Biophysics and Physicobiology
Published by the Biophysical Society of Japan
- Editor-in-chief
- : Haruki Nakamura
- Online ISSN
- : 2189-4779
- Journal Impact Factor (2024)
- : 1.6
- DOAJ (The Directory of Open Access Journals) archive for BPPB:
- PMC (PubMed Central) archive for BPPB:
- B2J service at bioRxiv is available
- Either CC BY-NC-SA 4.0 or CC BY 4.0 by the authors’ preference
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News
| 21 May, 2025 | As of May 2025, a short caption for the Graphical Abstract is requested for each BPPB paper except the category of Commentary & Perspective or Editorial. |
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| 12 May, 2025 | As of May 2025, each article published in BPPB may be licensed under either the Creative Commons Attribution (CC BY) 4.0 license or the Creative Commons Attribution-NonCommercial-ShareAlike (CC BY-NC-SA) 4.0 license, depending on the authors’ selection. |
| 01 Jan., 2025 | Because of the minor corrections about the manuscript style, the pages of “Instruction for Authors” and "Quick Guide to Prepare Manuscript" for Biophysics and Physicobiology have been slightly updated. The Template files have also been replaced. |
| 14 Nov., 2024 | Special Issue: "IUPAB2024 Congress in Kyoto" has been published. |
| 29 Aug., 2024 | The article "Editorial: IUPAB2024 Congress in Kyoto" has been published in the Special Issue together with total 1,339 Abstracts of the oral and poster presentations as the Supplementary Materials. |
| 29 May, 2024 | Special Issue: "Singularity Biology and Beyond" has been published. |
| 27 May, 2024 | Publication of "The Oosawa Lectures on DIY Statistical Mechanics" has been completed as the Special Issue of Biophysics and Physicobiology of Volume 18. |
| 30 Jan., 2024 | The “Instruction for Authors” for Biophysics and Physicobiology has been updated. In particular, our policy for the articles prepared with the aid of Large Language Models and/or Generative AI is added. |
| 30 Jun., 2023 | 2022 Journal Impact Factor of Biophysics and Physicobiology is given as 1.5 by Clarivate. |
| 21 Mar., 2023 | Special Issue: "Recent Advances in Retinal Protein Research" has been published. |
Recent Articles
Advance online publication Protein–ligand affinity prediction via Jensen-Shannon divergence of molecular dynamics simulation trajectories Kodai Igarashi, Masahito Ohue DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0015 ReceivedFebruary 20, 2025 AcceptedJuly 11, 2025 ReleasedJuly 16, 2025 |
Advance online publication HulaChrimson: A Chrimson-like cation channelrhodopsin discovered using freshwater metatranscriptomics from Lake Hula Hiroto Takahashi, Shunki Takaramoto, Takashi Nagata, Shai Fainsod, Yoshitaka Kato, Oded B？j？, Keiichi Inoue DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0014 ReceivedApril 14, 2025 AcceptedJuly 03, 2025 ReleasedJuly 05, 2025 |
Advance online publication Cytoskeleton as a generator of characteristic physical properties of plant cells: ‘cell wall,’ ‘large vacuole,’ and ‘cytoplasmic streaming’ Amari Toshiki, Noriko Nagata, Motoki Tominaga, Hirotomo Takatsuka DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0013 ReceivedJanuary 31, 2025 AcceptedJune 18, 2025 ReleasedJune 20, 2025 |
Method and Protocol A method for isolating and cryopreserving intact mitochondria with improved integrity and functionality Arima Okutani, Jannatul Naima, Asaka Ogihara, Taihei Motoichi, Ikuroh Ohsawa, Yoshihiro Ohta DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0012 ReceivedApril 07, 2025 AcceptedMay 14, 2025 ReleasedMay 16, 2025 |
