Activities
List of Publication
(as of 1. March 2022)Articles in journals: (with peer review)
2024
Dynamics of Centipede Locomotion Revealed by Large-Scale Traction Force Microscopy,
Rieu,J.P., Delanoë-Ayari1,H.,Barentin1,C., Nakagaki,T. and Kuroda,S.,
J. R. Soc. Interface 21: 20230439.
DOI: https://doi.org/10.1098/rsif.2023.0439 (12pp) 2024
Published on 2024.5.29
2022
Gait switching with phase reversal of locomotory waves in the centipede Scolopocryptops rubiginosus"
Kuroda,S., Uchida,N., Nakagaki,T.
Bioinspiration & Biomimetics 17 026005
DOI: https://doi.org/10.1088/1748-3190/ac482d (18pp) 2022
Published on 2022.3.8
2020
Thermal Conductivity and Thermal Diffusivity of Slime Mold (Physarum Polycephalum),
Maki,S., Kuroda,S.,Fujiwara,S., Tanaka,S., Erzalia,E., Kato,M., Higo,K., Arata,T., Nakagaki,T.,
Biomedical Journal of Scientific & Technical,
DOI: http://dx.doi.org/10.26717/BJSTR.2020.31.005090 (5pp) 2020
Physiological properties of Cantor coding-like iterated function system in the hippocampal CA1 network,
Fukushima,Y., Yamaguti,Y.,Kuroda,S.,Aihara,T., Tsuda,I. and Tsukada,M.,
Cognitive Neurodynamics,
DOI: https://doi.org/10.1007/ (8pp) 2020
2017
A Mathematical Model for Adaptive Vein Formation during Exploratory Migration of Physarum polycephalum: Routing while Scouting,
Schenz,D., Shima,Y., Kuroda,S., Nakagaki,T., Ueda,K.
J. Phys. D: Appl. Phys 50: 434001 (14pp) 2017
Published on 2017.9.28
[pdf]
Localization of Photoperiod Responsive Circadian Oscillators in the Mouse Suprachiasmatic Nucleus
Yoshikawa,T., Inagaki,N., Takagi,S., Kuroda,S., Yamasaki,M., Watanabe,M., Honma,S., Honma,K.-I.
Scientific reports 7:8210 (13pp) 2017
Published on 2017.8.15
Behavioural differentiation induced by environmental variation when crossing a toxic zone in an amoeba,
Kunita, I., Ueda,K., Akita,D., Kuroda,S., Nakagaki,T.
J. Phys. D: Appl. Phys, 50: 354002 (15pp) 2017
Published on 2017.8.7,
Current reinforcement model reproduces centre-in-centre vein trajectory of Physarum polycephalum,
Akita,D.,Schenz,D.,Kuroda,S.,Sato,K.,Ueda,K.,Nakagaki,T.
Development, Growth & Differentiation, DOI:10.1111/dgd.12384, 2017
Published on 2017.7.13
Dissociation of Per1 and Bmal1 circadian rhythms in the suprachiasmatic nucleus in parallel with behavioral outputs,
Ono,D., Honma,S., Nakajima,Y., Kuroda,S., Enoki,R., Honma,K.,
PNAS, doi:10.1073/pnas.1613374114, 2017
published on 2017.4.17
Dual origins of the intracellular circadian calcium rhythm in the suprachiasmatic nucleus,
Enoki,R., Ono,D., Kuroda,S., Honma,S., Honma,K-I.
Scientific Reports 7, 41733, 2017
Experimental models for Murray's Law,
Akita,D.. Kunita,I. Fricker,M.D., Kuroda,S., Sato,K., Nakagaki,T.
J. Phys. D: Appl. Phys., 50, 024001 (11pp), 2017
Physical ethology of unicellular organism,
Kuroda,S., Takagi,S., Saegusa,T., Nakagaki,T.,
In Brain Evolution by Design (eds. Shigeno,S., Murakami,Y. Nomura,T) (Springer, New York) , pp.3-23, 2017
2016
A ciliate memorizes the geometry of a swimming arena,
Kunita,I., Yamaguchi,T., Tero,A., Akiyama,M., Kuroda,S., Nakagaki,T.
J. R. Soc. Interface, 13: 20160155, 2016
2015
Allometry in Physarum plasmodium during free locomotion : Size versus shape, speed and rhythm,
Kuroda,S., Takagi,S., Nakagaki,T., Ueda,T.
The Journal of Experimental Biology, 218. 3729-3738. doi: 10.1242/jeb.124354, 2015
(link to paper) (pdf in HUSCUP) [pdf]
Common mechanics in crawling locomotion of limbless and legged animals,
Kuroda,S. Tanaka,Y. Nakagaki,T.
