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Shoichi Toyabe

Section

Graduate School of Engineering

Job title

Professor

Degree

博士（理学）（東京大学）
修士（理学）（東京大学）

researchmap

https://researchmap.jp/7000010897

J-GLOBAL ID

201501014926255688

e-Rad No.

40453675

Research History 5

2023/04 - Present

Institute for Molecular Science, National Institutes of Natural Sciences
2021/04 - Present

Tohoku University
2014/07 - 2021/03

Tohoku University
2011/10 - 2014/06

ミュンヘン大学 (LMU Munich)　物理学部　フンボルト財団リサーチフェロー
2007/04 - 2011/09

Chuo University　Faculty of Science and Engineering, Department of Physics

Education 3

The University of Tokyo

2004/04 - 2007/03
The University of Tokyo

2002/04 - 2004/03
The University of Tokyo　Faculty of Science　Department of Physics

- 2002/03

Professional Memberships 2

日本生物物理学会
日本物理学会

Research Interests 4

Stochastic thermodynamics
Biological molecular motor
Nonequilibrium Phyics
Biophysics

Research Areas 1

Natural sciences / Bio-, chemical, and soft-matter physics /

Awards 5

青葉工学振興会賞

2018/12
CAS Visiting Fellowship

2018/09　Center for Advanced Studies, Ludwig-Maximillians-Universität München
Young Scientist Award

2012/03　Japan Physical Society　Measurement of fluctuations and validation of thermodynamic relations under nonequilibrium states
Research Fellow

2011/10　Alexander von Humboldt Foundation
Early Research in Biophysics Award

2011/09　Biophysical Society of Japan　Single-molecule thermodynamics of molecular motor

Papers 50

Cooperative stator assembly of bacterial flagellar motor mediated by rotation. International-journal

Kenta I Ito, Shuichi Nakamura, Shoichi Toyabe

Nature communications　12　(1)　3218-3218　2021/05/28

DOI： 10.1038/s41467-021-23516-y 　

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Cooperativity has a central place in biological regulation, providing robust and highly-sensitive regulation. The bacterial flagellar motor implements autonomous torque regulation based on the stator's dynamic structure; the stator units bind to and dissociate from the motor dynamically in response to environmental changes. However, the mechanism of this dynamic assembly is not fully understood. Here, we demonstrate the cooperativity in the stator assembly dynamics. The binding is slow at the stalled state, but externally forced rotation as well as driving by motor torque in either direction boosts the stator binding. Hence, once a stator unit binds, it drives the rotor and triggers the avalanche of succeeding bindings. This cooperative mechanism based on nonequilibrium allostery accords with the recently-proposed gear-type coupling between the rotor and stator.
Optimal Rectification without Forward-Current Suppression by Biological Molecular Motor

Yohei Nakayama, Shoichi Toyabe

Physical Review Letters　126　(20)　2021/05/20

DOI： 10.1103/PhysRevLett.126.208101 　

ISSN： 0031-9007

eISSN： 1079-7114
Asymmetric enzyme kinetics of F1 -ATPase induced by rotation-assisted substrate binding Peer-reviewed

Yohei Nakayama, Shoichi Toyabe

Physical Review Research　7　(2)　023213　2025/06/02
Publisher: American Physical Society (APS)
DOI： 10.1103/physrevresearch.7.023213 　

eISSN： 2643-1564

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We demonstrate asymmetric enzyme kinetics of a biomolecular motor F1−ATPase between synthesis and hydrolysis of adenosine triphosphate (ATP). Our experiments show that ATP hydrolysis follows Michaelis-Menten kinetics, but ATP synthesis, which is an F1-ATPase's primary biological role, deviates from it. Specifically, the synthesis rate is sustained even at low substrate concentrations. Analysis of a theoretical model consistent with the experimental results reveals that ATP synthesis implements a rotation-assisted mechanism, in which a limited binding rate at low substrate concentration is partially compensated for by rotation to an angle where the binding rate is high. The results may imply that F1−ATPase implements a regulatory mechanism of enhancing substrate binding for ATP synthesis. Published by the American Physical Society 2025
Acceleration of enzymatic reaction-diffusion kinetics by intermediate state

Akihiro Fukuda, Yohei Nakayama, Shoichi Toyabe

2025/05/22

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Biological molecular motors are high-performance nanomachines that convert chemical energy into mechanical motion via chemomechanical coupling. Their reaction cycles typically comprise a series of intermediate chemical states between the initial and final primary states. However, the influence of these intermediate states on motor performance has not yet been fully explored. In this study, we investigate the impact of intermediate states on the motor kinetics using a reaction-diffusion model. In most cases, the intermediate states accelerate the motor by lowering the effective barrier height. This acceleration is particularly pronounced when an external load is applied to the motor, implying the practical importance of the intermediate states. The intermediate states can also slow down the reaction in some cases, such as the slow reaction limit with asymmetric kinetics. Our findings provide practical insights into the design principles behind the high performance of biological molecular motors, as well as the development of efficient artificial molecular motors.
Experimental demonstration of kinetic proofreading inherited in ligation-based information replication

Hiroyuki Aoyanagi, Yasuhiro Magi, Shoichi Toyabe

2025/05/13

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We experimentally demonstrate that information replication by templated ligation of DNA strands inherits a kinetic proofreading mechanism and achieves significant error suppression through cascade replication. A simple simulation model derived from the experimental results shows that templated ligation has a significant advantage over replication by polymerization for error suppression of long strands. This mechanism provides a plausible route for high-fidelity replication in prebiotic chemistry and illustrates how physical principles such as nonequilibrium kinetics and network architecture can drive reliable molecular information replication. The approach also offers new strategies for error suppression in biotechnology.
Efficiently driving F$_1$ molecular motor in experiment by suppressing nonequilibrium variation

