Article
Chemistry, Physical
Chinami Takashima, Junji Seino, Hiromi Nakai
Summary: This efficient algorithm for local unitary transformation, based on a spin-free infinite-order two-component relativistic method assisted by a one-center relativistic two-electron integral (TEI) database, is numerically assessed for various molecules and found to have lower computational cost compared to conventional methods, especially for small and medium-sized molecules.
CHEMICAL PHYSICS LETTERS
(2021)
Article
Physics, Multidisciplinary
Bijan Bagchi, Rahul Ghosh, Christiane Quesne
Summary: This study investigates the (1 + 1)-dimensional Dirac equation with position-dependent mass within the potential algebra of so(2,1) while considering a spatially varying Fermi velocity and an external pseudoscalar potential. Solutions to the three cases arising from so(2,1) are explored through a point canonical transformation.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
Review
Chemistry, Multidisciplinary
Hiromi Nakai
Summary: This article focuses on the theoretical developments of two-component relativistic quantum chemistry calculations, aiming for high efficiency and accuracy. It introduces new computation schemes, such as the local unitary transformation scheme, the divide-and-conquer scheme, and the frozen core potential scheme, as well as the accompanying coordinate expansion scheme with a transfer recurrence relation scheme.
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN
(2021)
Article
Mathematics
Dan Barbasch, Chao-Ping Dong, Kayue Daniel Wong
Summary: This paper computes the Dirac cohomology of irreducible unitary Harish-Chandra modules of complex classical groups viewed as real reductive groups, and shows that unitary representations with nonzero Dirac cohomology are induced from unipotent representations.
ADVANCES IN MATHEMATICS
(2022)
Article
Chemistry, Physical
Luca Nanni
Summary: The theory of relativity is not covered in theoretical chemistry courses, but it plays a significant role in studying the electronic structure of heavy elements. The laws of relativity, initially deemed unusual for chemistry, provide fundamental tools for investigating the properties of heavy atoms. Chemists can learn to master this relatively unfamiliar subject by studying the electronic structure of heavy elements and becoming familiar with its elegant formalism.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Albert Musaelian, Simon Batzner, Anders Johansson, Lixin Sun, Cameron J. Owen, Mordechai Kornbluth, Boris Kozinsky
Summary: This study introduces Allegro, a local equivariant deep neural network interatomic potential architecture that achieves excellent accuracy and scalability in quantum chemistry and molecular simulations.
NATURE COMMUNICATIONS
(2023)
Article
Mathematics, Applied
Lukas Heriban, Matej Tusek
Summary: This sentence describes the one-dimensional Dirac operator with a singular interaction term.
JOURNAL OF MATHEMATICAL ANALYSIS AND APPLICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Jeong Ryeol Choi
Summary: In this work, a theoretical model is proposed to analyze the quantum characteristics of a superconducting flux qubit-oscillator. By using a unitary transformation approach, quantum solutions are obtained and the energy levels of the combined system (qubit + resonator) are analyzed in detail. The coupling between the qubit and the resonator induces bifurcation of the resonator states, enabling quantum nondemolition dispersive measurements of the qubit states.
Article
Chemistry, Multidisciplinary
Shaosheng Yue, Hui Zhou, Ya Feng, Yue Wang, Zhenyu Sun, Daiyu Geng, Masashi Arita, Shiv Kumar, Kenya Shimada, Peng Cheng, Lan Chen, Yugui Yao, Sheng Meng, Kehui Wu, Baojie Feng
Summary: This study investigates the existence and properties of one-dimensional Dirac fermions in Si nanoribbons (SiNRs) through various experimental and theoretical approaches. The results provide a theoretical explanation and establish SiNRs as a platform for studying one-dimensional Dirac materials.