Journal of SICE, 54, 248-253, 2015 (in Japanese)
(pdf in HUSCUP) (link to paper)
2014
Attempts to retreat from a dead-ended long capillary by backward swimming in Paramecium,
Kunita,I., Kuorda,S., Ohki,K., Nakagaki,T.,
Frontiers in microbiology, 5, 270, doi:10.3389/fmicb.2014.00270, 2014
Common mechanics of mode switching in locomotion of limbless and legged animals,
Kuroda,S., Tanaka,Y., Kunita,I., Ishiguro,A., Kobayashi,R., Nakagaki,T.,
J. R. Soc. Interface, 11: 20140205 , 2014
link to the abstract (eprint in HUSCUP)
2012
Topological specificity and hierarchical network of the circadian calcium rhythm in the suprachiasmatic nucleus,
Enoki, R., Kuroda, S., Ono, D., Hasan, M. T., Honma, S., Ueda, T., Honma, K.
PNAS, 109:21498-503, doi:10.1073/pnas.1214415110, 2012
2010
A mathematical model for Cantor coding in the hippocampus.
Yamaguti, Y., Kuroda, S., Fukushima, Y., Tsukada, M., Tsuda, I.
Neural Networks 24, 43--53, 2010
2009
Iterated function systems in the hippocampal CA1.
Kuroda, S., Fukushima, Y., Yamaguti, Y., Tsukada, M.,Tsuda, I.
Cognitive Neurodynamics 3, 205--222, 2009
2007
Spatial clustering property and its self-similarity in membrane potentials of hippocampal CA1 pyramidal neurons for a spatio-temporal input sequence.
Fukushima, Y., Tsukada, M., Tsuda, I., Yamaguti, Y., Kuroda, S.
Cognitive Neurodynamics 1, 305--316, 2007
2004
A complex systems approach to an interpretation of dynamic brain activity II : Does Cantor coding provide a dynamic model for the formation of episodic memory.
Tsuda, I., Kuroda, S.
Lecture Notes in Computer Science 3146, 129--139, 2004
2001
Cantor coding in the hippocampus.
Tsuda, I., Kuroda, S.
Japan journal of industrial and applied mathematics 18, 249--281, 2001
DOI:10.13140/2.1.4878.8480
eprint in HUSCUP (link to paper)
Articles in proceedings: (with peer review)
2013
Inhibitory network dependency in Cantor coding,
Fukushima,Y., Isomura,Y., Yamaguti,Y., Kuroda,S., Tsuda,I., Tsukada,M.
in Advances in Cognitive Neurodynamics (III):
Proceedings of the Third International Conference on Cognitive Neurodynamics 2011, (ed.) Yamaguchi,Y., :
635-640
2011
Emergence of iterated function systems in the hippocampal CA1.
Kuroda, S., Fukushima, Y., Yamaguti, Y., Tsukada, M., Tsuda, I.
in Advances in Cognitive Neurodynamics (II): Proceeding of the Second International Conference on Cognitive Neurodynamics at Hangzhou, China, November 2009,
103--106.
(KurodaS-ETAL_2009d.pdf) (http://www.springerlink.com/content/r9k11653w475p024/)
Representation of time-series by a self-similar set in a model of hippocampal CA1.
Yamaguti, Y., Kuroda, S., Tsuda, I.
in Advances in Cognitive Neurodynamics (II): Proceeding of the Second International Conference on Cognitive neurodynamics at Hangzhou, China, November 2009,
97--101.
(http://www.springerlink.com/content/n3h28473w4245550/)
2009
Coding mechanisms in hippocampal networks for learning and memory.
Fukushima, Y., Tsukada, M., Tsuda, I., Yamaguti, Y., Kuroda, S.
in Advances in Neuro-Information Processing: 15th International Conference, ICONIP 2008, Auckland, New Zealand, November 25-28, 2008, Revised Selected Papers, Part I,
LNCS 5506, 72--79
(http://dx.doi.org/10.1007/978-3-642-02490-0_9)
2008
Physiological evidence for Cantor coding output in hippocampal CA1.
Fukushima, Y., Yoneyama, M., Tsukada, M., Tsuda, I., Yamaguti, Y., Kuroda, S.
in Advances in Cognitive Neurodynamics: Proceedings of the International Conference on Cognitive Neurodynamics at Shanghai, China, November 2007,
43--45
A mathematical model for the hippocampus: towards the understanding of episodic memory and imagination,
Tsuda, I., Yamaguti, Y., Kuroda, S., Fukushima, Y., Tsukada, M.
Progress of Theoretical Physics Supplement: Proceedings of the 22nd Nishinomiya-Yukawa Memorial Symposium, Oct 15-20, 2007, Kyoto, Japan,
173, 99--108.