Takahide Mishima, Deepak Gupta, Yohei Nakayama, W. Callum Wareham, Takumi Ohyama, David A. Sivak, Shoichi Toyabe

2025/05/02

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F$_1$-ATPase (F$_1$) is central to cellular energy transduction. Forcibly rotated by another motor F$_\mathrm{o}$, F$_1$ catalyzes ATP synthesis by converting mechanical work into chemical free energy stored in the molecule ATP. The details of how F$_\mathrm{o}$ drives F$_1$ are not fully understood; however, evaluating efficient ways to rotate F$_1$ could provide fruitful insights into this driving since there is a selective pressure to improve efficiency. Here, we show that rotating F$_1$ with an angle clamp is significantly more efficient than a constant torque. Our experiments, combined with theory and simulation, indicate that the angle clamp significantly suppresses the nonequilibrium variation that contributes to the futile dissipation of input work.
Experimentally achieving minimal dissipation via thermodynamically optimal transport

Shingo Oikawa, Yohei Nakayama, Sosuke Ito, Takahiro Sagawa, Shoichi Toyabe

2025/03/03

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Optimal transport theory, originally developed in the 18th century for civil engineering, has since become a powerful optimization framework across disciplines, from generative AI to cell biology. In physics, it has recently been shown to set fundamental bounds on thermodynamic dissipation in finite-time processes. This extends beyond the conventional second law, which guarantees zero dissipation only in the quasi-static limit and cannot characterize the inevitable dissipation in finite-time processes. Here, we experimentally realize thermodynamically optimal transport using optically trapped microparticles, achieving minimal dissipation within a finite time. As an application to information processing, we implement the optimal finite-time protocol for information erasure, confirming that the excess dissipation beyond the Landauer bound is exactly determined by the Wasserstein distance - a fundamental geometric quantity in optimal transport theory. Furthermore, our experiment achieves the bound governing the trade-off between speed, dissipation, and accuracy in information erasure. To enable precise control of microparticles, we develop scanning optical tweezers capable of generating arbitrary potential profiles. Our work establishes an experimental approach for optimizing stochastic thermodynamic processes. Since minimizing dissipation directly reduces energy consumption, these results provide guiding principles for designing high-speed, low-energy information processing.
Blocking uncertain mispriming errors of PCR. International-journal

Takumi Takahashi, Hiroyuki Aoyanagi, Simone Pigolotti, Shoichi Toyabe

Biophysical journal　123　(20)　3558-3568　2024/10/15

DOI： 10.1016/j.bpj.2024.09.008 　

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The polymerase chain reaction (PCR) plays a central role in genetic engineering and is routinely used in various applications, from biological and medical research to the diagnosis of viral infections. PCR is an extremely sensitive method for detecting target DNA sequences, but it is substantially error prone. In particular, the mishybridization of primers to contaminating sequences can result in false positives for virus tests. The blocker method, also called the clamping method, has been developed to suppress mishybridization errors. However, its application is limited by the requirement that the contaminating template sequence be known in advance. Here, we demonstrate that a mixture of multiple blocker sequences effectively suppresses the amplification of contaminating sequences even in the presence of uncertainty. The blocking effect was characterized by a simple model validated by experiments. Furthermore, the modeling allowed us to minimize the errors by optimizing the blocker concentrations. The results highlighted an inherent robustness of the blocker method in that fine-tuning the blocker concentrations is not necessary. Our method extends the applicability of PCR and other hybridization-based techniques, including genome editing, RNA interference, and DNA nanotechnology, by improving their fidelity.
Collective gradient sensing by dilute swimming bacteria without clustering

Tatsuro Kai, Takahiro Abe, Natsuhiko Yoshinaga, Shuichi Nakamura, Seishi Kudo, Shoichi Toyabe

Physical Review Research　6　(3)　L032061　2024/09/10
Publisher: American Physical Society (APS)
DOI： 10.1103/physrevresearch.6.l032061 　

eISSN： 2643-1564

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We characterize the taxis enhancement of swimming bacteria by collective migration without apparent clustering. We confine a dilute suspension in a shallow channel and evaluate the thermotaxis response to local heating and diffusion. By combining cell tracking analysis and numerical simulation based on simple modeling, we show that the alignment interaction suppresses orientation fluctuation, strengthens migration bias, and also prevents the dispersion of accumulated population. The results show a prominent example of how a collective motion of active matter implements a biological function. Published by the American Physical Society 2024
Design of artificial molecular motor inheriting directionality and scalability

Kenta I. Ito, Yusuke Sato, Shoichi Toyabe

Biophysical Journal　2024/02
Publisher: Elsevier BV
DOI： 10.1016/j.bpj.2024.02.026 　

ISSN： 0006-3495
Error-suppression mechanism of PCR by blocker strands. International-journal

Hiroyuki Aoyanagi, Simone Pigolotti, Shinji Ono, Shoichi Toyabe

Biophysical journal　2023/02/23

DOI： 10.1016/j.bpj.2023.02.028 　

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The polymerase chain reaction (PCR) is a central technique in biotechnology. Its ability to amplify a specific target region of a DNA sequence has led to prominent applications, including virus tests, DNA sequencing, genotyping, and genome cloning. These applications rely on the specificity of the primer hybridization and therefore require effective suppression of hybridization errors. A simple and effective method to achieve that is to add blocker strands, also called clamps, to the PCR mixture. These strands bind to the unwanted target sequence, thereby blocking the primer mishybridization. Because of its simplicity, this method is applicable to a broad nucleic-acid-based biotechnology. However, the precise mechanism by which blocker strands suppress PCR errors remains to be understood, limiting the applicability of this technique. Here, we combine experiments and theoretical modeling to reveal this mechanism. We find that the blocker strands both energetically destabilize the mishybridized complex and sculpt a kinetic barrier to suppress mishybridization. This combination of energetic and kinetic biasing extends the viable range of annealing temperatures, which reduces design constraint of the primer sequence and extends the applicability of PCR.
Optimal Control of the F<inf>1</inf>-ATPase Molecular Motor

