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Volume 22, 2025
Issue 2
Story of the Cover
Volume 22, 2025
Issue 2
Story of the Cover
Volume 22, 2025
Issue 1
Story of the Cover
Volume 22, 2025
Issue 1
Story of the Cover

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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.
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.

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Recent Articles

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
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   

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   

Review Article (Invited)
Unraveling the fastest myosin: Discovery history and structure-function relationships of algae Chara myosin XI
Kohji Ito, Takeshi Haraguchi

DOIhttps://doi.org/10.2142/biophysico.bppb-v21.0016
ReceivedMarch 07, 2024   
AcceptedJuly 11, 2024   
ReleasedJuly 17, 2024   

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