Toyabe S, Braun D
Cooperative ligation breaks sequence symmetry and stabilizes early molecular evolution.
arXiv:1802.06544, to appear in Phys. Rev. X. (2019)

生体分子モーター -進化が生んだ超高性能ナノマシンー
精密工学会誌 84(11), 905 (2018)

Sato K, Nakamura S, Kudo S, Toyabe S,
Evaluation of the duty ratio of bacterial flagellar motor by a dynamic load control.
arXiv:1806.06470 (2018)

Tahara H, Takabe K, Sasaki Y, Kasuga K, Kawamoto A, Koizumi N, Nakamura S.
The mechanism of two-phase motility in the spirochete Leptospira: Swimming and crawling.
Sci. Adv. 4, eaar7975 (2018)

生物工学会誌 96(4), p195-199(2018)

Sasaki Y, Kawamoto A, Tahara H, Kasuga K, Sato R, Ohnishi M, Nakamura S, Koizumi N.
 Leptospiral flagellar sheath protein FcpA interacts with FlaA2 and FlaB1 in Leptospira biflexa.
PLOS One 13, e0194923 (2018)

CSJカレントレビュー26「分子マシンの科学 分子の動きとその機能を見る」,p91-96. 化学同人(2017)

Takabe K, Kawamoto A, Tahara H, Kudo S, Nakamura S.
Implications of coordinated cell-body rotations for Leptospira motility.
Biochem. Biophys. Res. Commun., 491, p1040-1046 (2017)

Terahara N, Noguchi Y, Nakamura S, Kami-ike N, Ito M, Namba K, Minamino T.
Load- and polysaccharide-dependent activation of the Na+-type MotPS stator in the Bacillus subtilis flagellar motor.
Sci. Rep. 7: 46081 (2017)

Takabe K, Tahara H, Md. Islam S, Affroze S, Kudo S, and Nakamura S.
Viscosity-dependent variations in the cell shape and swimming manner of Leptospira.
Microbiology 163, p153-160 (2017)

Nakamura S, Md. Islam S.
Motility of Spirochetes. Methods in Microbiology 1593 “The Bacterial Flagellum, Methods and Protocols”, p243–251. Springer (2017)

S. Toyabe
物性研究 6, 064211 (2017) (Lecture notes in Japanese)

Sakamoto Y, Toyabe S
Assembly of a functional and responsive microstructure by heat bonding of DNA-grafted colloidal brick
Sci. Rep. 7, 9104 (2017)

Abe T, Nakamura S, Kudo S.
Bioconvection induced by bacterial chemotaxis in a capillary assay.
Biochem. Biophys. Res. Commun. 483, p277-282 (2017)

Toyabe S
Decoding Fluctuation: Diffusional Analysis of Biological Molecular Motors
J. Phys. Soc. Jpn. News Comments, 13, 07 (2016) (News article)

Affroze S, Md. Islam S, Takabe K, Kudo S, Nakamura S.
Characterization of leptospiral chemoreceptors using a microscopic agar drop assay.
Curr. Microbiol. 73, 202-205. (2016)

Xu J, Nakamura S, Md. Islam S, Guo Y, Ihara K, Tomioka R, Masuda M, Yoneyama H, Isogai E.
Mannose-binding lectin inhibits the motility of pathogenic Salmonella by affecting the driving forces of motility and the chemotactic response.
PLoS One 11, e0154165  (2016)

Toyabe S., Sano M.
Nonequilibrium fluctuations in biological strands, machines, and cells (Review article).
J. Phys. Soc. Japan, 84,  102001 (2015)
Md. Shafiqul Islam, Yusuke V. Morimoto, Seishi Kudo, Shuichi Nakamura
H+ and Na+ are involved in flagellar rotation of the spirochete Leptospira
Biochem. Biophys. Res. Comm., 466, 196-200 (2015)

