Shoji Mitsuo

J-GLOBAL         Last updated: Sep 19, 2019 at 02:43
Shoji Mitsuo
University of Tsukuba
Center for Computational Sciences
Job title
Assistant Professor

Published Papers

庄司, 光男
アンサンブル : 分子シミュレーション研究会会誌   40(4) 222-222   Oct 2018
庄司, 光男
アンサンブル : 分子シミュレーション研究会会誌   40(4) 238-242   Oct 2018   [Refereed]
Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα
Yamamoto, Yuta;Takei, Kenta;Arulmozhiraja, Sundaram;Sladek, Vladimir;Matsuo, Naoya;Han, Song-Iee;Matsuzaka, Takashi;Sekiya, Motohiro;Tokiwa, Takaki;Shoji, Mitsuo;Shigeta, Yasuteru;Nakagawa, Yoshimi;Tokiwa, Hiroaki;Shimano, Hitoshi
Biochemical and biophysical research communications      May 2018
木間塚政人;佐藤竜馬;原田隆平;庄司, 光男;重田, 育照
Journal of Computer Chemistry, Japan   17(5) 222-224   Mar 2019   [Refereed]
<p>Antifreezing nature of an antifreezing proteins (AFPs) from Rhagium inquisitor, RiAFP, was assessed by means of molecular dynamics (MD) simulations of RiAFP adsorbing ice surface in water below melting temperature to investigate how RiAFP affec...
Kyan, Akane; Kayanuma, Megumi; Shoji, Mitsuo; Shigeta, Yasuteru
CHEMICAL PHYSICS LETTERS   725 114-118   Jun 2019   [Refereed]
Kimatsuka, Masato;Sato, Ryuma;Harada, Ryuhei;Shoji, Mitsuo;Shigeta, Yasuteru
Chemistry Letters   48(3) 223-226   Mar 2019   [Refereed]
Yamaguchi, Kizashi; Yamanaka, Shusuke; Isobe, Hiroshi; Shoji, Mitsuo; Miyagawa, Kouichi; Nakajima, Takahito; Kawakami, Takashi; Okumura, Mitsutaka
Physiologia plantarum   166(1:::SI) 44-59   Mar 2019   [Refereed]
The optimized geometries of the CaMn O (X=5, 6) cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) by large-scale quantum mechanics (QM) and molecular mechanics (MM) calculations are compared with recent serial femtosecond cryst...
Isobe, Hiroshi; Shoji, Mitsuo; Suzuki, Takayoshi; Shen, Jian-Ren; Yamaguchi, Kizashi
Journal of chemical theory and computation   15(4) 2375-2391   Apr 2019   [Refereed]
Photosynthetic water oxidation is catalyzed by a MnCaO-cluster in photosystem II through an S-state cycle. Understanding the roles of heterogeneity in each S-state, as identified recently by the EPR spectroscopy, is very important to gain a comple...
Kayanuma, Megumi; Shoji, Mitsuo; Shigeta, Yasuteru
The journal of physical chemistry. A   123(13) 2497-2502   Mar 2019   [Refereed]
The photoinduced ligand exchange reaction of Ru(II) complexes in aqueous solution was studied using density functional theory (DFT). The optimized structures of the lowest triplet state of cis-[Ru(bpy)(CHCN)] (bpy = bipyridine), cis-[Ru(bpy)(NH)],...
Tokiwa, Takaki; Shoji, Mitsuo; Sladek, Vladimir; Shibata, Naoki; Higuchi, Yoshiki; Kataoka, Kunishige; Sakurai, Takeshi; Shigeta, Yasuteru; Misaizu, Fuminori
Molecules (Basel, Switzerland)   24(1)    Jan 2019   [Refereed]
Geometric and electronic structure changes in the copper (Cu) centers in bilirubin oxidase (BOD) upon a four-electron reduction were investigated by quantum mechanics/molecular mechanics (QM/MM) calculations. For the QM region, the unrestricted de...
Shoji, Mitsuo; Isobe, Hiroshi; Yamaguchi, Kizashi
CHEMICAL PHYSICS LETTERS   714 219-226   Jan 2019   [Refereed]
Kayanuma, Megumi; Shoji, Mitsuo; Furuya, Kenji; Aikawa, Yuri; Umemura, Masayuki; Shigeta, Yasuteru
CHEMICAL PHYSICS LETTERS   714 137-142   Jan 2019   [Refereed]
Bulletin of the Chemical Society of Japan   91(10) 1465-1473   Jul 2018   [Refereed]
<p>We propose a new algorithm that can be practically applied for searching molecular conformations without specifying the explicit reaction coordinates in advance. The basic idea is to introduce repulsive interactions among all the sampling struc...