Articles in journals: (without peer review)
Honma,S. Ono,D. Enoki,R. Yoshikawa,T. Kuorda,S. and Honma.K.-I.,
(2016)
"Oscillator networks in the suprachiasmatic nucleus: Analysis of circadian parameters using time-laps images",
in: “Proceedings of 30th Anniversary Meeting of Sapporo Symposium on Biological Rhythms, Honma,K. ed., Hokkaido University Press (Sapporo),
33-41.
Kuroda, S.
(2004):
"On the dynamics of finite sequence of states in the hippocampus model",
Bussei Kenkyu 83, 142-149. (in Japanese)
(http://ci.nii.ac.jp/Detail/detail.do?LOCALID=ART0008412318&lang=ja)
Preprint
2018
Dynamic gait transition in the Scolopendromorpha scolopocryptops rubiginosus L. Koch centipede.
Kuroda,S. Uchida,N. Nakagaki,T. (2018).
bioRxiv doi:10.1101/312280
Posted on 2018.05.02
Books
Kuroda,S. and Kunita,I. (2015)
"Extraction of the rhythm of life"
in Introduction of animal experiments, vol3 (behavior),
Kyoritsu shuppan
(in japanese)
(http://www.kyoritsu-pub.co.jp/bookdetail/9784320057746)
Kuroda,S. and Nakagaki,T. (2014)
"Physics of biological phenomena : exploring equations of motion for biological behavior"
in Guidance of physics,
Nihonhyouronsha
(in japanese)
Presentation in International Conference
(Oral) (* invited)
Kuroda, S. "Emergent behaviour and short term adaptation in a unicellular organism (Parameciucm) : observation and modelling", Mathematical Science seminar (Math. Dept, Hokkaido Univ.), Co-organised with Colloquium series: Road to Physical Ethology (RIES, Hokkaido Univ.) (Mar 13, 2018, Sapporo)
* Kuroda,S. (2016) "Dynamic gait generation in the crawling locomotion: observation and modelling", HOKUDAI-NCTU Joint Symposium on Nano, Photo and Bio sciences in 2016, Oct 4-5, 2016, Sapporo, Japan. (http://tamaoki.es.hokudai.ac.jp/hokudai-nctu/)
* Kuroda,S. (2015) "Physical ethology and animal walking", CIAC 2015 Hakodate Workshop 3, Nov 8-9, 2015, Hakodate, Japan.
Ohki,K. Kuroda,S. Kunita,I. Nakagaki,T. (2015) "The space learningin a capillaryand its mechanism in Paramecium", 48th the japan society of protistology annual conference with special project of JSP-KSOP going meeting, Nov 6-8, 2015, Tokyo, Japan.
Hayase,Y. and Kuroda,S. and Kobayashi, R. (2015) "A mathematical model of locomotion of centipede", Joint meeting of 5th CJK and 25th JSMB, Aug 26-29, 2015, Kyoto, Japan.
Kuroda,S. and Nakagaki,T. (2015) "A mechano-mathematical model for adaptive crawling locomotion: from a case study of centipde", Joint meeting of 5th CJK and 25th JSMB, Aug 26-29, 2015, Kyoto, Japan.
* Kuroda,S. and Nakagaki,T. (2015) "Transition among possible modes in crawling locomotion", Mini-workshop on "A crossroad of biology and mathematics -Modeling and Computation-", Apr 30 - May 1, 2015, Hokkaido University, Sapporo, Japan.
* Kuroda,S. (2014) "Scaling in the Physarum amoeba during locomotion : Size vs speed, shape and rhythm", Mathematical aspects on boundary layer in reaction-diffusion phenomena, Nov 28, 2014, Meiji university, Tokyo, Japan.
Kuroda,S. and Nakagaki,T. (2014) "General mechanics for environment-coupled crawling locomotion: from amoeba to snail, earthworm, centipede and beyond.", The joint annual meeting of the JSMB and SMB, Jul 28-Aug 1, Osaka, Japan.
* Kuroda,S. (2014) "Common mechanics of mode switching in locomotion of limbless and legged animals", CREST International symposium: Locomotion of animals, robotics and mathematics (Mar 20-21, 2014, Sapporo Japan)
* Kuroda,S. (2014) "On mechanics of peristaltic locomotion: transition among possible modes in crawling locomotion", Japan-Sweden research workshop on ethology and rheology of physarum and its related topics II (Feb 2014, Gavle, Sweden)
Kuroda,S., Fukushima,Y., Yamaguti,Y., Tsukada,M., Tsuda,I. (2009): “Emergence of iter-ated function systems in the hippocampal CA1” 2nd International Conference on Cognitive Neurodynamics (ICCN’09) (Nov 2009, Hangzhou, China)
Kuroda,S., Fukushima,Y., Yamaguti,Y., Tsukada,M., Tsuda,I. (2009): “Emergence of Contractive Affine Transformations in the Hippocampal CA1” 12th Japan-Slovenia Seminar on Nonlinear Science(Oct 2009, Maribor, Slovenia)
Kuroda,S., Yamaguti,Y., Fukushima,Y., Tsukada,M., Tsuda,I. (2007): “Iterated function systems in hippocampal CA1 neurons” 1st International Conference on Cognitive Neurody-namics (ICCN’07) (Nov 2007, Shanghai, China)
(Poster)
Kuroda,S. and Uchida,N. and Nakagaki,T. (2018) "Dynamic gait trainsition in the cenpede Scolopendromorpha scolopocryptops rubiginosus", International Congress in Neuroethology (15-20 July 2018, Brisbane, Australia)
Kuroda,S., Aonuma,H., Yasui,K., Ishiguro,A. (2017) "Adaptive locomotion in centipede : the role of body stiffness and morphology", AMAM 2017, June 27-30, Sapporo, Japan.