Hayashi R., Sasaki K, Nakamura S., Kudo S., Inoue Y., Noji H. and Hayashi K..
Giant acceleration of diffusion observed in a single-molecule experiment on F1-ATPase.
Phys. Rev. Lett. 114, 248101 (2015)
Nakamura S, Morimoto YV, Kudo S.
A lactose fermentation product produced by Lactococcus lactis subsp. lactis, acetate, inhibits the motility of flagellated pathogenic bacteria.
Microbiology 161, 701 (2015)
Xu J, Guo Y, Nakamura S, Islam Md. S, Tomioka R, Yoneyama H, Isogai E.
Mannose-Binding Lectin Impairs Leptospira Activity through the Inhibitory Effect on the Motility of Cell.
Microbiological Research 171, 21 (2015)
Guo Y, Fukuda T, Nakamura S, Bai L, Xu J, Kuroda K, Tomioka R, Yoneyama H, Isogai E.
Interaction between Leptospiral Lipopolysaccharide and Toll-like Receptor 2 in Pig Fibroblast Cell Line, and Inhibitory Effect of Antibody against Leptospiral Lipopolysaccharide on Interaction.
Asian Australas. J. Anim. Sci. 28: 273-279. (2015)

Toyabe S. and Muneyuki E.
Single molecule thermodynamics of ATP synthesis by F1-ATPase
New J. Phys. 17: 015008 (2015)
 Nakamura S.,
日本細菌学雑誌 69: 527-538 (2014)

Guo Y, Fukuda T, Donai K, Kuroda K, Masuda M, Nakamura S, Yoneyama H and Isogai E.
Leptospiral lipopolysaccharide stimulates the expression of toll-like receptor 2 and cytokines in pig fibroblasts.
Anim. Sci. J. in press. (2014)

Islam Md. S, Takabe K, Kudo S and Nakamura S.
Analysis of the chemotactic behaviour of Leptospira using microscopic agar-drop assay.
FEMS Microbiol. Lett. 365: 39-44. (2014)

Nakamura S, Minamino T, Kami-ike N, Kudo S and Namba K.
Effect of the MotB(D33N) mutation on stator assembly and rotation of the proton-driven bacterial flagellar motor.
BIOPHYSICS 10: 35-41. (2014)

Nakamura S., Leshansky A., Magariyama Y., Namba K., Kudo S..
Direct measurement of helical cell motion of the spirochete Leptospira.
Biophys. J. 106: 47-54. (2014)

Che YS, Nakamura S, Morimoto YV, Kami-Ike N, Namba K, Minamino T.
Load-sensitive coupling of proton translocation and torque generation in the bacterial flagellar motor.
Mol. Microbiol. 91:175-184. (2014)

Muneyuki E. and Toyabe S.
a chapter in "1分子ナノバイオ計測" (化学同人) edited by Hiroyuki Noji (in Japanese)
see Amazon.co.jp

Muneyuki E., Toyabe S., and Ueno H.
FoF1 モーター
a book chapter in "1分子生物学" (化学同人) edited by Yoshie Harada and Shin-ichi Ishiwata (in Japanese) see Amazon.co.jp 

Castillo DJ, Nakamura S., YV. Morimoto, YS Che, N. Kami-ike, Kudo S., T. Minamino, K. Namba.
The C-terminal periplasmic domain of MotB is responsible for load-dependent control of the number of stators of the bacterial flagellar motor.
BIOPHYSICS 9: 173-181. (2013)

Kishikawa J, Ibuki T, Nakamura S, Nakanishi A, Minamino T, Miyata T, Namba K, Konno H, Ueno H, Imada K, Yokoyama K.
Common evolutionary origin for the rotor domain of rotary ATPases and flagellar protein export apparatus.
PLoS One. 8:e64695. (2013)

Takabe K, Nakamura S, Ashihara M, Kudo S.
Effect of osmolarity and viscosity on the motility of pathogenic and saprophytic Leptospira.
Microbiol. Immunol. 57:236-9. (2013)

