階層分子システム解析研究部門 論文・発表一覧
- Akiko Ueno, Fumiko Takida, Tomoki Kita, Takuro Ishii, Tomoki Himiyama, Takuya Mabuchi & Yasunori Okamoto
 A cytokine-based designer enzyme with an abiological multinuclear metal center exhibits intrinsic and extrinsic catalysis
 Nature Communications 16, 6781; doi: 10.1038/s41467-025-61909-5 (2025) 
- T. Ehara, Y. Yoneda, T. Yoshida, T. Ogawa, Y. Konishi, T. Ono, A. Muranaka, H. Kuramochi, K. Miyata, and K. Onda
 Dynamic Excited-State Localization Induced by Jahn?Teller Distortion Observed by Coherent Vibrational Spectroscopy
 J. Am. Chem. Soc. 147, 26446-26455 (2025). 
- Mukaiyama A, Furuike Y, Ito-Miwa K., Onoue Y, Horiuchi K, Kondo K, Yamashita E, Akiyama S
 Evolutionary Origins of Self-sustained Kai Protein Circadian Oscillators in Cyanobacteria
 Nature Communications 16 4541; doi: 10.1038/s41467-025-59908-7 (2025) 
- Takahiro Kosugi, Mikio Tanabe, Nobuyasu Koga
 De novo design of ATPase based on a blueprint optimized for harboring the P-loop motif
 Protein Science 34, e70132; https://doi.org/10.1002/pro.70132 (2025). 
- Furuike Y, Onoue Y, Saito S, Mori T, Akiyama S
 The priming phosphorylation of KaiC is activated by the release of its autokinase autoinhibition
 
- 小杉貴洋
 タンパク質複合体の合理的改造
 生体の科学 76, 2, 131-135 (2025). 
- Y. Yoneda, T. Konishi, K. Suga, S. Saito, and H. Kuramochi
 Excited-State Aromatization Drives Nonequilibrium Planarization Dynamics
 J. Am. Chem. Soc. 147, 12051-12060 (2025). 
- H. Watanabe, M. Iwamura, K. Nozaki, T. Takanashi, H. Kuramochi, and T. Tahara
 Torsional Structural Relaxation Caused by Pt?Pt Bond Formation in the Photoexcited Dimer of Pt(II) N ? C ? N Complex in Solution
 J. Phys. Chem. Lett., 16, 1, 406-414 (2025). 
- K. Suga, K. Ochiai, Y. Yoneda, H. Kuramochi, and S. Saito
 An Energy-Tunable Dual Emission Mechanism of the Hybridized Local and Charge Transfer (HLCT) and the Excited State Conjugation Enhancement (ESCE)
 Chem. Eur. J. e202404376 (2024). 
- Y. Yoneda and H. Kuramochi
 Room-Temperature Solution Fluorescence Excitation Correlation Spectroscopy
 J. Phys. Chem. Lett. 15, 8533-8539 (2024). 
- Inobe T, Sakaguchi R, Obita T, Mukaiyama A, Koike S, Yokoyama T, Mizuguchi M, Akiyama S
 Structural insights into rapamycin-induced oligomerization of a FRB?FKBP fusion protein
 
- Akiyama S, Furuike Y
 Autonomous Disassembly of circadian clock system of cyanobacteria at dawn
 Circadian Clocks in 2024, 89-97 (2025) 
- H. Kuramochi, T. Tsutsumi, K. Saita, Z. Wei, M. Osawa, P. Kumar, L. Liu, S. Takeuchi, T. Taketsugu, and T. Tahara
 Ultrafast Raman Observation of the Perpendicular Intermediate Phantom State of Stilbene Photoisomerization
 Nat. Chem. 16, 22-27 (2024). 
- Koya Sakuma, Naohiro Kobayashi, Toshihiko Sugiki, Toshio Nagashima,Toshimichi Fujiwara, Kano Suzuki, Naoya Kobayashi, Takeshi Murata, Takahiro Kosugi, Rie Tatsumi-Koga, and Nobuyasu Koga
 Design of complicated all-α protein structures
 Nature Structural and Molecular Biology; doi.org/10.1038/s41594-023-01147-9 (2024). 