Deepak Gupta, Steven J. Large, Shoichi Toyabe, David A. Sivak

Journal of Physical Chemistry Letters　13　(51)　11844-11849　2022/12/29

DOI： 10.1021/acs.jpclett.2c03033 　

eISSN： 1948-7185
分子がはたらくということ Invited

中山洋平, 鳥谷部祥一

現代化学　30　2021/08
生体分子モーターの動作メカニズムとエネルギー論

鳥谷部祥一

ペトロテック = Petrotech : 石油学会情報誌　44　(6)　421-425　2021/06
Publisher: 石油学会 ; 1978-
ISSN： 0386-2763
Experimental characterization of autonomous heat engine based on minimal dynamical-system model Peer-reviewed

Shoichi Toyabe, Yuki Izumida

Physical Review Research　2　(3)　033146　2020/07/27
Publisher: American Physical Society (APS)
DOI： 10.1103/physrevresearch.2.033146 　

eISSN： 2643-1564

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The autonomous heat engine is a model system of autonomous nonequilibrium systems like biological cells, exploiting nonequilibrium flow for operations. As the Carnot engine has essentially contributed to the equilibrium thermodynamics, autonomous heat engine is expected to play a critical role in the challenge of constructing nonequilibrium thermodynamics. However, the high complexity of the engine involving an intricate coupling among heat, gas flow, and mechanics has prevented simple modeling. Here, we experimentally characterized the nonequilibrium dynamics and thermodynamics of a low-temperature-differential Stirling engine, which is a model autonomous heat engine. Our experiments demonstrated that the core engine dynamics are quantitatively described by a minimal dynamical model with only two degrees of freedom. The model proposes a novel concept that illustrates the engine as a thermodynamic pendulum driven by a thermodynamic force. This work will open a new approach to explore the nonequilibrium thermodynamics of autonomous systems based on a simple dynamical system.
Tight Chemomechanical Coupling of the F1 Motor Relies on Structural Stability. International-journal Peer-reviewed

Mana Tanaka, Tomohiro Kawakami, Tomoaki Okaniwa, Yohei Nakayama, Shoichi Toyabe, Hiroshi Ueno, Eiro Muneyuki

Biophysical journal　119　(1)　48-54　2020/07/07

DOI： 10.1016/j.bpj.2020.04.039 　

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The F1 motor is a rotating molecular motor that ensures a tight chemomechanical coupling between ATP hydrolysis/synthesis reactions and rotation steps. However, the mechanism underlying this tight coupling remains to be elucidated. In this study, we used electrorotation in single-molecule experiments using an F1βE190D mutant to demonstrate that the stall torque was significantly smaller than the wild-type F1, indicating a loose coupling of this mutant, despite showing similar stepping torque as the wild-type. Experiments on the ATPase activity after heat treatment and gel filtration of the α3β3-subcomplex revealed the unstable structure of the βE190D mutant. Our results suggest that the tight chemomechanical coupling of the F1 motor relies on the structural stability of F1. We also discuss the difference between the stepping torque and the stall torque.
Harnessing random low Reynolds number flow for net migration Peer-reviewed

Takeru Morita, Toshihiro Omori, Yohei Nakayama, Shoichi Toyabe, Takuji Ishikawa

Physical Review E　101　(6)　063101　2020/06
Publisher: American Physical Society (APS)
DOI： 10.1103/physreve.101.063101 　

ISSN： 2470-0045

eISSN： 2470-0053
Cooperative stator assembly of bacterial flagellar motor for autonomous torque regulation

Kenta I. Ito, Shuichi Nakamura, Shoichi Toyabe

2020/04/27
Publisher: Cold Spring Harbor Laboratory
DOI： 10.1101/2020.04.26.059089 　

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<title>ABSTRACT</title>Cooperativity has a central place in biological regulation, providing robust and highly-sensitive regulation. The bacterial flagellar motor (BFM) implements autonomous torque regulation by the nonequilibrium structure of the stators; the stators assemble at high load and disperse at low load. It would be natural to suppose that the stator packing is affected by stator-stator interaction. However, the cooperativity among the stators has rarely been explored. Here, we evaluated the energetics and kinetics of the stator assembly by combining dynamic load control of a single motor and the trajectory analysis based on statistical mechanics. We demonstrate that the BFM exploits the dynamic cooperativity of the stator binding for the autonomous torque regulation. The cooperative assembly leads to a discontinuous phase transition and hysteresis, which may implement torque regulation with high sensitivity and robustness.
Session 2SDA-Nonequilibrium energetics of biological molecular machines. International-journal Peer-reviewed

Shoichi Toyabe, Chun-Biu Li, Kazushi Kinbara

Biophysical reviews　12　(2)　273-274　2020/04

DOI： 10.1007/s12551-020-00634-3 　
Efficiencies of molecular motors: a comprehensible overview. International-journal Peer-reviewed

Chun-Biu Li, Shoichi Toyabe

Biophysical reviews　12　(2)　419-423　2020/04

DOI： 10.1007/s12551-020-00672-x 　

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Many biological molecular motors can operate specifically and robustly at the highly fluctuating nano-scale. How these molecules achieve such remarkable functions is an intriguing question that requires various notions and quantifications of efficiency associated with the operations and energy transduction of these nano-machines. Here we give a short review of some important concepts of motor efficiencies, including the thermodynamic, Stokes, and generalized and transport efficiencies, as well as some implications provided by the thermodynamic uncertainty relations recently developed in nonequilibrium physics.
Origin of Species in Template-directed Ligation