Guo Y, Nakamura S, Ando T, Yoneyama H, Kudo S, and Isogai E.
The inhibition effect of antiserum on the motility of Leptospira.
Curr. Microbiol. 66:359-64. (2013)

Morimoto Y.V., Nakamura S, Hiraoka K.D., Namba K, Minamino T.
Distinct roles of highly conserved charged residues at the MotA-FliG interface in bacterial flagellar motor rotation.
J. Bacteriol.195:474-81. (2013)

Toyabe S. and Muneyuki E.
Experimental thermodynamics of single molecular motor
biophysics 9, 91 (2013) (Review article)  

Toyabe S. and Muneyuki E.
Information-to-free-energy conversion: utilizing thermal fluctuations
biophysics 9, 107 (2013) (Review article)  

Muneyuki E. and Toyabe S.
Demonstration of Maxwell's demon
a chapter in "ナノスケール・ミクロスケールから見えるビッグな世界" (Chuo University Press, 2013)  (in Japanese)
see amazon.co.jp

Miyazaki S., Matsumoto M., Brier S. B., Higaki T., Yamada T., Okamoto T., Ueno H., Toyabe S., and Muneyuki E.
Properties of electrogenic activity of bacteriorhodopsin
Eur. Biophys. J. 42, 257 (2013)  

Kikuchi Y., Naka Y., Osakabe H., Okamoto T., Masaike T., Ueno H., Toyabe S., and Muneyuki E.
Thermodynamic analyses of nucleotide binding to an isolated monomeric β subunit and the α3β3γ subcomplex of F1-ATPase
Biophys. J. 105, 2541 (2013)  

Toyabe S., Ueno H., and Muneyuki E.
Recovery of state-specific potential of molecular motor from single-molecule trajectory
EPL 97, 40004 (2012)

Toyabe S. and Muneyuki E.
生物物理 52, 136 ( 2012)  (Review article in Japanese)

Faulds-Pain A., Birchall C., Aldridge C., Smith W.D., Grimaldi G.., Nakamura S., Miyata T., Gray J., Li G., Tang J.X., Namba K., Minamino T. and Aldridge P.D.
Flagellin redundancy in Caulobacter crescentus and its implications for flagellar filament assembly.
J. Bacteriol. 193, 2695-2707. (2011)

Minamino T., Imada K., Kinoshita M., Nakamura S., Morimoto Y.V. and Namba K.
Structural insight into the rotational switching mechanism of the bacterial flagellar motor.
PLoS Biol. 9:e1000616. (2011)

中村修一, 南野徹
化学と生物, 49巻1号, 22-31 (2011) (review in Japanese)

Toyabe S., T. Watanabe-Nakayama, T. Okamoto, Kudo S., and Muneyuki E.
Thermodynamic efficiency and mechanochemical coupling of F1-ATPase
Proc. Natl. Acad. Sci. USA 108, 17951 (2011)  

Toyabe S.
科学 81, 1142 (2011)  (Review article in Japanese)

Toyabe S.
物性研究 96, 11 (2011)  
- for a conference "Physics of Nonequilibrium Systems -Fluctuation and Collective Behavior-" at YITP (in Japanese)

Fujii S., Kanaizuka K., Toyabe S., Kobayashi K., Muneyuki E., and Haga M.
Fabrication and Placement of a Ring Structure of Nanoparticles by a Laser-Induced Micronanobubble on a Gold Surface
Langmuir 27, 8605 (2011) 

Morimoto Y.V.*, Nakamura S.*, Kami-ike N., Namba K. and Minamino T. (*equal contribution)
Charged residues in the cytoplasmic loop of MotA are required for stator assembly in to the bacterial flagellar motor.
Mol. Microbiol. 78: 1117-1129. (2010)

