiconductor-molecule interface. These simulations illustrate how environments such as hydrogen-bonding water molecules and an extended material surface impact the dynamical process on the atomistic level. Depending on how the molecule is chemisorbed on the surface, excited state electron transfer from the molecule to the semiconductor surface can inhibit ultrafast proton transfer within the molecule. This work elucidates how heterogeneous environments influence the balance between the quantum mechanical proton transfer and excited electron dynamics. The periodic RT-NEO-TDDFT approach is applicable to a wide range of other photoinduced heterogeneous processes.

physics.chem-ph↗

arXiv2023

Electronic Excitation Response of DNA to High-energy Proton Radiation in Water

The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer therapies. In particular, the dependence of different types of DNA damage on high-energy protons represents a significant knowledge void. Here we employ first-principles real-time time-dependent density functional theory simulation, using a massively-parallel supercomputer, to unravel the quantum-mechanical details of the energy transfer from high-energy protons to DNA in water. The calculations reveal that protons deposit significantly more energy onto the DNA sugar-phosphate side chains than onto the nucleobases, and greater energy transfer is expected onto the DNA side chains than onto water. As a result of this electronic stopping process, highly energetic holes are generated on the DNA side chains as a source of oxidative damage.

cond-mat.soft↗

arXiv2022

First-Principles Demonstration of Non-adiabatic Thouless Pumping of Electrons in A Molecular System

We demonstrate nonadiabatic Thouless pumping of electrons in trans-polyacetylene in the framework of Floquet engineering using first-principles theory. We identify the regimes in which the quantized pump is operative with respect to the driving electric field for a time-dependent Hamiltonian. By employing the time-dependent maximally localized Wannier functions in real-time time-dependent density functional theory simulation, we connect the winding number, a topological invariant, to a molecular-level understanding of the quantized pumping. While the pumping dynamics constitutes the opposing movement of the Wannier functions that represent both double and single bonds, the resulting current is unidirectional due to the greater number of double-bond electrons. Using a gauge-invariant formulation called dynamical transition orbitals, an alternative viewpoint on the nonequilibrium dynamics is obtained in terms of the particle-hole excitation. A single time-dependent transition orbital is found to be largely responsible for the observed quantized pumping. In this representation, the pumping dynamics manifests itself in the dynamics of this single orbital as it undergoes changes from its π bonding orbital character at equilibrium to acquiring resonance and antibonding character in the driving cycle. The work demonstrates the Floquet engineering of the nonadiabatic topological state in an extended molecular system, paving the way for experimental realization of the new quantum material phase.

cond-mat.mtrl-sci↗

arXiv2022

Nuclear-Electronic Orbital Approach to Quantization of Protons in Periodic Electronic Structure Calculations

The nuclear-electronic orbital (NEO) method is a well-established approach for treating nuclei quantum mechanically in molecular systems beyond the usual Born-Oppenheimer approximation. In this work, we present a strategy to implement the NEO method for periodic electronic structure calculations, particularly focused on multicomponent density functional theory (DFT). The NEO-DFT method is implemented in an all-electron electronic structure code, FHI-aims, using a combination of analytical and numerical integration techniques as well as a resolution of the identity scheme to enhance computational efficiency. After validating this implementation, proof-of-concept applications are presented to illustrate the effects of quantized protons on the physical properties of extended systems such as two-dimensional materials and liquid-semiconductor interfaces. Specifically, periodic NEO-DFT calculations are performed for a trans-polyacetylene chain, a hydrogen boride sheet, and a titanium oxide-water interface. The zero-point energy effects of the protons, as well as electron-proton correlation, are shown to noticeably impact the density of states and band structures for these systems. These developments provide a foundation for the application of multicomponent DFT to a wide range of other extended condensed matter systems.

physics.comp-ph↗

arXiv2022

Electron dynamics in extended systems within real-time time-dependent density functional theory

Due to a beneficial balance of computational cost and accuracy, real-time time-dependent density functional theory has emerged as a promising first-principles framework to describe electron real-time dynamics. Here we discuss recent implementations around this approach, in particular in the context of complex, extended systems. Results include an analysis of the computational cost associated with numerical propagation and when using absorbing boundary conditions. We extensively explore the shortcomings for describing electron-electron scattering in real time and compare to many-body perturbation theory. Modern improvements of the description of exchange and correlation are reviewed. In this work, we specifically focus on the Qb@ll code, which we have mainly used for these types of simulations over the last years, and we conclude by pointing to further progress needed going forward.

cond-mat.mtrl-sci↗

arXiv2019

Ab Initio Bethe-Salpeter Equation Approach to Neutral Excitations in Molecules with Numeric Atom-Centered Orbitals

The Bethe-Salpeter equation (BSE) based on GW quasiparticle levels is a successful approach for calculating the optical gaps and spectra of solids and also for predicting the neutral excitations of small molecules. We here present an all-electron implementation of the GW+BSE formalism for molecules, using numeric atom-centered orbital (NAO) basis sets. We present benchmarks for low-lying excitation energies for a set of small organic molecules, denoted in the literature as "Thiel's set". Literature reference data based on Gaussian-type orbitals are reproduced to about one meV precision for the molecular benchmark set, when using the same GW quasiparticle energies and basis sets as the input to the BSE calculations. For valence correlation consistent NAO basis sets, as well as for standard NAO basis sets for ground state density-functional theory with extended augmentation functions, we demonstrate excellent convergence of the predicted low-lying excitations to the complete basis set limit. A simple and affordable augmented NAO basis set denoted "tier2+aug2" is recommended as a particularly efficient formulation for production calculations. We finally demonstrate that the same convergence properties also apply to linear-response time-dependent density functional theory within the NAO formalism.

cond-mat.mtrl-sci↗