鳥谷部祥一, BRAUN Dieter

生物物理　60　(5)　2020

ISSN： 1347-4219
Evaluation of the Duty Ratio of the Bacterial Flagellar Motor by Dynamic Load Control. International-journal Peer-reviewed

Kento Sato, Shuichi Nakamura, Seishi Kudo, Shoichi Toyabe

Biophysical journal　116　(10)　1952-1959　2019/05/21

DOI： 10.1016/j.bpj.2019.04.004 　

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The bacterial flagellar motor is one of the most complex and sophisticated nanomachineries in nature. A duty ratio D is a fraction of time that the stator and the rotor interact and is a fundamental property to characterize the motor but remains to be determined. It is known that the stator units of the motor bind to and dissociate from the motor dynamically to control the motor torque depending on the load on the motor. At low load, at which the kinetics such as proton translocation speed limits the rotation rate, the dependency of the rotation rate on the number of stator units N implies D: the dependency becomes larger for smaller D. Contradicting observations supporting both the small and large D have been reported. A dilemma is that it is difficult to explore a broad range of N at low load because the stator units easily dissociate, and N is limited to one or two at vanishing load. Here, we develop an electrorotation method to dynamically control the load on the flagellar motor of Salmonella with a calibrated magnitude of the torque. By instantly reducing the load for keeping N high, we observed that the speed at low load depends on N, implying a small duty ratio. We recovered the torque-speed curves of individual motors and evaluated the duty ratio to be 0.14 ± 0.04 from the correlation between the torque at high load and the rotation rate at low load.
Cooperative Ligation Breaks Sequence Symmetry and Stabilizes Early Molecular Replication Peer-reviewed

Shoichi Toyabe, Dieter Braun

Phys. Rev. X　9　011056　2019/03
生体分子モーター ―進化が生んだ超高性能ナノマシン― Invited Peer-reviewed

鳥谷部祥一

精密工学会誌　84　(11)　905-908　2018/11

DOI： 10.2493/jjspe.84.905 　
生命現象における非平衡揺らぎとその応用 Invited

鳥谷部祥一

物性研究　6　(4)　2017/11
Assembly of a functional and responsive microstructure by heat bonding of DNA-grafted colloidal brick. International-journal Peer-reviewed

Yuki Sakamoto, Shoichi Toyabe

Scientific reports　7　(1)　9104-9104　2017/08/22

DOI： 10.1038/s41598-017-09804-y 　

ISSN： 2045-2322
Decoding Fluctuation: Diffusional Analysis of Biological Molecular Motors Invited Peer-reviewed

S. Toyabe

J. Phys. Soc. Jpn.　85　064004　2016/06

DOI： 10.7566/JPSJNC.13.07 　
Nonequilibrium Fluctuations in Biological Strands, Machines, and Cells Invited Peer-reviewed

Shoichi Toyabe, Masaki Sano

JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN　84　(10)　102001　2015/10

DOI： 10.7566/JPSJ.84.102001 　

ISSN： 0031-9015
Single molecule thermodynamics of ATP synthesis by F-1-ATPase Peer-reviewed

Shoichi Toyabe, Eiro Muneyuki

NEW JOURNAL OF PHYSICS　17　015008　2015/01

DOI： 10.1088/1367-2630/17/1/015008 　

ISSN： 1367-2630
Thermodynamic analyses of nucleotide binding to an isolated monomeric β subunit and the α3β3γ subcomplex of F1-ATPase. International-journal Peer-reviewed

Yohsuke Kikuchi, Yusuke Naka, Hidemitsu Osakabe, Tetsuaki Okamoto, Tomoko Masaike, Hiroshi Ueno, Shoichi Toyabe, Eiro Muneyuki

Biophysical journal　105　(11)　2541-8　2013/12/03

DOI： 10.1016/j.bpj.2013.10.018 　

ISSN： 0006-3495

eISSN： 1542-0086
Properties of the electrogenic activity of bacteriorhodopsin. International-journal Peer-reviewed

Shizuma Miyazaki, Makoto Matsumoto, Søren Bo Brier, Toshihiro Higaki, Takumi Yamada, Tetsuaki Okamoto, Hiroshi Ueno, Shoichi Toyabe, Eiro Muneyuki

European biophysics journal : EBJ　42　(4)　257-65　2013/04

DOI： 10.1007/s00249-012-0870-0 　

ISSN： 0175-7571

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In this study, we analyzed the photoelectric current generated by bacteriorhodopsin adsorbed on a polymer film, "Lumirror" (Muneyuki et al. in FEBS Lett 427:109-114, 1998). We could examine the photoelectric current over a wide range of light intensity and pH values using the same membrane owing to the mechanical and chemical stability of the thin polymer film. We analyzed the photoelectric current by comparison with a simple equivalent electric circuit. Analysis of experimental results obtained at different light intensities suggested that the electromotive force of the bacteriorhodopsin was independent of light intensity. The pH dependence of the photoelectric current suggested that the bacteriorhodopsin could generate a maximum electromotive force at approximately pH 6.
Experimental thermodynamics of single molecular motor. Peer-reviewed

Shoichi Toyabe, Eiro Muneyuki

Biophysics (Nagoya-shi, Japan)　9　91-8　2013

DOI： 10.2142/biophysics.9.91 　

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Molecular motor is a nano-sized chemical engine that converts chemical free energy to mechanical motions. Hence, the energetics is as important as kinetics in order to understand its operation principle. We review experiments to evaluate the thermodynamic properties of a rotational F1-ATPase motor (F1-motor) at a single-molecule level. We show that the F1-motor achieves 100% thermo dynamic efficiency at the stalled state. Furthermore, the motor reduces the internal irreversible heat inside the motor to almost zero and achieves a highly-efficient free energy transduction close to 100% during rotations far from quasistatic process. We discuss the mechanism of how the F1-motor achieves such a high efficiency, which highlights the remarkable property of the nano-sized engine F1-motor.
Information-to-free-energy conversion: Utilizing thermal fluctuations. Peer-reviewed