Nakamura S., Kami-ike N., Yokota J.P., Minamino, T. and K. Namba.
Evidence for symmetry in the elementary process of bidirectional torque generation by the bacterial flagellar motor.
Proc. Natl. Acad. Sci. USA. 107:17616-17620. (2010)

Toyabe S., Sagawa T., Ueda M., Muneyuki E., and Sano M.
Experimental demonstration of information-to-energy conversion and validation of the generalized Jarzynski equality
Nature Physics 6, 988 (2010) - see also News&Views, Nature News, and YouTube

Toyabe S., Okamoto T., Watanabe-Nakayama T., Taketani h., Kudo S., and Muneyuki E.
Nonequilibrium energetics of a single F1-ATPase molecule
Phys. Rev. Lett. 104, 198103 (2010)

Toyabe S. and Muneyuki E.
Single-molecule nonequilibrium energetics of a molecular-motor F1-ATPase
物性研究 95, 320 (2010)
- for a conference "4th Mini-symposium on Liquids" (in Japanese)

Fujii S., Kobayashi K., Kanaizuka K., Okamoto T., Toyabe S., Muneyuki E., and Haga M.
Observation of DNA pinning at laser focal point on Au surface and its application to single DNA nanowire and cross-wire formation
Bioelectrochemistry 80, 26 (2010)

Fujii S., Kobayashi K., Kanaizuka K., Okamoto T., Toyabe S., Muneyuki E., and Haga M.
Manipulation of Single DNA Using a Micronanobubble Formed by Local Laser Heating on a Au-coated Surface
Chem. Lett. 39, 92 (2010)

Nakamura, S., Morimoto, Y.V., Kami-ike, N., Minamino, T., and K. Namba.
Role of conserved prolyl residue (Pro173) of MotA in the mechanochemical reaction cycle of the proton-driven flagellar motor of Salmonella.
J. Mol. Biol. 393:300-307. (2009)

Nakamura S., Kami-ike N., Yokota J.P., Kudo S., Minamino T., and Namba K.
Effect of intracellular pH on the torque-speed relationship of bacterial proton-driven flagellar motor.
J. Mol. Biol. 386:332-338. (2008)

Che Y-S., Nakamura S., Kojima S., Kami-ike N., Namba K., and Minamino T.
Suppressor analysis of the MotB(D33E) mutation to probe bacterial flagellar motor dynamics coupled with proton translocation.
J. Bacteriol. 190:6660-6667. (2008)

Toyabe S. and M. Sano
Evaluating Energy Dissipation of a Brownian Particle in a Viscoelastic Fluid
Phys. Rev. E 77, 041403 (2008)

Watanabe-Nakayama T., Toyabe S., Kudo S., Sugiyama S., Yoshida M., and Muneyuki E.
Effect of external torque on the ATP-driven rotation of F1-ATPase
Biochem. Biophys. Res. Comm. 366, 951 (2008)

Toyabe S., Jiang H. R., Nakamura T., Murayama Y., and Sano M.
Experimental Test of a New Equality: Measuring Heat Dissipation in an Optically Driven Colloidal System
Phys. Rev. E 75, 011122 (2007)

T. Goto, S. Kudo and Y. Magariyama
Asymmetric Swimming Motion of Singly Flagellated Bacteria near a Rigid Surface.
a book chapter in Bio-mechanisms of Swimming and Flying, 3-15 (2007)

可視化情報学会論文集,27(3), 15-21 (2007)

Nakamura S., Adachi Y., Goto T. and Magariyama Y.
Improvement in motion efficiency of the spirochete Brachyspira pilosicoli in viscous environments.
Biophys. J. 90:3019–3026. (2006)

Y. Hayashibara, T. Agui, T. Ito, M. Oohaba, E. Koyanagi, T. Sekine, M. Takeuchi, and S. Kudo
Educational program with making automatic machines continuously from the basic to the applications.
J. Robotics and Mechatronics,18, 215-221 (2006)

