last modified：2024/11/21
Assistant Professor SUMIKAMA, Takashi
Faculty, Affiliation
WPI Nano Life Science Institute
College and School Educational Field
Laboratory
Academic Background
Career
Japan Science and Technology Agency PRESTO researcher(2020/11-2024/05)
Kanazawa University Nano Life Science Institute Assistant Professor(2020/04-)
Kanazawa University Nano Life Science Institute Postdoctoral Fellow(2018/04-2020/03)
University of Fukui School of Medical Sciences Assistant Professor(2010/02-2018/03)
Institute for Molecular Science Postdoctoral Fellow(2008/10-2010/01)
Nagoya University Graduate School of Science Postdoctoral Fellow(2008/04-2008/09)
Year & Month of Birth
Academic Society
The Physiological Society of Japan
The Biophysical Society of Japan
The Molecular Biology Society of Japan
The Biophysical Society
Award
○Papers of the Month(2019/09)
○Irisawa Memorial Promotion Award for Young Physiologists(2018/03)
○Best paper award(2017/07)
○Best presentation award(2017/03)
○Excellent paper award(2016/11)
Specialities
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Speciality Keywords
Research Themes
Books
Papers
- Voltage sensors of a Na+ channel dissociate from the pore domain and form inter-channel dimers in the resting state Ayumi Sumino,Takashi Sumikama,Mikihiro Shibata,Katsumasa Irie Nature Communications 14 7835 2023/12/19
- Computation of topographic and three-dimensional atomic force microscopy images of biopolymers by calculating forces Takashi Sumikama Biophysical Reviews 15 2059 2023/11/27
- Updating view of membrane transport proteins by simulation studies Takashi Sumikama,Ben Corry,Junichi Ono,Chigusa Kobayashi,Kei-ichi Okazaki Biophysics and Physicobiology 20 e200041 2023/11/02
- The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel Katsumasa Irie,Yoshinori Oda,Takashi Sumikama,Atsunori Oshima,Yoshinori Fujiyoshi Nature Communications 14 1 4236 2023/07/15
- Imaging single CaMKII holoenzymes at work by high-speed atomic force microscopy Shotaro Tsujioka,Ayumi Sumino,Yutaro Nagasawa,Takashi Sumikama,Holger Flechsig,Leonardo Puppulin,Takuya Tomita,Yudai Baba,Takahiro Kakuta,Tomoki Ogoshi,Kenichi Umeda,Noriyuki Kodera,Hideji Murakoshi,Mikihiro Shibata Science Advances 9 26 eadh1069 2023/06/30
- Antithetic effects of agonists and antagonists on the structural fluctuations of TRPV1 channel Ayumi Sumino,Yimeng Zhao,Daichi Mukai,Takashi Sumikama,Leonardo Puppulin,Motoyuki Hattori,Mikihiro Shibata Proceedings of the National Academy of Sciences of the United States of America 120 20 e2301013120 2023/05/16
- Intuitive interpretation of heterochromatin and euchromatin through rapid Hi-C analysis Takashi Sumikama,Takeshi Fukuma bioRxiv 2022/10/28
- Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality Takashi Sumikama,Filippo Federici Canova,David Z. Gao,Marcos Penedo,Keisuke Miyazawa,Adam S. Foster,Takeshi Fukuma The Journal of Physical Chemistry Letters 13 5365 2022/06/09
- Vectorial insertion of a β-helical peptide into membrane: A theoretical study on polytheonamide B Mahroof Kalathingal,Takashi Sumikama,Shigetoshi Oiki,Shinji Saito 120 4786 2021/09
- Conductance selectivity of Na+ across the K+ channel via Na+ trapped in a tortuous trajectory Kenichiro Mita,Takashi Sumikama,Masayuki Iwamoto,Yuka Matsuki,Kenji Shigemi,Shigetoshi Oiki Proceedings of the National Academy of Sciences 118 12 e2017168118 2021/03/23
- Computed Atomic Force Microscopy Images of Chromosomes by Calculating Forces with Oscillating Probes Takashi Sumikama,Adam S. Foster,Takeshi Fukuma Journal of Physical Chemistry C 124 3 2213 2020/01
- Queueing arrival and release mechanism for K+ permeation through a potassium channel Takashi Sumikama,Shigetoshi Oiki Journal of Physiological Sciences 69 6 919 2019/08
- High-speed AFM reveals accelerated binding of agitoxin-2 to a K+ channel by induced fit Ayumi Sumino,Takashi Sumikama,Takayuki Uchihashi,Shigetoshi Oiki Science Advances 5 7 eaax0495 2019/07
