| 1. |
Yoshiaki Niidome, Hiromu Matsumoto, Ryo Hamano, Koichiro Kato, Tsuyohiko Fujigaya, Tomohiro Shiraki, Polymer Wrapping State Changes at Defect Sites of Locally Functionalized Single-Walled Carbon Nanotubes, The Journal of Physical Chemistry C, 10.1021/acs.jpcc.3c07692, 2024.03. |
| 2. |
Takashi Miyano, Yasunori Ayukawa, Takahisa Anada, Ichiro Takahashi, Hiroko Furuhashi, Shoji Tokunaga, Akie Hirata, Naoki Nakashima, Koichiro Kato, Haruhisa Fukuda, Association Between Reduced Posterior Occlusal Contact and Alzheimer’s Disease Onset in Older Japanese Adults: Results from the LIFE Study, Journal of Alzheimer's Disease, 10.3233/jad-230449, 97, 2, 871-881, 2024.01, Background: An association between poor oral health and cognitive decline has been reported. Most of these studies have considered the number of teeth as a criterion, only a few studies have analyzed the relationship between occlusal status and Alzheimer’s disease (AD). Objective: To elucidate whether posterior occlusal contact is associated with AD, focusing on the Eichner classification, among an older population aged 65 years or older in Japan. Methods: This study used monthly claims data of National Health Insurance in Japan from April 2017 to March 2020. The outcome was newly diagnosed AD defined according to ICD-10 code G30. The number of teeth was estimated by dental code data, and occlusal contact was divided into three categories, namely A, B, and C, according to the Eichner classification. Multivariate Cox proportional hazards models were used to analyze the association between a new diagnosis of AD and the Eichner classification. Results: A total of 22,687 participants were included, 560 of whom had newly diagnosed AD during a mean follow-up period of 12.2 months. The AD participants had a lower proportion of Eichner A and a higher proportion of Eichner C. After adjusting for covariates, hazard ratios (95% confidence intervals) with Eichner B and C were 1.34 (1.01–1.77) and 1.54 (1.03–2.30), respectively. Conclusion: In older people aged≥65 years old, reduced posterior occlusal contact as well as tooth loss have an impact on AD. This study emphasizes the importance of paying attention to occlusal contacts to reduce the risk of AD.. |
| 3. |
Ryo Kanada, Atsushi Tokuhisa, Yusuke Nagasaka, Shingo Okuno, Koichiro Amemiya, Shuntaro Chiba, Gert-Jan Bekker, Narutoshi Kamiya, Koichiro Kato, Yasushi Okuno, Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model., Journal of chemical theory and computation, 10.1021/acs.jctc.3c00889, 20, 1, 7-17, 2024.01, In all-atom (AA) molecular dynamics (MD) simulations, the rugged energy profile of the force field makes it challenging to reproduce spontaneous structural changes in biomolecules within a reasonable calculation time. Existing coarse-grained (CG) models, in which the energy profile is set to a global minimum around the initial structure, are unsuitable to explore the structural dynamics between metastable states far away from the initial structure without any bias. In this study, we developed a new hybrid potential composed of an artificial intelligence (AI) potential and minimal CG potential related to the statistical bond length and excluded volume interactions to accelerate the transition dynamics while maintaining the protein character. The AI potential is trained by energy matching using a diverse structural ensemble sampled via multicanonical (Mc) MD simulation and the corresponding AA force field energy, profile of which is smoothed by energy minimization. By applying the new methodology to chignolin and TrpCage, we showed that the AI potential can predict the AA energy with significantly high accuracy, as indicated by a correlation coefficient (R-value) between the true and predicted energies exceeding 0.89. In addition, we successfully demonstrated that CGMD simulation based on the smoothed hybrid potential can significantly enhance the transition dynamics between various metastable states while preserving protein properties compared to those obtained with conventional CGMD and AAMD.. |
| 4. |
Naoki Tanaka, Aoi Hamasuna, Itsuki Yamaguchi, Koichiro Kato, Tsuyohiko Fujigaya, Pyridine-mediated B–B bond cleavage of tetrahydroxydiboron to synthesize n-doped SWCNTs with long-term air stability, Scientific Reports, 10.1038/s41598-023-48847-2, 13, 1, 2023.12, Abstract
