Trans-Hierarchical Molecular Systems Achievements
- 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）.
- 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).
- 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)
- 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)
- 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).
- 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).
- 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)
- 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)
- 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).
- 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)
- 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)
- 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 dynamic 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
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)
- 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 Mathematical Physics 57, 102702 (41 Pages) (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)
- G. KOBAYASHI
Development of H- Conductor and the Application Possibility as a Solid Electrolyte
Energy Device 3(6), 1-6 (2016) (in Japansese)
- 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 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 Research 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)
- Akiyama S
Interplay of Chronobiology & Synchrotron Radiation Research
J. JSSRR 29(2), 56-63 (2016) (in Japanese)
- 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
Nucl. Instrum. Methods Phys. Res., Sect. B 369, 40-44 (2016)
- Abe J, Mukaiyama A, Akiyama S
Slow ATP Hydrolysis Reaction Designed in the Atomic Structure of Circadian Clock Protein KaiC
SPring-8/SACLA Information 21, 2-4 (2016) (in Japanese)
- R. KOGA and N. KOGA
De Novo Computational Protein Design: Toward Custom Made Generation of Protein Structures
Kagaku 71, 42-46 (2016) (in Japanese)
- 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)
- Akio Hosoya, Koji Maruyama, and Yutaka Shikano
Operational derivation of Boltzmann distribution with Maxwell's demon model
Scientific Reports 5, 17011 (9pages) (2015)
- Mukaiyama A, Abe J, Son S, Akiyama S
Atomic-Scale Origins of Slowness in the Cyanobacterial Circadian Clock
Jikkenigaku 33, 3119-3122 (2015) (in Japanese)
- Kentaro Soma, Stan Konings, Genki Kobayashi and Seiji Takeda
B12-O-05 Towards Dynamic Electron Holographic Analysis of Solid State Electrochemical Devices at Operating Condition
Microscopy 64, i21 (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)
- 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)
- 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)
- S. Tsusima, W. Hung, P. Deevanhxay, G. Kobayashi, R. Kanno, S. Hirai
In Situ X-ray Visualization of the Lithiation Process in a Porous Graphite Electrode in an Operating Li-Ion Cell
ChemElectroChem 2, 1535-1540 (2015)
- Abe J, Hiyama T B, Mukaiyama A, Son S, Mori T, Saito S, Osako M, Wolanin J,
Yamashita E, Kondo T, and Akiyama S
Atomic-scale Origins of Slowness in the Cyanobacterial Circadian Clock
Science 349, 312-316 (2015)
- Giuseppe Di Molfetta, Lauchlan Honter, Ben B. Luo, Tatsuaki Wada, and Yutaka Shikano
Massless Dirac Equation from Fibonacci Discrete-Time Quantum Walk
Quantum Studies: Mathematics and Foundations 2, 243 - 252 (10pages) (2015)
Erratum to: Massless Dirac Equation from Fibonacci Discrete-Time Quantum Walk Quantum Studies: Mathematics and Foundations 2, 253 - 254 (2pages) (2015)
- Mukaiyama A, Osako M, Hikima T, Kondo T, and Akiyama S
A protocol for preparing nucleotide-free KaiC monomer
BIOPHYSICS 11, 79-84 (2015)
- Yutaka Shikano
These from Bits