Regular Article A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape Junichi Higo, Kota Kasahara, Shun Sakuraba, Gert-Jan Bekker, Narutoshi Kamiya, Ikuo Fukuda, Takuya Takahashi, Yoshifumi Fukunishi DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0011 ReceivedJanuary 10, 2025 AcceptedApril 24, 2025 ReleasedApril 26, 2025 |
Method and Protocol A low-cost electric micromanipulator and its application to single-cell electroporation Kazuma Shimizu, Norihiko Nishimura, Manato Oku, Chika Okimura, Yoshiaki Iwadate DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0010 ReceivedNovember 07, 2024 AcceptedApril 24, 2025 ReleasedApril 26, 2025 |
Regular Article Structure-activity relationship of PET-degrading cutinase regulated by weak Ca2+ binding and temperature Fumiya Kondo, Narutoshi Kamiya, Gert-Jan Bekker, Satoshi Nagao, Nobutaka Numoto, Hiroshi Sekiguchi, Nobutoshi Ito, Masayuki Oda DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0009 ReceivedMarch 10, 2025 AcceptedApril 22, 2025 ReleasedApril 24, 2025 |
Review Article Genetically-encoded temperature indicators for thermal biology Tetsuichi Wazawa, Ryohei Ozaki-Noma, Lu Kai, Shun-ichi Fukushima, Tomoki Matsuda, Takeharu Nagai DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0008 ReceivedDecember 14, 2024 AcceptedApril 03, 2025 ReleasedApril 08, 2025 |
Method and Protocol Time-resolved small-angle X-ray scattering system development for the biological macromolecules at SACLA: A pilot study Nobutaka Shimizu, Fangjia Luo, Tomoyuki Tanaka, Kensuke Tono, Keiko Yatabe, So Iwata, Eriko Nango DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0007 ReceivedOctober 23, 2024 AcceptedMarch 25, 2025 ReleasedMarch 27, 2025 |
Regular Article Gliding direction of Mycoplasma mobile correlates with the curved configuration of its cell shape Kana Suzuki, Daisuke Nakane, Masaki Mizutani, Takayuki Nishizaka DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0006 ReceivedJanuary 17, 2025 AcceptedFebruary 17, 2025 ReleasedFebruary 26, 2025 |
Regular Article Exploring hydrophilic sequence space to search for uncharted foldable proteins by AlphaFold2 Naoki Tomita, Hiroki Onoda, Leonard M. G. Chavas, George Chikenji DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0005 ReceivedNovember 06, 2024 AcceptedJanuary 30, 2025 ReleasedFebruary 01, 2025 |
Regular Article Improvement in positional accuracy of neural-network predicted hydration sites of proteins by incorporating atomic details of water-protein interactions and site-searching algorithm Kochi Sato, Masayoshi Nakasako DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0004 ReceivedNovember 14, 2024 AcceptedJanuary 27, 2025 ReleasedJanuary 30, 2025 |
Regular Article Product release and substrate entry of aldehyde deformylating oxygenase revealed by molecular dynamics simulations Masataka Yoshimura, Munehito Arai DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0003 ReceivedDecember 16, 2024 AcceptedDecember 27, 2024 ReleasedJanuary 09, 2025 |
Regular Article Measurement of protoplasmic streaming over the entire body of Physarum plasmodium, and estimation of the transport and mixing of protoplasma through the intricate vein network Yo Sato, Charles Fosseprez, Yukinori Nishigami, Katsuhiko Sato, Hiroshi Orihara, Toshiyuki Nakagaki DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0002 ReceivedJuly 17, 2024 AcceptedDecember 24, 2024 ReleasedJanuary 09, 2025 |