Shoichi Toyabe, Eiro Muneyuki

Biophysics (Nagoya-shi, Japan)　9　107-12　2013

DOI： 10.2142/biophysics.9.107 　

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Maxwell's demon is a hypothetical creature that can convert information to free energy. A debate that has lasted for more than 100 years has revealed that the demon's operation does not contradict the laws of thermodynamics; hence, the demon can be realized physically. We briefly review the first experimental demonstration of Maxwell's demon of Szilard's engine type that converts information to free energy. We pump heat from an isothermal environment by using the information about the thermal fluctuations of a Brownian particle and increase the particle's free energy.
Utilizing Thermal Fluctuations: Experimental Demonstration of Information-heat Engine Invited Peer-reviewed

Shoichi Toyabe, Eiro Muneyuki

Seibutsu Butsuri　52　(3)　136-139　2012/05
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.52.136 　

ISSN： 0582-4052 1347-4219

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We review the relationship between information and thermodynamics, especially with focusing on the issues surrounding the Maxwell's demon. Furthermore, we briefly introduce our experimental demonstration of an "information-heat engine", which can pump heat from an isothermal environment by using information about the system's microscopic degrees of freedom.<br>
Recovery of state-specific potential of molecular motor from single-molecule trajectory Peer-reviewed

Shoichi Toyabe, Hiroshi Ueno, Eiro Muneyuki

EPL　97　(4)　40004　2012/02

DOI： 10.1209/0295-5075/97/40004 　

ISSN： 0295-5075
Thermodynamic efficiency and mechanochemical coupling of F1-ATPase. International-journal Peer-reviewed

Shoichi Toyabe, Takahiro Watanabe-Nakayama, Tetsuaki Okamoto, Seishi Kudo, Eiro Muneyuki

Proceedings of the National Academy of Sciences of the United States of America　108　(44)　17951-6　2011/11/01

DOI： 10.1073/pnas.1106787108 　

ISSN： 0027-8424
Fabrication and placement of a ring structure of nanoparticles by a laser-induced micronanobubble on a gold surface. International-journal Peer-reviewed

Sho Fujii, Katsuhiko Kanaizuka, Shoichi Toyabe, Katsuaki Kobayashi, Eiro Muneyuki, Masa-aki Haga

Langmuir : the ACS journal of surfaces and colloids　27　(14)　8605-10　2011/07/19

DOI： 10.1021/la201616s 　

ISSN： 0743-7463
情報を自由エネルギーに変換する(非平衡系の物理-非平衡ゆらぎと集団挙動-,研究会報告)

鳥谷部祥一

物性研究　96　(1)　11-14　2011/04/05
Publisher: 物性研究刊行会
ISSN： 0525-2997
情報と熱と悪魔―熱運動を利用する Invited

Shoichi Toyabe

Kagaku　81　(11)　1142-1145　2011
Publisher: 岩波書店
ISSN： 0022-7625
Single-molecule nonequilibrium energetics of a molecular-motor F_1-ATPase(4th Mini-Symposium on Liquids -Liquid in Life-) :

95　(3)　320-322　2010/12/05
Publisher:
ISSN： 0525-2997
Experimental demonstration of information-to-energy conversion and validation of the generalized Jarzynski equality

Shoichi Toyabe, Takahiro Sagawa, Masahito Ueda, Eiro Muneyuki, Masaki Sano

NATURE PHYSICS　6　(12)　988-992　2010/12

DOI： 10.1038/NPHYS1821 　

ISSN： 1745-2473
Observation of DNA pinning at laser focal point on Au surface and its application to single DNA nanowire and cross-wire formation. International-journal Peer-reviewed

Sho Fujii, Katsuaki Kobayashi, Katsuhiko Kanaizuka, Tetsuaki Okamoto, Shoichi Toyabe, Eiro Muneyuki, Masa-Aki Haga

Bioelectrochemistry (Amsterdam, Netherlands)　80　(1)　26-30　2010/11

DOI： 10.1016/j.bioelechem.2010.04.004 　

ISSN： 1567-5394
Nonequilibrium energetics of a single F1-ATPase molecule. International-journal Peer-reviewed

Shoichi Toyabe, Tetsuaki Okamoto, Takahiro Watanabe-Nakayama, Hiroshi Taketani, Seishi Kudo, Eiro Muneyuki

Physical review letters　104　(19)　198103-198103　2010/05/14

DOI： 10.1103/PhysRevLett.104.198103 　

ISSN： 0031-9007

eISSN： 1079-7114
Manipulation of Single DNA Using a Micronanobubble Formed by Local Laser Heating on a Au-coated Surface

Sho Fujii, Katsuaki Kobayashi, Katsuhiko Kanaizuka, Tetsuaki Okamoto, Shoichi Toyabe, Eiro Muneyuki, Masa-aki Haga

CHEMISTRY LETTERS　39　(2)　92-93　2010/02

DOI： 10.1246/cl.2010.92 　

ISSN： 0366-7022

eISSN： 1348-0715
Nonequilibrium Energetics of a Single F1-ATPase Molecule

Shoichi Toyabe, Tetsuaki Okamoto, Takahiro Watanabe-Nakayama, Hiroshi Taketani, Seishi Kudo, Eiro Muneyuki

Physical Review Letters　104　198103　2010

DOI： 10.1103/PhysRevLett.104.198103 　
Energy dissipation of a Brownian particle in a viscoelastic fluid (vol 77, art no 041403, 2008)