Article
Computer Science, Interdisciplinary Applications
G. Gaigalas, D. Kato
Summary: The latest version of the grasp2018 package extends the multiconfigurational Dirac-Hartree-Fock method to account for crystal field effects in complex systems. Instead of using simplified treatments, this program uses a fully ab-initio method to handle crystal field effects, with examples provided in the source directory for CF_Hamiltonian program usage.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Alan Sena Pinheiro, Ricardo Gargano, Paulo Henrique Gomes dos Santos, Luiz Guilherme Machado de Macedo
Summary: This study investigated relativistic effects and Gaunt effects in polyatomic E121X(3) (X = F, Cl, Br) using different Hamiltonians. Results showed the importance of relativistic effects in obtaining reliable vibrational frequencies and the potential of using X2C spin-free Hamiltonian for cost-effective research on polyatomics, including superheavy elements. The comparison between ELF and Mulliken population analysis indicated bonding similarity between LaBr3 and E121Br(3).
JOURNAL OF MOLECULAR MODELING
(2021)
Article
Chemistry, Multidisciplinary
Gerardo Gonzalez, S. A. Alexander, R. L. Coldwell
Summary: This paper investigates the decay rate calculation formulas for relativistic hydrogenic atom. Previous formulas are based on two-component atomic wavefunctions, while this paper derives the working formulas using four-component wavefunctions and shows that both methods yield identical results.
JOURNAL OF MATHEMATICAL CHEMISTRY
(2023)
Article
Physics, Multidisciplinary
Sara Hassoul, Salah Menouar, Hamid Benseridi, Jeong Ryeol Choi
Summary: This paper investigates the quantum dynamics of general time-dependent three coupled oscillators through an alternative approach based on unitary transformation. By decoupling the system and diagonalizing the transformed Hamiltonian, the coupled oscillatory subsystems are completely decoupled, enabling the development of an exact theory for mechanical treatment of the originally-coupled systems without any restrictions on the time-varying parameters.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2022)
Article
Mathematics, Applied
Yunhui He
Summary: Local Fourier analysis (LFA) plays an important role in predicting the convergence factor of multigrid methods for discretizations of PDEs. The study demonstrates that the LFA representation for d-dimensional PDEs is independent of the placement of degrees of freedom (DoFs), providing a simple and unified way to compute symbols of discrete operators. This simple representation can aid in generalizing the implementation of LFA for different discretizations and higher order methods.
NUMERICAL LINEAR ALGEBRA WITH APPLICATIONS
(2021)
Article
Physics, Multidisciplinary
Meng-Li Qin, Xiao-Yong Wen, Cui-Lian Yuan
Summary: This paper investigates the relativistic Toda lattice system with one perturbation parameter alpha, abbreviated as RTL_(alpha) system, and constructs an integrable lattice hierarchy associated with it. Multi-soliton solutions, higher-order rational and semi-rational solutions are derived using the discrete generalized Darboux transformation. Numerical simulations show that a small noise has very little effect on soliton propagation.
COMMUNICATIONS IN THEORETICAL PHYSICS
(2021)
Article
Electrochemistry
Yusuke Onabuta, Masahiro Kunimoto, Fumimasa Ono, Yasuhiro Fukunaka, Hiromi Nakai, Giovanni Zangari, Takayuki Homma
Summary: This study investigates the morphological and structural characteristics of Zn electrodeposition with the addition of Pb. It is found that distinctive pillar-like Zn grows in the presence of Pb, with a specific orientation. Understanding the behavior of such deposited atoms provides insights into the effects and working mechanisms of additives.