- Furuike Y, Yamashita E, Akiyama S
 Structure-function relationship of KaiC around dawn
 Biophysics and Physicobiology; doi: 10.2142/biophysico.bppb-v21.0001 (2023) 
- 小杉 貴洋
 タンパク質設計技術で分子モーターを加速する
 現代化学 632, 11, 24-27 (2023) 
- R. Kimura, Y. Yoneda, H. Kuramochi, and S. Saito
 Environment-Sensitive Fluorescence of COT-Fused Perylene Bisimide Based on Symmetry-Breaking Charge Separation
 Photochemical & Photobiological Sciences 22, 2541-2522; doi.org/10.1007/s43630-023-00468-4 (2023). 
- S. Minami, N. Kobayashi, T. Sugiki, T. Nagashima, T. Fujiwara, R. Tatsumi-Koga, G. Chikenji, N. Koga
 Exploration of novel αβ-protein folds through de novo design
 Nature Structural & Molecular Biology 30, 1132-1140; doi.org/10.1038/s41594-023-01029-0 (2023). 
- T. Kosugi, T. Iida, M. Tanabe, R. Iino, N Koga.
 Design of allosteric sites into rotary motor V1-ATPase by restoring lost function of pseudo-active sites
 Nature Chemistry, 15, 1591-1598; doi.org/10.1038/s41557-023-01256-4 (2023). 
- Y. Yoneda and H. Kuramochi
 Rapid-Scan Resonant Two-Dimensional Impulsive Stimulated Raman Spectroscopy of Excited States
 The Journal of Physical Chemistry A 127, 24, 5276-5286; doi.org/10.1021/acs.jpca.3c02489 (2023) 
- D. Yoshioka, Y. Yoneda, I. Y. Chang, H. Kuramochi, K. Hyeon-Deuk, and Y. Kobayashi
 Quasi-Reversible Photoinduced Displacement of Aromatic Ligands from Semiconductor Nanocrystals
 ACS Nano 17, 12, 11309-11317; doi.org/10.1021/acsnano.2c12578 (2023). 
- 小杉 貴洋
 タンパク質設計技術で目指す未来
 現代化学 622, 34-36 (2022). 
- 倉持 光, 田原 太平
 フェムト秒時間分解時間領域ラマン分光で観る光化学反応の超高速構造ダイナミクス
 光化学 53, 3, 132-137 (2022). 
- Akihiro Otomo, Takahiro Kosugi
 Tackle "Molecular Engine" by early-career researchers
 Biophysics and Physicobiology 19, e190039; doi.org/10.2142/biophysico.bppb-v19.0039 (2022). 
- Makito Miyazaki, Takahiro Kosugi
 Uncovering the design principles of supramolecular assemblies through manipulation of the structures, dynamics, and functions
 Biophysics and Physicobiology 19, e190031; doi.org/10.2142/biophysico.bppb-v19.0031 (2022). 
- 古賀 理恵, 小杉 貴洋, 古賀 信康
 de novoデザインタンパク質―生物がもたないタンパク質を設計できる時代
 実験医学増刊 40, 12, 2046-2054(2022). 
- Mukaiyama A, Furuike Y, Yamashita E, Akiyama S
 Highly sensitive tryptophan fluorescence probe for detecting rhythmic conformational changes of KaiC in the cyanobacterial circadian clock system
 Biochemical Journal 479, 14, 1505-1515; doi: 10.1042/BCJ20210544 (2022). 