Toyabe S. and Sano M.
Spatial Suppression of Error Catastrophe in a Growing Pattern
Physica D 203,1 (2005)

Y. Takano, S. Kudo, M. Nishitoba, and Y. Magariyama
Analyses on Deformation of Helical Flagella of Salmonella.
JSME International J., C,48, 513-520 (2005)

Y. Magariyama, M. Ichiba, K. Nakata, K. Baba, T. Ohtani, S. Kudo, T. Goto
Difference in bacterial motion between forward and backward swimming caused by the wall effect.
Biophys J. 88, 3648-3658 (2005)
S. Kudo, N. Imai, M. Nishitoba, S. Sugiyama, and Y. Magariyama
Asymmetric swimming pattern of Vibrio alginolyticus cells with single-polar flagella.
FEMS Microbiol. Letters,242, 221-225 (2005)

Y. Magariyama, S. Kudo, T. Goto and Y. Takano
An Engineering Perspective on Swimming Bacteria: High-Speed Flagellar Motor, Intelligent Flagellar Filaments, and Skillful Swimming in Viscous Environments
Bio-mechanisms of Swimming and Flying, 1-12 (2004)

S. Sugiyama, Y. Magariyama and S. Kudo
Forced rotation of Na+-driven flagellar motor in a coupling-ion free environment.
Biochimica et Biophysica Acta,1656,32-36 (2004)

Y. Takano, K. Yoshida, S. Kudo, M. Nishitoba and Y. Magariyama
Analysis of small deformation of Helical flagellum of swimming Vibrio alginolyticus.
JSME International J., C,46, 1241-1247 (2003)

Y. Magariyama and S. Kudo
A Mathematical Explanation of an Increase in Bacterial Swimming Speed with Viscosity in Linear-Polymer Solutions.
Biophys. J. 83,733-739 (2002)

基礎としての物理学 (生命科学の基礎シリーズ第2巻)
実教出版 (2002)

Y. Magariyama, S. Masuda, Y. Takano, T. Ohtani, and S. Kudo
Difference between forward and backward swimming speeds of the single-polar-flagellated bacterium, Vibrio alginolyticus.
FEMS Microbiol. Letters 205, 343-347 (2001)
Y. Magariyama, S. Sugiyama and S. Kudo
Bacterial swimming speed and rotation rate of bundled flagella.
FEMS Microbiol. Letters,199,125-129 (2001)

日本機械学会誌,104, 602-603 (2001)

日本機械学会誌,103, 38-41 (2000)

トライボロジスト 44, 420-425 (1999)

パリティ,13, 4-12

S. Kojima, T. Atsumi, K. Muramoto, S. Kudo, I. Kawagishi and M. Homma
Vibrio alginolyticus mutants resistant to phenamil, a specific inhibitor of the sodium-driven flagellar motor.
J. Mol. Biol. 265, 310-318 (1997)

応用物理学会、有機分子・バイオエレクトロニクス分科会・会誌 8, 131-140 (1997)

K. Muramoto, Y. Magariyama, M. Homma, I. Kawagishi, S. Sugiyama, Y. Imae and S. Kudo
Rotational fluctuation of the sodium-driven flagellar motor of Vibrio alginolyticus induced by binding of inhibitors
J. Mol. Biol. 259, 687-695 (1996)
日本ロボット学会誌,14, 1125-1128 (1996)

菌血症モデルにおける白血球レオロジー —毛細血管モデルを用いた観察—.
Proc. 8th Jikei Symp. on Hemorheology, 53-60 (1996)

Y. Magariyama, S. Sugiyama, K. Muramoto, I. Kawagishi, Y. Imae and S. Kudo
Simultaneous Measurement of Bacterial Flagellar Rotation Rate and Swimming Speed.
Biophys. J. 69, 2154-2162 (1995)