Shoichi Toyabe, Masaki Sano

PHYSICAL REVIEW E　77　(5)　2008/05

DOI： 10.1103/PhysRevE.77.059902 　

ISSN： 1539-3755
Energy dissipation of a Brownian particle in a viscoelastic fluid. International-journal Peer-reviewed

Shoichi Toyabe, Masaki Sano

Physical review. E, Statistical, nonlinear, and soft matter physics　77　(4 Pt 1)　041403-041403　2008/04

DOI： 10.1103/PhysRevE.77.041403 　

ISSN： 1539-3755
Effect of external torque on the ATP-driven rotation of F1-ATPase. International-journal Peer-reviewed

Takahiro Watanabe-Nakayama, Shoichi Toyabe, Seishi Kudo, Shigeru Sugiyama, Masasuke Yoshida, Eiro Muneyuki

Biochemical and biophysical research communications　366　(4)　951-7　2008/02/22

DOI： 10.1016/j.bbrc.2007.12.049 　

ISSN： 0006-291X

eISSN： 1090-2104
Experimental test of a new equality: measuring heat dissipation in an optically driven colloidal system. International-journal Peer-reviewed

Shoichi Toyabe, Hong-Ren Jiang, Takenobu Nakamura, Yoshihiro Murayama, Masaki Sano

Physical review. E, Statistical, nonlinear, and soft matter physics　75　(1 Pt 1)　011122-011122　2007/01

DOI： 10.1103/PhysRevE.75.011122 　

ISSN： 1539-3755
Spatial Suppression of Error Catastrophe in a Growing Pattern

Shoichi Toyabe, Masaki Sano

Physica D　203　1　2005

DOI： 10.1016/j.physd.2005.02.011

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Books and Other Publications 4

生物物理学 (物理学アドバンストシリーズ)

鳥谷部祥一

日本評論社　2022/08/30

ISBN: 453578972X
１分子生物学

宗行英朗, 鳥谷部祥一, 上野博史

化学同人　2014/10/10

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原田慶恵 (編集), 石渡信一 (編集)
１分子ナノバイオ計測

宗行英朗, 鳥谷部祥一

化学同人　2014/06/30

ISBN: 9784759807530

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野地博行編
ナノスケール・ミクロスケールから見えるビックな世界

宗行英朗, 鳥谷部祥一

中央大学出版　2013/10

ISBN: 9784805792087

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新藤斎編著

Research Projects 14

沙川情報エネルギー変換プロジェクト

沙川貴大

Offer Organization: 科学技術振興機構

System: 戦略的な研究開発の推進戦略的創造研究推進事業 ERATO

Institution: 東京大学

2023 - 2028

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現在実用化されている計算機は原理的な限界よりもはるかに大量のエネルギーを消費していると見られており、莫大な計算量に伴うエネルギー消費量の増加が深刻な問題となっています。今後さらに計算量が増大することが予想されることから、高速な情報処理と高いエネルギー効率を同時に実現する新機軸となる学理の創出が期待されています。このような背景の中で、本プロジェクトでは、「いかにして、トレードオフ関係にある高速な情報処理と高いエネルギー効率を同時に達成するか」という課題を設定し、その原理限界と、原理限界達成に向けた方法を明らかにするために、研究総括が先駆者となって発展した「情報熱力学」の成果を通じ、理論と実験の両面で取り組みます。具体的には、古典から量子にわたる実験系で、熱ゆらぎ・量子ゆらぎの観測と制御により情報と熱力学的エネルギーの変換を検証することにより、情報処理に必要なエネルギーの原理限界を明らかにします。それらの知見を統合して統一的な理論を構築し、「情報と熱力学的エネルギーの相互変換の原理限界」の学理の確立を目指します。本研究を通じて、将来的には新しい計算機の概念の構築につながることが期待されます。
Optimal Transport Protocols for Biomolecular Machinery - Approaching the Principle Limits of Control of Microscopic Systems

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (B)

Institution: Tohoku University

2023/04/01 - 2027/03/31
エラー制御の物理が生み出す革新的バイオ技術

鳥谷部祥一

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 挑戦的研究(萌芽)

Institution: 東北大学

2023/06/30 - 2026/03/31
人工分子モーターが切り拓く「自律的ナノマシンの実験物理学」

鳥谷部祥一

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 基盤研究(B)

Institution: 東北大学

2019/04/01 - 2023/03/31

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本年度から，DNAオリガミベースの「やわらかい」人工モーターの実現に向けた研究を開始した．人工分子モーターは，ラチェット型と構造変化型の2つに分類することができる．ラチェット型はメカニズムがシンプルであるが，パフォーマンスは悪い．また，すでにある程度の研究の積み重ねがある．一方，構造変化型は複雑でありこれまでの実現例が存在しないが，大きなパフォーマンスが得られると期待できる．両者には一長一短があり，両方のアプローチで進めるのが良い．本年度は，これら２つのアプローチの両方でDNAオリガミベースの人工分子モーター実現に向けた研究を進めた．ラチェット型に関しては，燃料供給，構造で決まる方向性，スケーラビリティという重要な3つの要素をすべて満たすモーターは実現していない．そこで，従来型のバーントブリッジラチェット型モーターから出発し，これに燃料供給＋構造非対称を加えたモデルを構築し，数値計算によりその動作を確認した．その結果，新しい運動メカニズムを提案し，特に，一方向に運動し続ける条件を発見した．現在，論文を執筆中であり，近日中に投稿予定である．また，構造変化型に関しては，まず，脚となるヒンジ型構造を設計し，DNAオリガミで構造を作った．また，分子動力学法に基づいた数値計算で動作を確認した．構造が正しく出来ていることは透過型電子顕微鏡で確認できた．2021年度後半は，燃料の付加によるヒンジの折れ曲がりを確認していた．特に，電顕と電気泳動からは，燃料の結合が不十分であると推測され，現在，設計の見直しを行っている．また，電顕では静的な構造しか観察できないが，色違いの量子ドットを複数結合することで，蛍光顕微鏡で動的な構造変化を観察できる．このための準備として，カルボキシル基付き量子ドットへのDNA修飾ができることを確認した．
Statistical physics and energetics for autonomous motion and functional design in active molecular engines