Kawakami, Takashi; Miyagawa, Koichi; Sharma, Sandeep; Saito, Toru; Shoji, Mitsuo; Yamada, Satoru; Yamanaka, Shusuke; Okumura, Mitsutaka; Nakajima, Takahito; Yamaguchi, Kizashi
Journal of computational chemistry   40(2:::SI) 333-341   Oct 2018   [Refereed]
Both direct exchange and super-exchange interactions cooperate to realize inter-spin magnetic interaction in binuclear manganese complex Mn(IV) O (NHCHCO ) with a di-μ-oxo path. We revisited this spin system using DMRG CAS methods and CAS selectio...
Kurniawan, Isman; Kawaguehi, Kazutomo; Shoji, Mitsuo; Matsui, Toru; Shigeta, Yasuteru; Nagao, Hidemi
Bulletin of the Chemical Society of Japan   91(9) 1451-1456   Sep 2018   [Refereed]
Akter, Mahfuza; Tokiwa, Takaki; Shoji, Mitsuo; Nishikawa, Koji; Shigeta, Yasuteru; Sakurai, Takeshi; Higuchi, Yoshiki; Kataoka, Kunishige; Shibata, Naoki
Chemistry (Weinheim an der Bergstrasse, Germany)   24(68) 18052-18058   Aug 2018   [Refereed]
Bilirubin oxidase (BOD) belongs to the family of blue multicopper oxidases, and catalyzes the concomitant oxidation of bilirubin to biliverdin and the reduction of molecular oxygen to water via a four-electron reduction system. The active sites of...
Kayanuma, Megumi;Kidachi, Kaori;Shoji, Mitsuo;Komatsu, Yu;Sato, Akimasa;Shigeta, Yasuteru;Aikawa, Yuri;Umemura, Masayuki
Chem Phys Lett   687 178-183   Nov 2017   [Refereed]
Sato, Akimasa;Kitazawa, Yuya;Ochi, Toshiro;Shoji, Mitsuo;Komatsu, Yu;Kayanuma, Megumi;Aikawa, Yuri;Umemura, Masayuki;Shigeta, Yasuteru
Molecular Astrophysics   10 11-19   Mar 2018   [Refereed]
Seibutsu Butsuri   58(3) 127-133   May 2018   [Refereed]
<p>Photosystems are natural energy conversion systems evolved for over 2,700 million years. Among the photosystems, photosystem II (PSII) catalyzes the light-driven water decomposition reaction with the production of O2, protons and el...
Shoji, Mitsuo; Isobe, Hiroshi; Shigeta, Yasuteru; Nakajima, Takahito; Yamaguchi, Kizashi
The journal of physical chemistry. B   122(25) 6491-6502   Jun 2018   [Refereed]
The O release of the oxygen-evolving complex of the photosystem II (PSII) is one of the essential processes responsible for the highly efficient O production. Despite its importance, the detailed molecular mechanism is still unsolved. In the prese...
Sano, Shinsuke;Kawakami, Takashi;Yoshimura, Shohei;Shoji, Mitsuo;Yamanaka, Shusuke;Okumura, Mitsutaka;Nakajima, Takahito;Yamaguchi, Kizashi
Polyhedron   136(4) 159-169   Nov 2017   [Refereed]
Yamaguchi, Kizashi;Mitsuo, Shoji;Isobe, Hiroshi;Yamanaka, Shusuke;Kawakami, Takashi;Yamada, Satoru;Katouda, Michio;Nakajima, Takahito
Molecular Physics   116(5-6) 717-745   Mar 2018   [Refereed]
Sato, Akimasa;Kitazawa, Yuya;Ochi, Toshiro;Shoji, Mitsuo;Komatsu, Yu;Kayanuma, Megumi;Aikawa, Yuri;Umemura, Masayuki;Shigeta, Yasuteru
Molecular Astrophysics   10 11-19   Jan 2018   [Refereed]
Glycine, the simplest amino acid, has been intensively searched for in molecular clouds, and the comprehensive clarification of the formation path of interstellar glycine is now imperative. Among all the possible glycine formation pathways, we foc...