Regular Article Near-infrared spectroscopic study of blood flow changes in the dorsolateral prefrontal cortex during pain relief by odor stimulation Yuki Okamura, Shogo Takayama, Kengo Namiki, Fusako Koshikawa, Etsuro Ito DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0001 ReceivedJuly 26, 2024 AcceptedDecember 24, 2024 ReleasedDecember 26, 2024 |
Regular Article Neuron with well-designed ionic system Takayoshi Tsubo DOIhttps://doi.org/10.2142/biophysico.bppb-v21.0028 ReceivedOctober 15, 2024 AcceptedDecember 10, 2024 ReleasedDecember 13, 2024 |
Regular Article Comparative study of alpha-glucosidase inhibition of four Vietnamese medicinal plants Combretum quadrangulare, Dicranopteris linearis, Psychotria adenophylla, and Garcinia schomburgkiana: In vitro and in vivo studies Thi-Hong-Tuoi Do, Thuc-Huy Duong, Huu-Hung Nguyen, Thanh-Sang Vo, Ngoc-Hong Nguyen, Huong Thuy Le DOIhttps://doi.org/10.2142/biophysico.bppb-v21.0027 ReceivedJuly 23, 2024 AcceptedDecember 09, 2024 ReleasedDecember 13, 2024 |
Commentary and Perspective (Invited) Half a Century of Biophysics: A Comparison of Presentation Statistics from the 6th and 21st IUPAB Congresses Mikio Kataoka, Kuniaki Nagayama DOIhttps://doi.org/10.2142/biophysico.bppb-v21.e2013 ReceivedNovember 20, 2024 AcceptedDecember 05, 2024 ReleasedDecember 07, 2024 |
Regular Article Electrophysiological analysis of hyperkalemic cardiomyocytes using a multielectrode array system Kentaro Kito, Masahito Hayashi, Tomoyuki Kaneko DOIhttps://doi.org/10.2142/biophysico.bppb-v21.0026 ReceivedSeptember 11, 2024 AcceptedNovember 19, 2024 ReleasedNovember 21, 2024 |
Editorial Announcement of BPPB paper awards 2024 Haruki Nakamura DOIhttps://doi.org/10.2142/biophysico.bppb-v21.0025 ReceivedNovember 06, 2024 AcceptedNovember 10, 2024 ReleasedNovember 12, 2024 |
Method and Protocol Rapid in vitro method to assemble and transfer DNA fragments into the JCVI-syn3B minimal synthetic bacterial genome through Cre/loxP system Atsuko Uenoyama, Hana Kiyama, Mone Mimura, Makoto Miyata DOIhttps://doi.org/10.2142/biophysico.bppb-v21.0024 ReceivedAugust 05, 2024 AcceptedNovember 05, 2024 ReleasedNovember 07, 2024 |
Regular Article Inducing aggresome and stable tau aggregation in Neuro2a cells with an optogenetic tool Shigeo Sakuragi, Tomoya Uchida, Naoki Kato, Boxiao Zhao, Toshiki Takahashi, Akito Hattori, Yoshihiro Sakata, Yoshiyuki Soeda, Akihiko Takashima, Hideaki Yoshimura, Gen Matsumoto, Hiroko Bannai DOIhttps://doi.org/10.2142/biophysico.bppb-v21.0023 ReceivedMay 17, 2024 AcceptedOctober 26, 2024 ReleasedOctober 29, 2024 |
Commentary and Perspective (Invited) Constructing virtual DNA-nanomachines Nathan Nunes Evangelista, Masahiro Takinoue DOIhttps://doi.org/10.2142/biophysico.bppb-v21.e2011 ReceivedJuly 05, 2024 AcceptedOctober 21, 2024 ReleasedOctober 22, 2024 |
Commentary and Perspective (Invited) Using interactive deep learning to track cells: A report on a 3-day hands-on training program at IUPAB 2024 Lissy M Hartmann, Samara Bridge DOIhttps://doi.org/10.2142/biophysico.bppb-v21.e2010 ReceivedAugust 26, 2024 AcceptedOctober 18, 2024 ReleasedOctober 19, 2024 |
Commentary and Perspective (Invited) DNA nanomachine tutorial Huong T. Vu DOIhttps://doi.org/10.2142/biophysico.bppb-v21.e2009 ReceivedSeptember 17, 2024 AcceptedOctober 15, 2024 ReleasedOctober 17, 2024 |