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Institution: Kyushu University

2018/06/29 - 2023/03/31
Structure formation of functional nano-sized structure by nano 3D pen

TOYABE Shoichi, SAKAMOTO yuki, KAI tatsuro

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Challenging Research (Exploratory)

Institution: Tohoku University

2017/06/30 - 2019/03/31

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In this research project, we aimed to develop a novel "nano 3D pen" technology by combining the "colloidal particle 3D printer" technology developed we developed previously and the technology to aggregate small particles using a temperature gradient. We expect that the "nano 3D pen" will realize a dynamic and diverse function nano-molecule robot and a platform for spatially arranging biomolecules and cells in an arbitrary pattern. In this project, we established the technology of structure formation modified by hairpin DNA strands by laser scanning, which is the core of "nano 3D pen" technology. On the other hand, the problem remains in the shaping speed, and it is necessary to devise the optimization of the solution conditions and the sequence design of the hairpin DNA used for connecting particles.
揺らぐ非平衡構造によるフィードバック制御：べん毛モーターのトルク発生機構の解明

鳥谷部祥一

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 新学術領域研究(研究領域提案型)

Institution: 東北大学

2016/04/01 - 2018/03/31

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H28年度に構築したトルクスピードカーブ測定法を発展させ，以下の成果を挙げた． 1. 固定子の蛍光観察．蛍光たんぱく質を融合した固定子を用い，固定子のモーターへの結合数を蛍光強度から測定できる系を構築した．この実験系は，すでに他研究室で実現されているが，当研究室では，回転電場法と組み合わせることで，今後，トルク発生と固定子脱着の同時観察に挑戦する．特に，負荷をON/OFFさせて蛍光強度変化のタイミングを測定することで，固定子の結合・解離の時定数の負荷依存性を決定することを目指す．これらの実験から仮説を検証し，固定子の結合解離メカニズムを究明する． 2. 解析法の改良．テザードセル法では，回転の揺らぎが小さいため，実験系のノイズの影響が大きくなり，測定に大きな問題が生じていた．そこで，Speck-Seifertの等式[Speck and Seifert, EPL 74, 391(2006)]を用い，回転速度から角度ごとの局所的な平均速度を引くことで，実験系のノイズを著しく減らすことに成功し，揺らぎの高精度測定が可能となった．これにより，より正確なトルクスピードカーブが得られるようになった． 3. 変異型モーターのトルクスピードカーブの測定．プロトンの流れが遅い変異型（M206IおよびD33E），および，固定子がなく回転ブラウン運動をする変異型（ΔMotAB）を用い，トルクスピードカーブを測定した．これまで，M206Iはゼロトルクスピードが低く，また，D33Eはストールトルクおよびゼロトルクスピードが低いことが知られていた．回転電場法を用いた本研究においても，同様の傾向が得られ，測定法の妥当性を実証することができた．以上の2および3について論文を執筆中である．
Symmetry breaking of sequence information and emergence of genetic information in templated ligation system

Toyabe Shoichi

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Young Scientists (A)

Institution: Tohoku University

2015/04/01 - 2018/03/31

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The emergence of molecular species, which can stably keep and replicate its genetic information, is central to the origin of life. However, the mechanism leading to such emergence remains unknown. Here, on the basis of our previously proposed mechanism for the spontaneous emergence of molecular-species-like structure in templated ligation reaction, we investigated the detailed conditions for this emergence and the interaction between multiple molecular species. In addition, control of information replication error in the templated ligation was achieved.
分子モーターとDNAオリガミのハイブリッドで「感覚を持つ分子ロボット」を創る

鳥谷部祥一

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 新学術領域研究(研究領域提案型)

Institution: 東北大学

2015/04/01 - 2017/03/31

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自律的な人工微小ロボットの実現は，ナノテクノロジーの目標の１つである．ロボットであるからには動かしたいが，アクチュエーターを造るのが難しい．一方で，生体内では超高性能のアクチュエーターである分子モーターが働いている．そこで，この分子モーターをアクチュエーターとして利用することで，自律的な分子ロボットの実現を目指した．我々は，船体となるマイクロメートルサイズの粒子に，アクチュエーターとして回転分子モーターである F1-ATPaseの固定子を接着し，その回転軸に DNAオリガミで造ったスクリューを結合することで，バクテリアのように遊泳するロボットをデザインした．まず，DNAオリガミで造ったねじれた円柱を重合させることで，スクリューとなるらせん状の構造体を設計通りに実現することができた．構造は AFMや全反射顕微鏡を用いた蛍光観察等で確認した．さらに，このスクリュー， F1-ATPase, プラスチック粒子を組み合わせて構造体を組み立てることに成功した．しかし，これだけでは明らかな遊泳運動を観察することはできなかった．ひとつの原因として，F1-ATPase１分子によって生じる推進力が弱いことが考えられた．そこで，モーターの並列化による推進力の増強を試みた．粒子の片側のみを金蒸着した「ヤヌス粒子」を作成し，F1-ATPaseは，その反対側のみに接着するようにした．実際，F1-ATPase分子がほぼ片側のみに結合することを蛍光観察で確認できた．しかし，このヤヌス粒子を用いても，明らかな遊泳運動は観察できなかった．蛍光観察で詳細に見てみると，粒子表面で異なるモーターに結合したDNAオリガミ同士が凝集してしまっているように見えた．現在，この凝集を抑えて遊泳運動を観察するために，オリガミ作成条件の再検討を行っている．
Development of nano-particle 3D printer and realization of dynamic and multi-functional molecular robots