Shoji, Mitsuo; Isobe, Hiroshi; Shigeta, Yasuteru; Nakajima, Takahito; Yamaguchi, Kizashi
CHEMICAL PHYSICS LETTERS   698 138-146   Apr 2018   [Refereed]
Yamaguchi, Kizashi; Shoji, Mitsuo; Isobe, Hiroshi; Yamanaka, Shusuke; Kawakami, Takashi; Yamada, Satoru; Katouda, Michio; Nakajima, Takahito
MOLECULAR PHYSICS      Dec 2018   [Refereed]
Kawakami, Takashi; Sano, Shinsuke; Saito, Toru; Sharma, Sandeep; Shoji, Mitsuo; Yamada, Satoru; Takano, Yu; Yamanaka, Shusuke; Okumura, Mitsutaka; Nakajima, Takahito; Yamaguchi, Kizashi
MOLECULAR PHYSICS   115(17-18) 2154-2167   Mar 2017   [Refereed]
Ujiie, Yuzuru; Tanaka, Wataru; Hanaoka, Kyohei; Harada, Ryuhei; Kayanuma, Megumi; Shoji, Mitsuo; Murakawa, Takeshi; Ishida, Toyokazu; Shigeta, Yasuteru; Hayashi, Hideyuki
The journal of physical chemistry. B   121(22) 5536-5543   May 2017   [Refereed]
Threonine synthase (ThrS) catalyzes the final chemical reaction of l-threonine biosynthesis from its precursor, O-phospho-l-homoserine. As the phosphate ion generated in its former half reaction assists its latter reaction, ThrS is recognized as o...
Shoji, Mitsuo; Isobe, Hiroshi; Nakajima, Takahito; Shigeta, Yasuteru; Suga, Michihiro; Akita, Fusamichi; Shen, Jian-Ren; Yamaguchi, Kizashi
Faraday discussions   198 83-106   Mar 2017   [Refereed]
Large-scale QM/MM calculations were performed to elucidate an optimized geometrical structure of a CaMn4O5 cluster with and without water insertion in the S3 state of the oxygen evolving complex (OEC) of photosystem II (PSII). The left (L)-opened ...
Abe, Yukihiro; Shoji, Mitsuo; Nishiya, Yoshiaki; Aiba, Hiroshi; Kishimoto, Takahide; Kitaura, Kazuo
Physical chemistry chemical physics : PCCP   19(15) 9811-9822   Mar 2017   [Refereed]
Monomeric sarcosine oxidase (MSOX) is a flavoprotein that oxidizes sarcosine to the corresponding imine product and is widely used in clinical diagnostics to test renal function. In the past decade, several experimental studies have been performed...
Yamaguchi, K.;Shoji, M.;Isobe, H.;Yamanaka, S.;Umena, Y.;Kawakami, K.;Kamiya, N.
MOLECULAR PHYSICS   115(5:::SI) 636-666   Feb 2017   [Refereed]
Solvation Energy of Proton: a Consistent Calculation Schemefor Acid Dissociation Constantsand Standard Hydrogen Electrode Potentials
Journal of Computer Chemistry, Japan   15(5) 184-191   2016
<p>We here review a scheme for estimating the acid dissociation constant (pKa) based on quantum-chemical calculations combined with a polarizable continuum model, where a parameter is determined for small refe...
Molecular dynamics study on the key catalytic intermediates of threonine synthase
Shoji, Mitsuo; Ujiie, Yuzuru; Harada, Ryuhei; Kayanuma, Megumi; Shigeta, Yasuteru; Murakawa, Takeshi; Hayashi, Hideyuki
PROTEIN SCIENCE   24(1:SI) 18-18   Oct 2015   [Refereed]
GPU-accelerated FMO Calculation with OpenFMO: Four-Center Inter-Fragment Coulomb Interaction
Journal of Chemical Software   14(3) 69-70   2015   [Refereed]
GPU acceleration of four-center (4C) inter-fragment Coulomb interaction term (IFC) for OpenFMO, a fragment molecular orbital calculation program, has been implemented and its performance was examined. FMO calculation has two time...
林, 秀行; 村川, 武志; 庄司, 光男
Vitamins   89(3) 162-163   Mar 2015   [Refereed]
Chemical Physics Letters   634 181-187   Aug 2015   [Refereed]
Computational costs with the use of the initial guesses formed by the divide-and-conquer approach are examined. For conventional density functional theory calculations, their computational costs rapidly increase as the system sizes increase, there...
Hanaoka, Kyohei; Tanaka, Wataru; Kayanuma, Megumi; Shoji, Mitsuo
CHEMICAL PHYSICS LETTERS   631 16-20   Jul 2015
Performance Benchmark of FMO Calculation with GPU-Accelerated Fock Matrix Preparation Routine
Journal of Chemical Software   13(6) 323-324   2015   [Refereed]
GPU acceleration for OpenFMO, a fragment molecular orbital calculation program, has been implemented and its performance was examined. We have developed a GPU-accelerated Fock matrix preparation routine without atomic operation and implemented it ...