Commentary and Perspective (Invited) GENESIS and CHARMM-GUI: Advances and applications from Hands-on training program C at RIKEN Nor Akmalyati Sulong, Vannajan Sanghiran Lee DOIhttps://doi.org/10.2142/biophysico.bppb-v21.e2008 ReceivedJuly 30, 2024 AcceptedOctober 09, 2024 ReleasedOctober 17, 2024 |
Editorial Hands-on Training Program Kumiko Hayashi DOIhttps://doi.org/10.2142/biophysico.bppb-v21.e2007 ReceivedSeptember 24, 2024 AcceptedOctober 07, 2024 ReleasedOctober 10, 2024 |
Review Article (Invited) Artificial cell system as a tool for investigating pattern formation mechanisms of intracellular reaction-diffusion waves Sakura Takada, Kei Fujiwara DOIhttps://doi.org/10.2142/biophysico.bppb-v21.0022 ReceivedSeptember 05, 2024 AcceptedOctober 08, 2024 ReleasedOctober 10, 2024 |
Commentary and Perspective (Invited) Experience report of Hands-on Training Program E: Exploring multi-cellular mechanics Asuka Takeda-Sakazume DOIhttps://doi.org/10.2142/biophysico.bppb-v21.e2006 ReceivedSeptember 04, 2024 AcceptedSeptember 19, 2024 ReleasedSeptember 21, 2024 |
Commentary and Perspective (Invited) IUPAB and BSJ meeting Kyoto: Reflections on hands on workshop “Real-time single-molecule experiments with optical tweezers and correlated fluorescence microscopy” with LUMICKS C-trap, emphasising the importance of practicing international and interdisciplinary science Karina New DOIhttps://doi.org/10.2142/biophysico.bppb-v21.e2005 ReceivedAugust 26, 2024 AcceptedSeptember 19, 2024 ReleasedSeptember 21, 2024 |
Databases and Computer Programs Data-driven score tuning for ChooseLD: A structure-based drug design algorithm with empirical scoring and evaluation of ligand–protein docking predictability Akihiro Masuda, Daichi Sadato, Mitsuo Iwadate DOIhttps://doi.org/10.2142/biophysico.bppb-v21.0021 ReceivedJune 03, 2024 AcceptedSeptember 20, 2024 ReleasedSeptember 21, 2024 |
Note Monitoring of enzymatic cleavage reaction of GST-fusion protein on biolayer interferometry sensor Sena Tarumoto, Sei Inoue, Rina Yanagimoto, Takashi Saitoh DOIhttps://doi.org/10.2142/biophysico.bppb-v21.0019 ReceivedAugust 13, 2024 AcceptedSeptember 13, 2024 ReleasedSeptember 18, 2024 |
Commentary and Perspective (Invited) Experience of Hands-on training program on DNA Nanomachine at IUPAB2024 Koki Yoshida DOIhttps://doi.org/10.2142/biophysico.bppb-v21.e2004 ReceivedJuly 07, 2024 AcceptedSeptember 09, 2024 ReleasedSeptember 13, 2024 |
Commentary and Perspective (Invited) Feeling a nanoworld with optical tweezers: Hands on training at IUPAB 2024 Zuzana Johanovská DOIhttps://doi.org/10.2142/biophysico.bppb-v21.e2003 ReceivedAugust 21, 2024 AcceptedSeptember 04, 2024 ReleasedSeptember 05, 2024 |
Review Article (Invited) Function of nodal cilia in left-right determination: Mechanical regulation in initiation of symmetry breaking Takanobu A. Katoh DOIhttps://doi.org/10.2142/biophysico.bppb-v21.0018 ReceivedJune 17, 2024 AcceptedSeptember 04, 2024 ReleasedSeptember 06, 2024 |
Commentary and Perspective (Invited) Hands-on training experience of C-trap Yuze Sun DOIhttps://doi.org/10.2142/biophysico.bppb-v21.e2002 ReceivedJuly 23, 2024 AcceptedAugust 13, 2024 ReleasedAugust 29, 2024 |
Editorial IUPAB2024 Congress in Kyoto Hiroyuki Noji DOIhttps://doi.org/10.2142/biophysico.bppb-v21.e2001 ReceivedAugust 07, 2024 AcceptedAugust 09, 2024 ReleasedAugust 29, 2024 |
Review Article (Invited) Chemical tongues as multipurpose bioanalytical tools for the characterization of complex biological samples Shunsuke Tomita, Hiroka Sugai DOIhttps://doi.org/10.2142/biophysico.bppb-v21.0017 ReceivedMay 27, 2024 AcceptedAugust 13, 2024 ReleasedAugust 20, 2024 |