K. Muramoto, I. Kawagishi, S. Kudo, Y. Magariyama, Y. Imae and M. Homma
High-speed Rotation and Speed Stability of the Sodium-driven Flagellar Motor in Vibrio alginolyticus
J. Mol. Biol. 251,50-58 (1995)

Y. Kikuchi, Y. Magariyama, S. Sugiyama and S. Kudo
 Leukocyte Rheology in a Model of Bacteria.
Microcirc. ann. 11, 31-32 (1995)

トライボロジスト,40, 488-493 (1995)

メカライフ 41, 38-39

Very fast flagellar rotation
Y. Magariyama, S. Sugiyama, K. Muramoto, Y. Maekawa, I. Kawagishi, Y. Imae and S. Kudo
Nature 371, 752 (1994)

機械の研究 46, 210-213 (1994)

技報 安川電機 58, 204-207 (1994)

M. Washizu, Y. Kurahashi, H. Iochi, O. Kurosawa, S.-I. Aizawa, S. Kudo, Y. Magariyama, and H .Hotani
Dielectrophoretic Measurement of Bacterial Motor Characteristics.
IEEE Trans. Industry Applicat. 29, 286-294 (1993)

材料科学,30, 210-214, (1993)

N. Kami-ike, S. Kudo and H. Hotani
Rapid changes in flagellar rotation induced by external electric pulses.
Biophys. J.,60,1350-1355 (1991)

生物物理 31, 38-40 (1991)

豊田中央研究所 R&D レビュー 26, 31-47 (1991)

東海化学工業会報 164, 1-4 (1991)

S. Kudo, Y. Magariyama and S.-I. Aizawa
Abrupt changes in flagellar rotation observed by laser dark-field microscopy.
Nature 346, 677-680 (1990)

工藤成史, 小澤正邦
論 複合振動子法によるセラミックスの弾性率測定(第1報)-簡易化と高精度化-.
日本セラミックス協会学術論文誌,98, 653-657 (1990)
小澤正邦, 工藤成史
日本セラミック協会学術論文誌,98, 987-990 (1990)

小澤正邦, 工藤成史
ファインセラミックス,53, 266-2741 (1990)

細胞,22, 267-270 (1990)
H. Okino, M. Isomura, S. Yamaguchi, Y. Magariyama, S. Kudo and S.-I. Aizawa
Release of Flagellar Filament-Hook-Rod Complex by a Salmonella typhimurium Mutant Defective in the M-Ring of the Basal Body.
J. Bacteriol.,171(4), 2075-2082 (1989)

S. Kudo and M. Ozawa
Evaluation and Minimization of Experimental Errors in Elastic Constants and Internal Friction Obtained by the Composite-Bar Method.
Jpn. J. Appl. Phys., 28 (Supplement 28-2),184-186 (1989)

S. Kudo, J. Mizuno and H. Hasegawa
Raman Microprobe Study of Phase Transfor-mation in Y2O3-PSZ.
Adv. Ceramics,24,103-108 (1988)
工藤成史, 水野二郎, 長谷川英雄
Y2O3-PSZ における応力誘起相変態の顕微ラマン観察.

S. Kudo
X-Ray Determination of Incommensurate Superlattices in K2SeO4 and (NH4)2BeF4.
Jpn. J. Appl. Phys.,21,255-258 (1982)

S. Kudo and T. Ikeda
Birefringence and Lattice Strain in K2SeO4.
J. Phys. Soc. Jpn.,50, 3681-3687 (1981)
S. Kudo and T. Ikeda
Hydrostatic Pressure Effect on the Dielectric Properties of K2SeO4.
J. Phys. Soc. Jpn.,50(3),(1981),733-734
S. Kudo and T. Ikeda
Elastic Compliance Anomalies in K2SeO4.
Jpn. J. Appl. Phys.,19(1),(1980),L45-L48

S. Kudo and T. Hikita
Brillouin Scattering Study of Ferroelectric (NH4)2BeF4.
J. Phys. Soc. Jpn.,45(5),(1978),1775-1776

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