Neutral radicals, including carbon radicals, are highly useful chemical species for the functionalization of semiconducting materials to change their electrical and optical properties owing to their high reactivity. However, boron radicals have been limited to synthetic and reaction chemistry, with rare utilization in materials science. In this study, a mixture of tetrahydroxydiboron (B2(OH)4) and pyridine derivatives was found to act as an electron dopant for single-walled carbon nanotubes (SWCNTs) because of the electron transfer from pyridine-mediated boron radicals generated by B–B bond dissociation to neutral radicals. In particular, the radical formed from a mixture of B2(OH)4 and 4-phenylpyridine ((4-Phpy)B(OH)2·) efficiently doped electrons into the SWCNT films; thus, n-type SWCNTs with long-term air stability for more than 50 days at room temperature were prepared. Furthermore, the experimental and theoretical surface analyses revealed that the formation of stable cations from ((4-Phpy)B(OH)2·) and the efficient interaction with SWCNTs due to their high planarity served as the mechanism for their stable doping.. |
| 5. |
Yin Kan Phua, Tsuyohiko Fujigaya, Koichiro Kato, Predicting the anion conductivities and alkaline stabilities of anion conducting membrane polymeric materials: development of explainable machine learning models, Science and Technology of Advanced Materials, 10.1080/14686996.2023.2261833, 24, 1, 2023.10, Anion exchange membranes (AEMs) are core components in fuel cells and water electrolyzers, which are crucial to realize a sustainable hydrogen society. The low anion conductivity and durability of AEMs have hindered the commercialization of AEM-based devices, and research and development (R&D) to improve AEM materials is often resource-intensive. Although machine learning (ML) is commonly used in many fields to accelerate R&D while reducing resource consumption, it is rarely used in the AEM field. Three problems hinder the adoption of ML models, namely, the low explainability of ML models; complication with expressing both homopolymers and copolymers in unity to train a single ML model; and difficulty in building a single ML model that comprehends various polymer types. This study presents the first ML models that solve all three problems. Our models predicted the anion conductivity for a diverse set of unseen AEM materials with high accuracy (root mean squared error = 0.014 S cm−1), regardless of their state (freshly synthesized or degraded). This enables virtual pre-synthesis screening of novel AEM materials, reducing resource consumption. Moreover, human-comprehensible prediction logic revealed new factors affecting the anion conductivity of AEM materials. Such capability to reveal new important variables for AEM materials design could shift the paradigm of AEM R&D. This proposed method is not limited to AEM materials, instead it presents a technology that is applicable to the diverse set of polymers currently available.. |
| 6. |
Koichiro Kato, Ami Yamamoto, Chiduru Watanabe, Kaori Fukuzawa, Application of Model Core Potentials to Zn- and Mg-containing Metalloproteins in the Fragment Molecular Orbital Method, Chem-Bio Informatics Journal, https://doi.org/10.1273/cbij.23.14, 23, 14-25, 2023.09. |
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Kotaro Koiwai, Kazue Inaba, Kana Morohashi, Sora Enya, Reina Arai, Hirotatsu Kojima, Takayoshi Okabe, Yuuta Fujikawa, Hideshi Inoue, Ryunosuke Yoshino, Takatsugu Hirokawa, Koichiro Kato, Kaori Fukuzawa, Yuko Shimada-Niwa, Akira Nakamura, Fumiaki Yumoto, Toshiya Senda, Ryusuke Niwa, An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo., The Journal of biological chemistry, 10.1074/jbc.RA119.011463, 295, 20, 7154-7167, 2020.05, Ecdysteroids are the principal steroid hormones essential for insect development and physiology. In the last 18 years, several enzymes responsible for ecdysteroid biosynthesis encoded by Halloween genes were identified and genetically and biochemically characterized. However, the tertiary structures of these proteins have not yet been characterized. Here, we report the results of an integrated series of in silico, in vitro, and in vivo analyses of the Halloween GST protein Noppera-bo (Nobo). We determined crystal structures of Drosophila melanogaster Nobo (DmNobo) complexed with GSH and 17β-estradiol, a DmNobo inhibitor. 17β-Estradiol almost fully occupied the putative ligand-binding pocket and a prominent hydrogen bond formed between 17β-estradiol and Asp-113 of DmNobo. We found that Asp-113 is essential for 17β-estradiol-mediated inhibition of DmNobo enzymatic activity, as 17β-estradiol did not inhibit and physically interacted less with the D113A DmNobo variant. Asp-113 is highly conserved among Nobo proteins, but not among other GSTs, implying that this residue is important for endogenous Nobo function. Indeed, a homozygous nobo allele with the D113A substitution exhibited embryonic lethality and an undifferentiated cuticle structure, a phenocopy of complete loss-of-function nobo homozygotes. These results suggest that the nobo family of GST proteins has acquired a unique amino acid residue that appears to be essential for binding an endogenous sterol substrate to regulate ecdysteroid biosynthesis. To the best of our knowledge, ours is the first study describing the structural characteristics of insect steroidogenic Halloween proteins. Our findings provide insights relevant for applied entomology to develop insecticides that specifically inhibit ecdysteroid biosynthesis.. |