- Furuike Y, Mukaiyama A, Koda S, Simon D, Ouyang D, Ito-Miwa K, Saito S, Yamashita E, Nishiwaki-Ohkawa T, Terauchi K, Kondo T, Akiyama S
 Regulation Mechanisms of the Dual ATPase in KaiC
 Proceedings of the National Academy of Sciences of the United States of America 119, e2119627119; doi: 10.1073/pnas.2119627119 (2022) 
- Furuike Y, Mukaiyama A, Ouyang D, Ito-Miwa K, Simon D, Yamashita E, Kondo T, Akiyama S
 Elucidation of Master Allostery Essential for Circadian Clock Oscillation in Cyanobacteria
 Science Advances 8, eabm8990; doi: 10.1126/sciadv.abm8990 (2022) 
- Furuike Y, Ouyang D, Tominaga T, Matsuo T, Mukaiyama A, Kawakita Y, Fujiwara S, Akiyama S
 Cross-scale Analysis of Temperature Compensation in the Cyanobacterial Circadian Clock System
 Communications Physics 5, 75; doi: 10.1038/s42005-022-00852-z (2022) 【プレスリリース】どうして生物の24時間リズムは安定なのか?ー水素原子の運動から迫る時計タンパク質の温度補償制御ー 生物の24時間リズム一定に保たれる理由 分子研、QSTなど解明 
 科学新聞, 10面, 2022年5月20日, 掲載
- Simon D, Mukaiyama A, Furuike Y, Akiyama S
 Slow and Temperature-compensated Autonomous Disassembly of KaiB-KaiC Complex
 Biophysics and Physicobiology 19, e190008; doi: 10.2142/biophysico.bppb-v19.0008 (2022) 
- Maruyama M, Furukawa Y, Kinoshita M, Mukaiyama A, Akiyama S, Yoshimura T
 Adenylate kinase 1 overexpression increases locomotor activity in medaka fish
 PLoS ONE 17, e0257967; doi: 10.1371/journal.pone.0257967 (2022) 
- 倉持 光, 竹内 佐年, 岩村 宗高, 田原 太平
 フェムト秒時間分解インパルシブ誘導ラマン分光による光誘起結合生成ダイナミクスの実時間構造追跡
 光学 51, 1, 8-14 (2022) 
- M. Mitsumoto, K. Sugaya, K. Kazama, R. Nakano, T. Kosugi, T. Murata, N. Koga,
 State-Targeting Stabilization of Adenosine A2A Receptor by Fusing a Custom-Made De Novo Designed α-Helical Protein
 International Journal of Molecular Sciences 22, 23, 12906 (13 pages) ; doi.org/10.3390/ijms222312906 (2021). 
- Akiyama S, Kamikubo H
 Beyond multi-disciplinary and cross-scale analyses of the cyanobacterial circadian clock system
 Biophysics and Physicobiology, doi.org/10.2142/biophysico.bppb-v18.031 (2021) 
- H. Murata, H. Imakawa, N. Koga, G. Chikenji
 The register shift rules for βαβ-motifs for de novo protein design
 PLoS ONE 16, 8, e0256895 (24 pages); doi.org/10.1371/journal.pone.0256895 (2021). 
- H. Kuramochi
 数サイクルパルスを用いた極限分光計測による複雑分子系のフェムト秒構造化学研究
 Molecular Science 15, 1, A0117; doi.org/10.3175/molsci.15.A0117 (2021). 
- 古賀 理恵, 古賀 信康
 タンパク質の合理設計技術開発
 化学と工業 74, 8, 576-578(2021). 
- Akiyama S
 Reasons for Seeking Information on the Molecular Structure and Dynamics of Circadian Clock Components in Cyanobacteria
 Circadian Rhythms in Bacteria and Microbiomes, 138-145 (2021) 
- Okumura M, Kanemura S, Matsusaki M, Lee YH, Akiyama S, Inaba K
 A unique leucine-valine adhesive motif supports structure and function of protein disulfide isomerase P5 via dimerization
 Structure 29, 1-14; doi.org/10.1016/j.str.2021.03.016 (2021) 
- A. Nakamura, N. Kobayashi, N. Koga, R. Iino,
 Positive Charge Introduction on the Surface of Thermostabilized PET Hydrolase Facilitates PET Binding and Degradation
 ACS Catalysis 11, 14, 8550-8564; doi.org/10.1021/acscatal.1c01204 (2021). 