- Capturing the Freeze-Drying Dynamics of NaCl Nanoparticles Using THz Spectroscopy Katsuhiro Ajito,Yuko Ueno,Jae-Young Kim,Takashi Sumikama Journal of the American Chemical Society 140 42 13793 2018/10
- Origins of Heat Evolution in Mixing Water and Dimethyl Sulfoxide Kazuko Mizuno,Takashi Sumikama,Yoshinori Tarnai,Masahiko Tani 2018 43rd International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz) 2018-September 2018/09
- A Letter to Editors —A Proposal for SEIBUTSU BUTSURI— Takashi SUMIKAMA Seibutsu Butsuri 58 2 108 2018
- Entrance of Channel Determines Ion Permeation Rate through the Kv1.2 Channel Takashi SUMIKAMA,Shigetoshi OIKI Seibutsu Butsuri 58 1 012 2018
- Structure and dynamics of solvent molecules inside the polytheonamide B channel in different environments: a molecular dynamics study Mahroof Kalathingal,Takashi Sumikama,Toshifumi Mori,Shigetoshi Oiki,Shinji Saito Physical Chemistry Chemical Physics 20 5 3334 2018
- Digitalized K+ Occupancy in the Nanocavity Holds and Releases Queues of K+ in a Channel Takashi Sumikama,Shigetoshi Oiki Journal of the American Chemical Society 138 32 10284 2016/08
- Origin of the Shape of Current-Voltage Curve through Nanopores: A Molecular Dynamics Study Takashi Sumikama Scientific Reports 6 25750 2016/05
- Structure and Dynamics of Membrane-embedded KcsA Potassium Channel Revealed by Atomic Force Microscopy Ayumi SUMINO,Daisuke YAMAMOTO,Takashi SUMIKAMA,Masayuki IWAMOTO,Takehisa DEWA,Shigetoshi OIKI Seibutsu Butsuri 55 1 005 2015
- Mechanism of ion permeation through a model channel: Roles of energetic and entropic contributions Takashi Sumikama,Shinji Saito,Iwao Ohmine Journal of Chemical Physics 139 16 165106 2013/10/28
- The Open Gate Structure of the Membrane-Embedded KcsA Potassium Channel Viewed From the Cytoplasmic Side Ayumi Sumino,Takashi Sumikama,Masayuki Iwamoto,Takehisa Dewa,Shigetoshi Oiki Scientific Reports 3 1063 2013/01
- Cycle Flux Algebra for Ion and Water Flux through the KcsA Channel Single-File Pore Links Microscopic Trajectories and Macroscopic Observables Shigetoshi Oiki,Masayuki Iwamoto,Takashi Sumikama PLoS ONE 6 1 e16578 2011/01
- A mesoscopic approach to understanding the mechanisms underlying the ion permeation on the discrete-state diagram Shigetoshi Oiki,Masayuki Iwamoto,Takashi Sumikama Journal of General Physiology 136 3 363 2010/09
- Mechanism of ion permeation in a model channel: Free energy surface and dynamics of K+ ion transport in an anion-doped carbon nanotube Takashi Sumikama,Shinji Saito,Iwao Ohmine Journal of Physical Chemistry B 110 41 20671 2006/10
Conference Presentations
- A development of rapid classification method of A/B compartments based on Hi-C and an insight into structural dynamics of A/B compartments(2023/05/11)
- Chromosome modeling by polymer simulation and comparison with 3D-AFM measurements(conference：5th Genome Biophysics Seminar)(2023/08/28)
- AFM image computations by force calculation and combined studies of AFM and MD simulations(conference：The First International Symposium of Nano Life Science: Nano Biotechnology, Biosensor, Computation (NanoBiocom2023))(2023/09/18)
- Computational and theoretical studies in collaboration with experiments to elucidate biological phenomena(conference：International Conference on Theoretical and High Performance Computational Chemistry 2024)(2024/04/21)
- Molecular mechanism of selective ion permeation through the K+ channels: A computational study(conference：The 10th Federation of the Asian and Oceanian Physiological Societies Congress)(2023/11/01)
- Selective ion permeation through the K+ channels and novel gating mechanism of the Na+ channel(conference：Annual Meeting of the Biophysical Society of Japan)(2023/11/15)
Others
Arts and Fieldwork
Patent
Theme to the desired joint research
Grant-in-Aid for Scientific Research
Competitive research funding,Contribution
Collaborative research,Consignment study
Classes (Bachelors)
Classes (Graduate Schools)
○Basic Computational Science(2021)
○Basic Computational Science(2020)