in It From Bit or Bit From It?, Chapter 10, 113-118 (Springer, Switzerland, 2015)
- Ryo Sakuma, Hashimoto Hideki, Genki Kobayashi, Tatsuo Fujii, Makoto Nakanishi, Ryoji Kanno, Mikio Takano, Jyun Takada
High-rate performance of a bacterial iron-oxide electrode for lithium-ion battery
Materials Letters 139, 414-417 (2015)
- Genki Kobayashi, Yuichi Sato
Solid electrolytes, basic and evaluation method of all solid-state secondary batteries
Electrochemistry 82, 1108-1113 (2014)
- J. Sugiyama, H. Nozaki, M. Harada, Y. Higuchi, J. Brewer, A. H. Jess, J. Eduardo, G. Kobayashi and R. Kanno
Variation of local magnetic enviroments in olivine-type compounds: Na0.7FePO4 and FePO4
Physical Review B 90, 014426/1-014426/10 (2014)
- Atsushi Noguchi, Yutaka Shikano, Kenji Toyoda, and Shinji Urabe
Aharonov-Bohm effect in the tunnelling of a quantum rotor in a linear Paul trap
Nature Communications 5, 3868 (2014)
- Hirokazu Kobayashi, Koji Nonaka, and Yutaka Shikano
Stereographical visualization of a polarization state using weak measurements with an optical-vortex beam
Physical Review A 89, 053816 (2014). Editor's Suggestion
- C. Hansen, K. Kubota, G. Kobayashi, M. Hirayama, R. Kanno
High-pressure synthesis and electrochemical properties of lighium transition metal oxides with layered rock-salt structure
Journal of Power Sources 252, 1-7 (2014)
- H. Hashimoto, G. Kobayashi, R. Sakuma, T. Fujii, N. Hayashi, T. Tomoko, R. Kanno, M. Takano, J. Takada
Bacterial nanometric amorphous Fe-based oxide: a otential lithium-ion battery anode material
ACS Applied Materials & Interfaces 6, 5374-5378 (2014)
- Kojima R, Okumura M, Masui S, Kanemura S, Inoue M, Saiki M, Yamaguchi H, Hikima T, Suzuki M, Akiyama S and Inaba K.
Radically Different Thioredoxin Domain Arrangement of ERp46, an Efficient Disulfide Bond Introducer of the Mammalian PDI Family
Structure 22, 431-443 (2014)
- Yutaka Shikano, Tatsaki Wada, and Junsei Horikawa
Discrete-time quantum walk with feed-forward quantum coin
Scientific Reports 4, 4427 (2014)
- Yuki Susa, Yutaka Shikano, and Akio Hosoya
Reply to "Comment on 'Optimal probe wave function of weak-value amplification' "
Physical Review A 87, 046102 (2 pages) (2013)
- Ali Ü. C. Hardal, Peng Xue, Yutaka Shikano, Özgür E. Müstecaplioglu, and Barry C. Sanders
Discrete-time quantum walk with nitrogen-vacancy centers in diamond coupled to a superconducting flux qubit
Physical Review A 88, 022303 (11 pages) (2013)
- Yutaka Shikano, Etsuo Segawa, Armando Perez, and Jingbo Wang
A Special Issue on Theoretical and Mathematical Aspects of Discrete Time Quantum Walks
Journal of Computational and Theoretical Nanoscience 10, 1555-1556 (2 pages) (2013)
- Meltem Gönülol, Ekrem Aydiner, Yutaka Shikano, and Özgür E. Müstecaplioglu
Survival Probability in a Quantum Walk on a One-Dimensional Lattice with Partially Absorbing Traps
Journal of Computational and Theoretical Nanoscience 10, 1596-1600 (5 pages) (2013)
- Yutaka Shikano
From Discrete Time Quantum Walk to Continuous Time Quantum Walk in Limit Distribution
Journal of Computational and Theoretical Nanoscience 10, 1558-1570 (12 pages) (2013)
- Tomoyuki Horikiri, Yasuhiro Matsuo, Yutaka Shikano, Andreas Löffler,Sven Höfling, Alfred Forchel, and Yoshihisa Yamamoto
Temperature Dependence of Highly Excited Exciton Polaritons in Semiconductor Microcavities
Journal of the Physical Society of Japan 82, 084709 (2013) .
- M. Iqbal, G. Kobayashi, M. Hirayama, R. Kanno
Synthesis, structure and electrochemical properties of layered La2Li2x(CO3)1-xO2+2x
Journal of Solid State Chemistry, 206, 14-19 (2013)
- R. Kimura, Y. Yoneda, H. Kuramochi, and S. Saito