- Nobuyasu Koga, Rie Koga, Gaohua Liu, Javier Castellanos, Gaetano T. Montelione & David Baker
 Role of backbone strain in de novo design of complex α/β protein structures
 Nature Communications volume 12, Article number: 3921; doi.org/10.10.38/s41467-021-2450-7 (2021) 
- H. Kuramochi and T. Tahara
 Tracking Ultrafast Structural Dynamics by Time-Domain Raman Spectroscopy
 Journal of the American Chemical Society 143, 26, 9699-9717; doi.org/10.1021/jacs.1c02545 (2021). 
- 古賀 理恵, 古賀 信康
 整合性原理に基づくタンパク質デザイン
 生物物理 , 60, 6, 325-330 (2020). 
- Rie Koga, Mami Yamamoto, Takahiro Kosugi, Naohiro Kobayashi, Toshihiko Sugiki, Toshimichi Fujiwara, and Nobuyasu Koga
 Robust folding of a de novo designed ideal protein even with most of the core mutated to valine
 Proceedings of the National Academy of Sciences of the United States of America ,doi.org/10.1073/pnas.2002120117(2020) 
- Ito-Miwa K, Furuike Y, Akiyama S, Kondo T
 Tuning the circadian period of cyanobacteria up to 6.6 days by the single amino acid substitutions in KaiC
 Proceedings of the National Academy of Sciences of the United States of America; doi.org/10.1073/pnas.2005496117 (2020) 
- Anzai I, Tokuda E, Handa S, Misawa H, Akiyama S, Furukawa Y
 Oxidative misfolding of Cu/Zn-superoxide dismutase triggered by non-canonical intramolecular disulfide formation
 Free Radical Biology and Medicine 147, 187-199; doi.org/10.1016/j.freeradbiomed.2019.12.017 (2020) 
- Mukaiyama A, Furuike Y, Akiyama S
 A kinetic mechanism gating the assembly of KaiB-KaiC complex in the cyanobacterial circadian clock system
 Biological Rhythms, 29-34 (2019) 
- Rie Koga , Nobuyasu Koga
 Consistency principle for protein design
 Biophysics and Physicobiology 16, 304-309; doi.org/10.2142/biophysico.16.0_304(2019) 
- 小杉 貴洋, 古賀 理恵, 古賀 信康
 合理デザインによる新規タンパク質の創出:現状とその可能性
 実験医学 37, 18, 3089-3095(2019). 
- H. Murakoshi, H. Horiuchi, T. Kosugi, M. Onda, A. Sato, N. Koga, J. Nabekura
 ShadowR: a novel chromoprotein with reduced non-specific binding and improved expression in living cells
 Scientific Reports 9, 12072; doi.org/ 10.1038/s41598-019-48604-4 (2019). 
- Ouyang D, Furuike Y, Mukaiyama A, Ito-Miwa K, Kondo T, Akiyama S
 Development and Optimization of Expression, Purification, and ATPase Assay of KaiC for Medium-Throughput Screening of Circadian Clock Mutants in Cyanobacteria
 International Journal of Molecular Science 20, 2789-2800; doi: 10.3390/ijms20112789 (2019) 
- Okumura M, Noi K, Kanemura S, Kinoshita M, Saio T, Inoue Y, Hikima T, Akiyama S, Ogura T, Inaba K
 Dynamic assembly of protein disulfide isomerase in catalysis of oxidative folding
 Nature Chemical Biology 15, 499-509; doi: 10.1038/s41589-019-0268-8 (2019) 
- S. Basak, R. P. Nobrega, D. Tavella, L.M. Deveau, N. Koga, R. Tatsumi-Koga, D. Baker, F. Massi, C. R. Matthews
 Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein
 Proceedings of the National Academy of Sciences of the United States of America 116, 14, 6806-6811; doi.org/10.1073/pnas.1818744116 (2019). 
