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
Gallery of the Recent Covers
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Issue 4
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News
| 04 Aug., 2025 | The promotional video for every article in BPPB except those of the category of Commentary and Perspective or Editorial will be released on YouTube as of Issue 3, Volume 22 (2025). |
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| 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. |
| 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 Physicochemical, functional, and evolutionary characteristics of protein loop regions in human and Escherichia coli proteomes Lin Zhang, Hafumi Nishi DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0031 ReceivedMay 27, 2024 AcceptedNovember 20, 2025 ReleasedNovember 22, 2025 |
Advance online publication Schiff base deprotonation and structural changes in a mouse UV-sensitive cone visual pigment revealed by FTIR spectroscopy at 77 K Yosuke Mizuno, Sora Arai, Kota Katayama, Hideki Kandori DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0030 ReceivedOctober 09, 2025 AcceptedNovember 15, 2025 ReleasedNovember 21, 2025 |
Advance online publication FTIR study of the wild-type and mutant proteins of a viral rhodopsin, OLPVR1 Mako Aoyama, Kota Katayama, Hideki Kandori DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0029 ReceivedOctober 07, 2025 AcceptedNovember 10, 2025 ReleasedNovember 12, 2025 |
Advance online publication Selection–diversification interplay in oligonucleotide chemical evolution Jiro Kakizaki, Ryo Mizuuchi DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0028 ReceivedSeptember 16, 2025 AcceptedNovember 01, 2025 ReleasedNovember 05, 2025 |
Editorial Announcement of BPPB paper awards 2025 Haruki Nakamura DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0027 ReceivedOctober 21, 2025 AcceptedOctober 21, 2025 ReleasedOctober 23, 2025 |
Regular Article Fractal dimensions for tumour-related cell types of prostate cancer on histopathology images using multiple-threshold box counting algorithm Anton Schwarz, Hidetaka Arimura, Yunhao Cui, Shun Shimabukuro, Qijing Lin, Yu Jin, Satoshi Kobayashi, Takashi Matsumoto, Masaki Shiota, Masatoshi Eto, Yoshinao Oda DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0026 ReceivedSeptember 04, 2025 AcceptedOctober 06, 2025 ReleasedOctober 18, 2025 |
Method and Protocol (Invited) A platform for analyzing translational control by RBPs at single-mRNA resolution in cells Hotaka Kobayashi, Robert H. Singer DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0025 ReceivedSeptember 01, 2025 AcceptedOctober 06, 2025 ReleasedOctober 08, 2025 |
Regular Article Molecular properties of a viral heliorhodopsin, V2HeR2 Ritsu Mizutori, Kota Katayama, Masae Konno, Keiichi Inoue, Oded Béjà, Hideki Kandori DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0024 ReceivedJune 24, 2025 AcceptedOctober 02, 2025 ReleasedOctober 04, 2025 |
Review Article (Invited) Stress fiber contraction induces cell body rotation in single keratocytes Chika Okimura DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0023 ReceivedJuly 25, 2025 AcceptedOctober 02, 2025 ReleasedOctober 04, 2025 |
Regular Article Finding differentially expressed genes between cell fates predicted by image-based deep learning Tomoaki Okaniwa, Kirill Kryukov, Katsuyuki Shiroguchi DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0022 ReceivedMay 02, 2025 AcceptedSeptember 24, 2025 ReleasedSeptember 26, 2025 |
Commentary and Perspective Interdisciplinary investigations into the biophysics of the origins of life Tony Z. Jia, Yutetsu Kuruma DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0021 ReceivedSeptember 08, 2025 AcceptedSeptember 10, 2025 ReleasedSeptember 12, 2025 |
Commentary and Perspective Approaching active matter from biophysics perspective Masayuki Hayakawa, Ibuki Kawamata DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0020 ReceivedAugust 25, 2025 AcceptedAugust 29, 2025 ReleasedAugust 30, 2025 |
Regular Article Visualization of peptidoglycan layer isolated from gliding diderm bacteria, Flavobacterium johnsoniae and Myxococcus xanthus, by quick-freeze deep-etch replica electron microscopy Yuhei O. Tahara, Tâm Mignot, Makoto Miyata DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0019 ReceivedFebruary 06, 2025 AcceptedAugust 22, 2025 ReleasedAugust 26, 2025 |
Regular Article Origin of the unique topology of the triangular water cluster in Rubrobacter xylanophilus rhodopsin Tomoyasu Noji, Msasaki Tsujimura, Keisuke Saito, Keiichi Kojima, Yuki Sudo, Hiroshi Ishikita DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0018 ReceivedApril 28, 2025 AcceptedAugust 21, 2025 ReleasedAugust 23, 2025 |
Regular Article Polymerization and stability of actin conjugated with polyethylene glycol Masaya Sagara, Kuniyuki Hatori DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0017 ReceivedMarch 10, 2025 AcceptedAugust 06, 2025 ReleasedAugust 08, 2025 |
Regular Article Characterizing deterioration of milk through bioimpedance spectroscopy Abhishek Mallick, Bishal Paul, Anirudhha Roy, Arijit Roy DOIhttps://doi.org/10.2142/biophysico.bppb-v22.0016 ReceivedApril 21, 2025 AcceptedJuly 29, 2025 ReleasedAugust 02, 2025 |
Regular Article 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 |
Regular Article 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 |
Review Article (Invited) 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 |