ELECTROCHEMISTRY COMMUNICATIONS
(2022)
Article
Plant Sciences
Hiromi Nakai, Daisuke Yasutake, Kensuke Kimura, I Kengo, Kota Hidaka, Toshihiko Eguchi, Tomoyoshi Hirota, Takashi Okayasu, Yukio Ozaki, Masaharu Kitano
Summary: This study analyzed the dynamics of carbon export from strawberry leaves under field conditions and the effects of carbohydrate availability coordination on these dynamics. During the daytime, leaf starch synthesis and carbon export rate increased when sucrose concentration exceeded a certain threshold. In the nighttime, carbon export rate decreased with decreasing starch concentrations. These results highlight the role of leaf carbohydrate availability coordination in carbon export dynamics.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2022)
Article
Chemistry, Physical
Yoshifumi Nishimura, Hiromi Nakai
Summary: This article presents extensions to quantum chemical nanoreactor molecular dynamics simulations for discovering complex reactive events. The species-selective algorithm allows the nanoreactor to effectively work on the desired reactants. The divide-and-conquer linear-scaling density functional tight-binding method is used for efficient simulations of large model systems. Two examples, the polymerization of propylene and cyclopropane mixtures and the aggregation of sodium chloride from aqueous solutions, demonstrate the promising potential of species-selective quantum chemical nanoreactor molecular dynamics in accelerating the sampling of multicomponent chemical processes under mild conditions.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Hiromi Nakai, Masato Kobayashi, Takeshi Yoshikawa, Junji Seino, Yasuhiro Ikabata, Yoshifumi Nishimura
Summary: Fragmentation and embedding schemes are crucial in applying quantum-chemical calculations to complex and attractive targets. This feature article discusses the DC-based schemes developed by the authors over the last two decades, inspired by the pioneering study of the DC self-consistent field method. Theoretical aspects of DC-based SCF, electron correlation, excited-state, and nuclear orbital methods are described, along with the introduction of two-component relativistic theory, quantum-mechanical molecular dynamics simulation, and three programs including DC-based schemes. Illustrative applications demonstrate the accuracy and feasibility of the DC-based schemes.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Dentistry, Oral Surgery & Medicine
Hidetake Tachinami, Kei Tomihara, Shin-ichi Yamada, Atsushi Ikeda, Shuichi Imaue, Hideaki Hirai, Hiromi Nakai, Tomoko Sonoda, Kazuto Kurohara, Yukio Yoshioka, Takumi Hasegawa, Tomofumi Naruse, Takashi Niiyama, Tetsu Shimane, Michihiro Ueda, Souichi Yanamoto, Masaya Akashi, Masahiro Umeda, Hiroshi Kurita, Akihiro Miyazaki, Naoya Arai, Ryuji Hayashi, Makoto Noguchi
Summary: The immune checkpoint inhibitor nivolumab has greatly improved the treatment of recurrent and metastatic oral cancer. However, the response rate to nivolumab remains low, and there is a need to identify predictors of response. This study evaluated the association between neutrophil-to-lymphocyte ratio (NLR) and nivolumab treatment outcome in oral squamous cell carcinoma (OSCC) patients.
BRITISH JOURNAL OF ORAL & MAXILLOFACIAL SURGERY
(2023)
Article
Chemistry, Physical
Takeshi Yoshikawa, Yasuhiro Ikabata, Hiromi Nakai, Kentaro Ogawa, Ken Sakata
Summary: Conical intersections (CIs) play a crucial role in various photophysical, photochemical, and photobiological processes, but the systematic interpretation of minimum energy CI (MECI) geometries is unclear. A previous study investigated the MECI between the ground and first excited electronic states (S0/S1 MECI) using frozen orbital analysis (FZOA), identifying two controlling factors. However, one of the factors was found to be invalid for spin-flip TDDFT (SF-TDDFT). This study revisited the controlling factors using FZOA for the SF-TDDFT method and confirmed the control factors of S0/S1 MECI through numerical applications of a revised formula.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Yoshifumi Nishimura, Hiromi Nakai
Summary: In this study, a large-scale quantum chemical calculation program, Dcdftbmd, was integrated with a Python-based advanced atomistic simulation program, i-PI. The implementation of a client-server model enabled hierarchical parallelization with respect to replicas and force evaluations. The established framework demonstrated that quantum path integral molecular dynamics simulations can be executed with high efficiency for systems consisting of a few tens of replicas and containing thousands of atoms. The application of the framework to bulk water systems, with and without an excess proton, demonstrated that nuclear quantum effects are significant for intra- and inter-molecular structural properties, including oxygen-hydrogen bond distance and radial distribution function around the hydrated excess proton.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Hiroki Uratani, Hiromi Nakai
Summary: In this study, real-time simulations were performed to investigate the charge-transfer processes in organic photovoltaic interfaces. The results revealed the importance of local structures and the coupling between nuclear and electronic dynamics in these processes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Chinami Takashima, Hiromi Nakai
Summary: The Cholesky decomposition and lower-upper decomposition methods were utilized to handle the two-electron integral matrices in an infinite-order two-component relativistic Hamiltonian. CD was used to calculate the symmetric TEI matrices, such as Coulomb-like and specific spin-free interaction terms, while LUD was used for the asymmetric TEI matrix, namely the Darwin-like term. Unitary transformation was performed on the decomposed matrices. Numerical assessments suggest that the proposed method can reduce the computational cost without sacrificing accuracy.