- Mukaiyama A, Ouyang D, Furuike Y, Akiyama S
 KaiC from a cyanobacterium Gloeocapsa sp. PCC 7428 retains functional and structural properties required as the core of circadian clock system
 International Journal of Biological Macromolecules 131, 67-73; doi: 10.1016/j.ijbiomac.2019.03.051 (2019) 
- 秋山 修志,古池 美彦,向山 厚
 変化し続ける概日時計のかたち
 時間生物学 24, 92-99 (2018) 
- Furukawa Y, Lim C, Tosha T, Yoshida K, Hagai T, Akiyama S, Watanabe S, Nakagome K, Shiro Y
 Identification of a novel zinc-binding protein, C1orf123, as an interactor with a heavy metal-associated domain
 PLoS One 13, e0204355; doi: 10.1371/journal.pone.0204355 (2018) 
- 秋山 修志
 芸は身を助く?
 生物物理 58, 181 (2018) 
- Mukaiyama A, Furuike Y, Abe J, Yamashita E, Kondo T, Akiyama S
 Conformational rearrangements of the C1 ring in KaiC measure the timing of assembly with KaiB
 Scientific Reports 8, 8803 (2018) 
- Akiyama S, Mukaiyama A, Abe J, Furuike Y
 Cyanobacterial circadian clock system: how and why can it be so slow and stable?
 Biological Clocks: with reference to suprachiasmatic nucleus, 73-77 (2017) 
- 小林 玄器
 ヒドリドイオン導電性酸水素化物
 セラミックス 52(12), 829-832 (2017) 
- 小林 玄器
 ヒドリドイオン導電体の開発と新型電池への応用可能性
 応用物理 86(12), 1084-1087 (2017) 
- Y.-R. Lin, N. Koga, R. Tatsumi-Koga, G. Liu, A. F. Clouser, G. T. Montelione and D.Baker
 Cyclic oligomer design with de novo αβ-proteins
 PROTEIN SCIENCE 26(11),2187-2194 , doi:10.1002/pro.3270(2017) 
- Nuemket N, Yasui N, Kusakabe Y, Nomura Y, Atsumi N, Akiyama S, Nango E, Kato Y, Kaneko M K, Takagi J, Hosotani M, Yamashita A
 Structural basis for perception of diverse chemical substances by T1r taste receptors
 Nature Communications 8, 15530 (2017) 
- K. Soma, S. Konings, R. Aso, N. Kamiuchi, G. Kobayashi, H. Yoshida, S. Takeda
 Detecting dynamics responses of materials and devices under an alternating electric potential by phase-locked transmission electron microscopy
 Ultramicroscopy 181, 27-41 (2017) 
- Yutaka SHIKANO
 How to Realize One-dimensional Discrete-time Quantum Walk by Dirac Particle
 Nature Interdisciplinary Information Sciences 23, 33-37(2017) 
- Anzai I, Tokuda E, Mukaiyama A, Akiyama S, Endo F, Yamanaka K, Misawa H, Furukawa Y
 A misfolded dimer of Cu/Zn-superoxide dismutase leading to pathological oligomerization in amyotrophic lateral sclerosis
 Protein Science 26, 484-496 (2017) 
- A. Watanabe, G. Kobayashi, N. Matsui, M. Yonemura, A. Kubota, K. Suzuki, M. Hirayama and R. Kanno
 Ambient Pressure Synthesis and H− Conductivity of LaSrLiH2O2
 Electrochemistry 85(2), 88-92 (2017) 
- 小林玄器
 ヒドリドイオン導電体
 固体物理, 51(12), 825-830 (2016) 
- Kanemura S, Okumura M, Yutani K, Ramming T, Hikima T, Appenzeller-Herzog C, Akiyama S, Inaba K
 Human ER Oxidoreductin-1α (Ero1α) Undergoes Dual Regulation through Complementary Redox Interactions with Protein-Disulfide Isomerase(PDI)
 Journal of Biological Chemistry 291, 23952-23964 (2016) 
- Furuike Y, Abe J, Mukaiyama A, Akiyama S
 Accelerating in vitro studies on circadian clock systems using an automated sampling device
 Biophysics and Physicobiology 13, 235-241; doi: 10.2142/biophysico.13.0_235 (2016) 
- S.Goto 
 Contact geometric descriptions of vector fields on dually flat spaces and their applications in electric circuit models and nonequilibrium statistical mechanics
 Journal of Matematical Physics 57, 102702 (41 Pages) (2016) 
- 秋山 修志
 概日時計因子の構造や動態を調べる意義とは?