Kuroda,S., Aonuma,H., Yasui,K., Ishiguro,A. (2016) "The role of body stiffness for adaptive locomotion in centipede", The 87th Anuual Meeting of the Zoological Society of Japan, Nov.17-18, Ginowan, Okinawa, Japan.
Kuroda,S. (2016) "Minimal model for crawling locomotion with dynamic gait generation", Patterns and Waves 2016, Aug 1-5, 2016, Sapporo, Japan.
Kuroda,S. and Nakagaki,T. (2015) "A mechano-mathematical model for adaptive crawling locomotion", AMAM 2015, June 22-25, 2015, Boston, USA
Aonuma,H. and Goda,M. and Kuorda,S. and Kano,T. and Owaki,D. and Ishiguro,A.. (2015) "ACricket switches locomotion patterns from walking to swimming by evaluating reaction forces from the environment", AMAM 2015, June 22-25, 2015, Boston, USA
Kuroda,S. and Nakagaki,T. (2015) "A mechano-mathematical model for adaptive crawling locomotion", SIAM 2015 for application of dynamical systems, May 17-21, 2015, Snow bird, USA
Kuroda,S. and Nakagaki (2015) "A mathematical model for adaptive crawling locomotion", Computational Biofluids in Physiology in Celebration of Arron Fogelson's 60th Birthday (May 14-15 2015, Salt lake city, USA)
Kuroda,S. and Nakagaki,T. (2014) "Transition among possible modes in crawling locomotion", Gordon Research Conference (Oscillations & Dynamic Instabilities in Chemical Systems), July 14-18 2014, Girona, Spain.
Kuroda,S. and Nakagaki,T. (2014) "Transition among possible modes in crawling locomotion", Gordon Research Seminar (Oscillations & Dynamic Instabilities in Chemical Systems), July 12-13 2014, Girona Spain.
Kuroda,S. (2013) "Transition among possible modes in crawling locomotion", The 14th RIES-Hokudai International Symposium on 網 [mou] (Dec 2013, Sapporo)
Kuroda,S., Tanaka,Y. Ito,T., Kunita,I., Ishiguro,A., Kobayashi,R., Nakagaki,T. (2013) ``Switching of possible modes in crawling locomotion'', Self-organization and emergent dynamics in active soft matter (Feb. 2013, Kyoto)
Kuroda,S., Takagi,S., Ueda,T.. (2011): “Allometry of the true slime mold: Size, shape and speed", 12th RIES-Hokudai International Symposium on 観 [kan] (Nov 2011, Sapporo)
Kuroda,S., Fukushima,Y., Yamaguti,Y., Tsukada,M., Tsuda,I. (2010): “Iterated function systems in the rat hippocampal CA1 area” 11th RIES-Hokudai International Symposium on 彫 [chou] (Mar 2010, Sapporo)
Kuroda, S., Yamaguti,Y., Fukushima,Y., Tsukada,M., Tsuda,I.(2009): “Emergence of contractive affine transformations in the Hippocampal CA1” 11th Dynamic Brain Forum (DBF’09), (Mar 2009, Atami Japan)
Kuroda,S., Yamaguti,Y., Fukushima,Y., Tsukada,M., Tsuda,I. (2008): “Emergence of contractive affine transformations in the Hippumcampal CA1” 10th RIES-Hokudai International Symposium on 綾 [aya] (Dec 2008, Sapporo)
Kuroda,S., Yamaguti,Y., Fukushima,Y., Tsukada,M., Tsuda,I. (2008): “Cantor Coding for Spatio-Temporal Patterns” 9th RIES-Hokudai International Symposium on 創 [sou] (Jan 2008, Sapporo)
Kuroda,S. (2007): “On a type of condition to discriminate spatiotemporal patterns in locally connected neural network” 10th Dynamic Brain Forum (DBF’07) (Mar 2007, Hakuba, Japan)