Toyabe Shoichi

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Challenging Exploratory Research

Institution: Tohoku University

2015/04/01 - 2017/03/31

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We developed a novel process for assembling microstructures that are functional, flexible, and dynamic. As an example, we present the assembly of a microscopic robot arm actuated by an external magnet. Diverse particles modified with DNA strands are used for the assembly, and the flexible connection formed by the DNA strands provides the control and dynamic capabilities of the microstructure. We believe that our study makes a significant contribution to the literature because it overcomes the limitations of assembling microstructures using conventional lithographic processes and opens a new possibility to reazlize microscale autonomous machines.
分子モーターの1分子トラジェクトリからポテンシャルを描く

鳥谷部祥一, 上野博史

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 挑戦的萌芽研究

Institution: 中央大学

2011 - 2011

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分子モーターは,化学エネルギーを力学運動に変換するナノサイズの化学エンジンである.したがって,そのエネルギー論を議論することは,分子モーターの動作原理を理解するうえで本質的である.特に,回転分子モーターF1-ATPaseは生体内で自由エネルギー変換の中心的な役割を担い,そのエネルギー論は生物学的にも重要である.F1-ATPaseはほぼ100%の自由エネルギー変換効率を持つことが知られており,なぜこのような高効率を実現できるのか,非平衡熱力学の観点からも興味深い.我々は,1分子トラジェクトリのみから,分子モーターの力学ポテンシャルを見積もる方法をすでに開発している.本研究課題では,この方法をF1-ATPaseに応用し,F1-ATPaseの高効率な自由エネルギー変換機構の仕組みを解明しようと試みた.我々は,光学系の調整と高度な画像処理により,露光時間40usで1秒間に9000枚の画像をリアルタイムでPCに記録できるシステムを構築した.このシステムを用いてF1-ATPaseの極めて時間分解能の高い1分子トラジェクトリを測定し,上記の方法を用いて解析した.その結果,F1-ATPaseの化学状態ごとの力学ポテンシャル,力学ポテンシャルが切り替わる瞬間の回転軸の角度,回転によって生じる熱散逸量などを,1分子トラジェクトリのみから推定することに成功した.そして,化学状態がランダムに切り替わるのではなく,中心の回転軸が少し進んだところでのみ状態が切り替わることを発見した.これは,F1-ATPaseが,"Diffusion-and-catch"と"Power stroke"の2つの機構を巧みに利用してトルクを発生していることを示唆している.これが,F1-ATPaseが高効率性を実現している理由の1つだと推測される.このような知見はある程度予想されてはいたものの,実験データから導き出したのは初めてであり画期的な成果と言える.
隠れた自由度を持つタンパク質-分子のパラメータ推定法

原田崇広, 鳥谷部祥一

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 特定領域研究

Institution: 東京大学

2009 - 2011

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タンパク質のダイナミクスの研究では、アミノ酸の数と同程度の膨大な自由度を考慮するのが一般的である。しかし、最近の1分子実験や分子シミュレーションの結果を統合すると、少なくともモータータンパク質など比較的大きな構造変化をするタンパク質は、その大域的で遅いダイナミグスは高々2～3程度の自由度で粗視化できることが分かってきた。このような実験結果を踏まえて、タンパク質のダイナミクスを低次元のLangevin系でモデル化する試みがされている。しかしタンパク質1分子の動きは直接観察出来ない。リンカーを介して結合されたプローブ粒子の動きから、タンパク質の動きや粗視化モデルの物性パラメータを推定する枠組みが必要となる。この問題に対してベイズ推定の枠組みで取り組み、隠れた自由度を持つ微小系に対するパラメータ推定法を構築し、Langevinモデルで数値実験を行いその有効性を確認した。一方で内部自由度の緩和時間よりもプローブの緩和時間が長くなるとき、推定結果が急激に不安定になる一種の相転移を初めて見出した。パラメータ推定が容易な領域では、観測時間に比例して推定誤差が減少していくことが確かめられ、我々の理論と一致する結果を得た。パラメータ推定では一般に、モデルパラメータが決まれば、経路確率の隠れた自由度に関する最大化で、隠れた自由度の最尤軌道も求めることができる。しかし、準安定状態が多数あるポテンシャルを含むLangevin系の場合、通常の緩和法では最尤軌道の計算コストが膨大になる。そこで、摂動展開を用いて最尤軌道の近似解を逐次的に構成する手法を考案した(往復法)。1分子実験の粗視化モデルで数値実験を行い、緩和法に比べて3桁以上速く解が収束することを確認した。さらに、初期条件と境界条件の選択によらず、ほぼ一意で適切な解が得られることを示した。
Exploring Fundamental Theory of Non-equilibrium Systems using Micro-manipulation

SANO Masaki, TOYABE Shoichi

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (A)

Institution: The University of Tokyo

2009 - 2011

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We succeeded to demonstrate the first realization of a Szilard-type Maxwell’s demon. We performed a nonequilibrium feedback manipulation of a Brownian particle based on information about its location achieves information-energy conversion. Moreover, a new nonequilibrium equality concerning the feedback control has been shown to hold. Furthermore, we realized self-propelling Janus particles by defocused laser irradiation. We found that the motion is caused by self-thermophoresis: i.e. migration due to a local temperature gradient induced by laser heating at the metal coated side of the Janus particle.
Measurement of nonequilibrium fluctuations of molecular motor F1-ATPase

TOYABE Shoichi

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Young Scientists (B)

Institution: Chuo University

2009 - 2010

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In order to reveal the energetics of rotary molecular motor F1-ATPase, we measured the response of F1-ATPase against a constant and periodic torque by using an electrorotation method. We found that F1-ATPase can convert the chemical free energy change of ATP hydrolysis to mechanical motion.

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