 生物物理 56, 266-270 (2016) 
- Anzai I, Toichi K, Tokuda E, Mukaiyama A, Akiyama S, Furukawa Y
 Screening of Drugs Inhibiting In vitro Oligomerization of Cu/Zn-Superoxide Dismutase with a Mutation Causing Amyotrophic Lateral Sclerosis
 Frontiers in Molecular Biosciences 3, 40; doi: 10.3389/fmolb.2016.00040 (2016) 
- 小林玄器
 ヒドリドイオン導電体の開発と電解質材料への応用可能性
 Energy Device 3(6), 53-58 (2016) 
- Kazutaka G. Nakamura, Kazuma Ohya, Hiroshi Takahashi, Tetsuya Tsuruta, Hiroya Sasaki, Shin-ichi Uozumi, Katsura Norimatsu, Masahiro Kitajima, Yutaka Shikano,  and Yosuke Kayanuma
 Spectrally resolved detection in transient-reflectivity measurements of coherent optical phonons in diamond
 Physical Review B 94, 024303 (7pages)( 2016) 
- S.Goto, R.W.Tucker and T.J. Walton
 The Dynamics of Compact Laser Pulses
 Journal of the Physics A:Mathematical and Theoretical 49, 265203 (11 pages) (2016) 
- Tomoyuki Horikiri, Makoto Yamaguchi, Kenji Kamide, Yasuhiro Matsuo, Tim Byrnes, Natsuko Ishida, Andreas Löffler, Sven Höfling, Yutaka Shikano, Tetsuo Ogawa, Alfred Forchel, and Yoshihisa Yamamoto
 High-energy side-peak emission of exciton-polariton condensates in high density regime
 Scientific Reports 6, 25655 (11pages) (2016) 
- Nango E, Akiyama S, Maki-Yonekura S, Ashikawa Y, Kusakabe Y, Krayukhina E, Maruno T, Uchiyama S, Nuemket N, Yonekura K, Shimizu M, Atsumi N, Yasui N, Hikima T, Yamamoto M, Kobayash Y, Yamashita A
 Taste substance binding elicits conformational change of taste receptor T1r heterodimer extracellular domains
 Scientific Reports 6, 25745; doi: 10.1038/srep25745 (2016) 
- G. Kobayashi, Y. Hinuma, S. Matsuoka, A. Watanabe, M. Iqbal, M. Hirayama, M. Yonemura, T. Kamiyama, I. Tanaka, R. Kanno
 Pure H-conduction in oxyhydrides
 Science 351, 1314-1317 (2016) 
- Abe J, Mukaiyama A, Akiyama S
 Absolute slowness encoded in the circadian clock protein KaiC
 SPring-8 Reserch Frontiers 2015, 24-25 (2016) 
 
- Furukawa Y, Anzai I, Akiyama S, Imai M, Cruz FJC, Saio T, Nagasawa K, Nomura T, and Ishimori K
 Conformational Disorder of the Most Immature Cu, Zn-Superoxide Dismutase Leading to Amyotrophic Lateral Sclerosis
 Journal of Biological Chemistry 291, 4144-4155 (2016) 
- 秋山 修志
 時間生物学と放射光科学の接点
 放射光 29, 56-63 (2016) 
- M. Iqbal, K. Suzuki, G. Kobayashi, G. Zhao, M. Hirayama, R. Kanno
 Lithium ion conduction in doped LaLiO2 system
 Solid State Ionics 285, 33-37 (2016) 
- Furukawa Y, Suzuki Y, Fukuoka M, Nagasawa K, Nakagome K, Shimizu H, Mukaiyama A, Akiyama S
 A molecular mechanism realizing sequence-specific recognition of nucleic acids by TDP-43
 Scientific Reports 6, 20576; doi: 10.1038/srep20576 (2016) 
- S.Goto, R. W.Tucker, T.J.Walton
 Classical Dynamics of Free Electromagnetic Laser Pulses
 Nuclear Instruments and Methods in Physics Research Section B : Beam Interactions with Materials and Atoms 369 , 40-44 (2016) 
- 阿部 淳,向山 厚,秋山 修志
 時計タンパク質KaiCの「遅さ」が刻み込まれた原子構造