Nagai, Masako; Kobayashi, Chika; Nagai, Yukifumi; Imai, Kiyohiro; Mizusawa, Naoki; Sakurai, Hiroshi; Neya, Saburo; Kayanuma, Megumi; Shoji, Mitsuo; Nagatomo, Shigenori
JOURNAL OF PHYSICAL CHEMISTRY B   119(4) 1275-1287   Jan 2015   [Refereed]
Kayanuma, Megumi; Hanaoka, Kyohei; Shoji, Mitsuo; Shigeta, Yasuteru
CHEMICAL PHYSICS LETTERS   623 8-13   Mar 2015   [Refereed]
Shoji, Mitsuo; Isobe, Hiroshi; Yamanaka, Shusuke; Suga, Michihiro; Akita, Fusamichi; Shen, Jian-Ren; Yamaguchi, Kizashi
Shoji, Mitsuo; Isobe, Hiroshi; Yamanaka, Shusuke; Suga, Michihiro; Akita, Fusamichi; Shen, Jian-Ren; Yamaguchi, Kizashi
CHEMICAL PHYSICS LETTERS   627 44-52   May 2015
Shigeta, Yasuteru; Harada, Ryuhei; Kayanuma, Megumi; Shoji, Mitsuo
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY   115(5:::SI) 300-308   Mar 2015   [Refereed]
Chemical Physics Letters   608 50-54   Jul 2014   [Refereed]
A novel procedure to generate initial broken-symmetry solutions is proposed. Conventional methods for the initial broken-symmetry solutions are the MO alter, HOMO-LUMO mixing and fragment methods. These procedures, however, are quite complex. Our ...
Molecular Physics   112(3-4) 393-397   Feb 2014   [Refereed]
Nitrous oxide (N2O), with a greenhouse effect 300 times that of CO2, is increasingly eliminated into the atmosphere. Using a hybrid quantum mechanics/molecular mechanics (QM/MM) method, we examined nitric oxide reductase-catalysed N2O formation, w...
3. トレオニン合成酵素における生成物リン酸イオンの触媒作用のQM/MMによる解析(第433回研究協議会研究発表要旨,ビタミンB研究委員会)
林, 秀行; 村川, 武志; 庄司, 光男; 氏家, 謙
Vitamins   87(10) 582   Oct 2013   [Refereed]
Fock Matrix Preparation in Fragment Molecular Orbital Method with GPGPU
情報処理学会論文誌. コンピューティングシステム   6(4) 26-37   Oct 2013   [Refereed]
GPU acceralated Fock matrix preparation routine in OpenFMO program has been implemented with CUDA. Atomic operation less algorithm was proposed and implemented for the Fock matrix preparation. Applying several speedup techniques, such as screening...
梅田, 宏明;塙, 敏博;庄司, 光男;朴, 泰祐
IPSJ SIG Notes   2013-HPC-138(19) 1-7   Feb 2013
分子軌道計算のボトルネックである G 行列計算について CUDA による GPGPU 化を行なった.G 行列計算においては行列への加算に排他制御が必要であることが最も大きな問題となっている.我々は行列加算について排他制御を行なわない G 行列計算手法を提案し,その実装を行なった.またスクリーニングや動的負荷分散,CPU 計算とのオーバーラップなど,多くの高速化の技法を実装することにより CPU 1 コアに対し 13 倍程度の性能を実現している.元の分子軌道計算プログラムの持つ OpenMP...
Shoji, Mitsuo;Hanaoka, Kyohei;Sato, Akimasa;Kondo, Daiki;Yang, Moon Young;Kamiya, Katsumasa;Shiraishi, Kenji
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY   113(3:::SI) 342-347   Feb 2013   [Refereed]

Conference Activities & Talks

第46回生体分子科学討論会   21 Jun 2019   
分子構造探索および反応経路探索のための新手法(GLAS 法)の提唱
Shoji, Mitsuo
第21回理論化学討論会   16 May 2018   
A new approach for searching stable molecular structures by introducing repulsive interactions among walkers
Shoji, Mitsuo
7thJCS   21 May 2018   
A new algorithm searching stable molecular structures and reaction pathways by introducing repulsive interactions among walkers
Shoji, Mitsuo
ICQC 2018   20 Jun 2019   
Shoji, Mitsuo
第18回日本蛋白質科学会年会   26 Jun 2018