| 8. |
Koichiro Kato, Kaori Fukuzawa, Yuji Mochizuki, Modeling of hydroxyapatite-peptide interaction based on fragment molecular orbital method, Chemical Physics Letters, 10.1016/j.cplett.2015.03.057, 629, 58-64, 2015.06, Abstract We have applied the four-body corrected fragment molecular orbital (FMO4) calculations to analyze the interaction between a designed peptide motif (Glu1-Ser2-Gln3-Glu4-Ser5) and the hydroxyapatite (HA) solid mimicked by a cluster model consisting of 1408 atoms. To incorporate statistical fluctuations, a total of 30 configurations were generated through classical molecular dynamics simulation with water molecules and were subjected to FMO4 calculations at the MP2 level. It was found that Ser5 plays a leading role in interacting with the phosphate moieties of HA via charge transfer and also that negatively charged Glu1 and Glu4 provide electrostatic stabilizations with the calcium ions.. |
| 9. |
Koichiro Kato, Takashi Koretsune, Susumu Saito, Energetics and electronic properties of twisted single-walled carbon nanotubes, Physical Review B - Condensed Matter and Materials Physics, 10.1103/PhysRevB.85.115448, 85, 11, 2012.03, We perform a systematic first-principles study of energetics and electronic properties of chiral carbon nanotubes (CNTs) in the density-functional theory. It is found that chiral CNTs possess slightly twisted ground-state geometries. Moderate-diameter CNTs show twisting-dependent electronic properties well classified by their chiral indices, while the electronic structures of small-diameter CNTs possess sizable but individually different twisting dependences, leading to metal-semiconductor transitions in some CNTs. The CNT having the widest fundamental gap is predicted to be the twisted (4,3) CNT. © 2012 American Physical Society.. |
| 10. |
Koichiro Kato, Susumu Saito, Geometries, electronic structures and energetics of small-diameter single-walled carbon nanotubes, Physica E: Low-Dimensional Systems and Nanostructures, 10.1016/j.physe.2010.07.025, 43, 3, 669-672, 2011.01, We study the detailed geometries, electronic structures and energetics of small-diameter single-walled carbon nanotubes in the framework of the density functional theory with the local density approximation. In the present work, we study 41 kinds of nanotubes including 16 chiral nanotubes. It is found that electronic properties of optimized nanotubes as well as their geometrical properties depend strongly on not only diameter but also chiral angle. The largest difference from graphene values for both bond lengths and bond angles is found in zigzag nanotubes among all the nanotubes with similar diameters. Interestingly, the bond length decreases relative to that of graphene when the angle between the bond direction and tube axis is less than about 22°. As for the electronic structures, because of significant curvature effect, the band gap values of small-diameter nanotubes are show significant deviation from the classification from the tight-binding study. Interestingly, we also find that so-called "near-armchair" nanotubes have large band gaps even in the small-diameter region. © 2010 ElsevierB.V. All rights reserved.. |
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Yasuhiko Tanaka, Yasuhiko Hirana, Yasuro Niidome, Koichiro Kato, Susumu Saito, Naotoshi Nakashima, Experimentally determined redox potentials of individual (n,m) single-walled carbon nanotubes, Angewandte Chemie - International Edition, 10.1002/anie.200902468, 48, 41, 7655-7659, 2009.09, Nanotubes reveal their potential: The fabrication of a thin film that retains isolated singlewalled nanotubes (SWNTs) allows the experimental determination of the redox potentials of many individual SWNTs that have different chirality indexes (n,m). The method is simple and applicable to all individual SWNTs whose near-IR photoluminescence (PL) is detectable (see picture). © 2009 Wiley-VCH Verlag GmbH &
Co. KGaA.. |