 SPring-8/SACLA利用者情報 21, 2-4 (2016) 
- 古賀理恵, 古賀信康
 計算機でゼロからタンパク質をデザイン - 望みのタンパク質分子のテーラーメイド創出を目指して
 化学 71, 42-46 (2016) 
- G. Kobayashi, Y. Irii, F. Matsumoto, A. Ito, Y. Ohsawa, S. Yamamoto, Y. Cui, J.-Y. Son, and Y. Sato
 Improving Cycling Performance of Li[Li0.2Ni0.18Co0.03Mn0.58]O2 through Combination of Al2O3-based Surface Modification and Stepwise Pre-cycling
 Journal of Power sources 303, 250-256 (2016)
- Yuta Fujihashi and Akihito Ishizaki
 Fluctuations in electronic energy affecting singlet fission dynamics and mixing with charge-transfer state: Quantum dynamics study
 Journal of the Physical Chemistry Letters 7, 363-369 (2016) 
- 石崎 章仁
 新著紹介, K. A. Dill and S. Bromberg, Molecular Driving Forces; Statistical Thermodynamics in Chemistry, Physics, Biology, and Nanoscience, Second Edition (Garland Science, London and New York, 2011)
 日本物理学会誌 70(12), 946 (2015) 
- Akio Hosoya, Koji Maruyama, and Yutaka Shikano
 Operational derivation of Boltzmann distribution with Maxwell's demon model
 Scientific Reports 5, 17011 (9pages) (2015) 
- 向山厚 , 阿部淳 , 孫世永 , 秋山修志
 タンパク質の化学反応が細胞内の時を計る
 実験医学 33, 3119-3122 (2015) 
- Kentaro Soma, Stan Konings, Genki Kobayashi and Seiji Takeda
 B12-O-05 Towards Dynamics Electron Holographic Analysis of Solid State Electrochemical Devices at Operating Condition
 Microscopy 64, i21 (2015) 
- Yu-Ru Lin, Nobuyasu Koga, Rie Tatsumi-Koga, Gaohua Liu, Amanda F. Clouser, Gaetano T. Montelione, David Baker
 Control over overall shape and size in de novo designed proteins
 Proceedings of the National Academy of Sciences of the United States of America 112(40), E5478-5485 (2015) 
- Kazutaka G. Nakamura, Yutaka Shikano, and Yosuke Kayanuma
 Influence of pulse width and detuning on coherent phonon generation
 Physical Review B 92, 144304 (7pages) (2015) 
- Yuta Fujihashi, Graham R. Fleming, and Akihito Ishizaki
 Influences of quantum mechanically mixed electronic and vibrational pigment states in 2D electronic spectra of photosynthetic systems: Strong electronic coupling cases
 Journal of the Chinese Chemical Society 63, 49-56 (8 pages) (2015) 
- Yusuf Turek, Hirokazu Kobayashi, Tomotada Akutsu, Chang-Pu Sun, and Yutaka Shikano
 Post-selected von Neumann measurement with Hermite-Gaussian and Laguerre-Gaussian pointer states
 New Journal of Physics 17, 083029 (17pages) (2015) 
- Yusuf Turek, Wulayimu Maimaiti, Yutaka Shikano, Chang-Pu Sun, and Mohammad Al-Amri
 Advantages of nonclassical pointer states in postselected weak measurements
 Physical Review A 92, 022109 (8pages) (2015) 
- Daniele M. Monahan, Lukas Whaley-Mayda, Akihito Ishizaki, and Graham R. Fleming
 Influence of weak vibrational-electronic couplings on 2D electronic spectra and inter-site coherence in weakly coupled photosynthetic complexes
 Journal of Chemical Physics 143, 065101 (2015) 
 
- Akiko Ueno, Fumiko Takida, Tomoki Kita, Takuro Ishii, Tomoki Himiyama, Takuya Mabuchi & Yasunori Okamoto