CHEMICAL PHYSICS LETTERS
(2023)
Article
Chemistry, Physical
Tatsuki Hanada, Hiroki Uratani, Hiromi Nakai
Summary: In this study, the feasibility of N?I phase transition by vibrational excitation using infrared irradiation is investigated. Nonadiabatic molecular dynamics approach combined with real-time electron dynamics at the level of a semiempirical quantum chemical model is used to simulate the photoinduced phase transition processes. The results highlight the importance of vibronic interactions in the phase transition, suggesting the possibility of N?I phase transition driven by vibrational excitations with infrared irradiation.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Permono Adi Putro, Aditya Wibawa Sakti, Faozan Ahmad, Hiromi Nakai, Husin Alatas
Summary: Extensive metadynamics simulations were conducted to accurately predict the maximum UV-Vis wavelength (Amax) values of capsanthin-based red natural dyes using the LC-TD-DFT-D4/?B97X/def2-SVP method, which exhibited the effect of conformational changes on calculated wavelengths. Additionally, the inexpensive and efficient LC-TD-DFTB method reproduced experimental ?(max) values insensitive to conformational changes.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Plant Sciences
Hiromi Nakai, Daisuke Yasutake, Kota Hidaka, Koichi Nomura, Toshihiko Eguchi, Gaku Yokoyama, Tomoyoshi Hirota
Summary: The allocation of carbon between sucrose and starch in plant leaves is a crucial factor affecting plant productivity. Previous studies have shown that strawberry plants accumulate starch in response to excess carbon from photosynthesis compared to sucrose storage capacity. This study aimed to investigate the role of starch in carbon allocation and whether the relationship between sucrose and starch is consistent across seasons. The results showed that starch production increased when sucrose concentration exceeded a certain threshold, indicating that starch serves as an overflow product during carbon allocation in strawberry leaves.
PLANT GROWTH REGULATION
(2023)
Article
Chemistry, Physical
Hiromi Nakai, Masato Kobayashi, Takeshi Yoshikawa, Junji Seino, Yasuhiro Ikabata, Yoshifumi Nishimura
Summary: Fragmentation and embedding schemes are crucial in quantum-chemical calculations for complex targets. This feature article presents various divide-and-conquer (DC)-based schemes developed by the authors, inspired by the pioneering study of DC self-consistent field method. It covers theoretical aspects of DC-based SCF, electron correlation, excited-state, and nuclear orbital methods, as well as the introduction of two-component relativistic theory, quantum mechanical molecular dynamics simulation, and three programs. Illustrative applications validate the accuracy and feasibility of the DC-based schemes.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Hiroki Uratani, Hiromi Nakai
Summary: This study presents real-time simulations of charge-transfer processes in donor-acceptor interfaces of organic photovoltaics using a new computational method. The results provide atomic resolution insights into the charge-transfer pathway and explain the dependence of charge transfer on excitation energy. Moreover, the study demonstrates the significant role of nuclear motion in modulating the molecular orbital energies and influencing the charge-transfer process.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Materials Science, Composites
Dhea Afrisa Darmawan, Evi Yulianti, Qolby Sabrina, Kensuke Ishida, Aditya Wibawa Sakti, Hiromi Nakai, Edi Pramono, Sun Theo Constan Lotebulo Ndruru
Summary: This study investigates the effect of lithium acetate salt on carboxymethyl cellulose-based solid polymer electrolytes. The results show that the complex of 30% (wt) LiCH3COO salt with CMC exhibits good ionic conductivity and thermal stability.
POLYMER COMPOSITES
(2023)
