Biophysics and Physicobiology最新文献

{"title":"Greetings from the President of Biophysical Society of Japan: Traditionally open culture for fostering creative biophysics.","authors":"Hiroyuki Noji","doi":"10.2142/biophysico.bppb-v18.024","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.024","url":null,"abstract":"In 2021, the Biophysical Society of Japan (BSJ), which was established in 1960, celebrated its 61st anniversary. For more than half a century, the BSJ has served as a vital platform for academic networking and exchange of knowledge in the biophysics field in Japan. Since its establishment, the BSJ has valued the international networking and knowledge exchange. This reflects our long contribution to the governance of the International Union of Pure and Applied Biophysics (IUPAB); BSJ has been producing many executive members in IUPAB: two IUPAB presidents, four IUPAB vice presidents, and six IUPAB councilors, including Setsuro Ebashi (1975-1978 president) and Kuniaki Nagayama (2008– 2011 president). This year, Takayuki Nishizaka was elected as one of the IUPAB councilors for 2021–2024. In Asia, previous BSJ members have established the Asian Biophysics Association with other associated societies, thereby significantly contributing to the promotion of biophysics in Asia. Furthermore, our society holds annual conferences in English with an aim of expanding the role of our society in biophysics from the domestic to an international platform. In recent years, our annual conference has included 1300-1400 participants, including many oversea participants. This indicates our society is growing as one of the largest international biophysics conferences. To further boost the international contribution of our society, we applied for the IUPAB Congress and won the bid in the second trial to hold the 21st IUPAB Congress in Kyoto to be held in 2023, which was later postponed to 2024 along with the rescheduling of the 20th International Botanical Congress in Brazil from 2020 to 2021 due to the ongoing COVID19 pandemic. The 21st IUPAB Congress of 2024 will be merged with the BSJ annual meeting as a joint congress, which will offer participants great opportunities to exchange cutting-edge research ideas with globally leading scientists. The joint congress will also bring blended flavors of biophysics from each region of the world, in particular, biophysics in Japan and Asian-Oceanian countries. Thus, we are positively reshaping the BSJ by attracting global scientists with the aim of contributing to the growth of biophysics research worldwide. Our society is also open to researchers from associated disciplines, such as physics, chemistry, and nanoscience. This stems from our belief that creative ideas often originate from different intersecting fields, as biophysics itself represent the amalgam of biology and physics. Therefore, the BSJ greatly values the open culture to enhance the exchange of new ideas among researchers from various research fields. Another characteristic feature of the BSJ is that our society is open for young students and early career researchers, not only regarding scientific networking, but also social governance. Along with this policy, our society highly appreciates the activity of the Society of Young Scientists in Biophysics, Wakateno-ka","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"224-225"},"PeriodicalIF":0.0,"publicationDate":"2021-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ee/ac/18_224.PMC8511463.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39675947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improve publishing procedures of Biophysics and Physicobiology.","authors":"Haruki Nakamura","doi":"10.2142/biophysico.bppb-v18.023","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.023","url":null,"abstract":"From October 2021, publishing procedures of the Biophysics and Physicobiology (BPPB) are improved for rapid publication of every accepted article, and for reduction of the publication cost that the authors have to pay. The details are described in the updated “Instruction for Authors” on the web page of the BPPB [1] and only the outline is presented here. After the Editor-in-Charge accepts publication of the individual article, the authors submit their manuscript as the final post-print form using the Template that can be downloaded from the web page of “Instruction for Authors”. The authors may submit their manuscript by using the Template even at the first submission procedure before reviewing. The submission site with S1M (ScholarOne Manuscripts) system [2] will automatically convert their manuscript to the PDF file, but if the converted PDF file is incorrect, the authors are requested to provide their own PDF file, which the authors construct by themselves. The publication office adds some information on the PDF file, such as the new DOI of the article, and the received and accepted dates. The publication office makes no particular type setting, as far as the authors prepare and submit the final post-print form using the Template by themselves. For proof reading, the authors are requested only to confirm the PDF file with some information added by the publication office. The above procedures could greatly reduce the publication time and cost, once the post-print form is prepared by the authors. For preparing the post-print form using the Template without complicated rules, the style of articles is changed as follows: (1) Double column setting is changed to single column setting (2) The bibliographic style of the Reference list is slightly changed without using “italic” or “bold-face” fonts (3) From Volume 19 published in 2022, each article is identified by the newly introduced “Article ID”, not by page numbers. (4) E-mail address of the corresponding author is not always necessary. Instead, the ORCID iD [3] should be always indicated. (5) The authors are always requested to submit “Graphical Abstract” except for articles in the category of “Editorial” or “Commentary and Perspective” The Editorial board members desire this improvement could encourage more authors in the world to submit their best papers to the BPPB. In addition, Manuscript Transfer system (B2J) from bioRxiv to the BPPB has been available since November 2020, in order to save authors time by transmitting their manuscript files and metadata directly from bioRxiv to the BPPB. About more details, see the web site of bioRxiv [4]. The authors are requested to input some additional information on the BPPB web site after transmitting their manuscript. Finally, we will always make our best to publish the BPPB, and would highly appreciate your cooperation with us.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"223"},"PeriodicalIF":0.0,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/9c/c8/18_223.PMC8492105.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39563877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease.","authors":"Daisuke Kuroda, Kouhei Tsumoto","doi":"10.2142/biophysico.bppb-v18.022","DOIUrl":"10.2142/biophysico.bppb-v18.022","url":null,"abstract":"<p><p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), spread rapidly around the globe. The main protease encoded by SARS-CoV-2 is essential for processing of the polyproteins translated from the viral RNA genome, making this protein a potential drug target. A recently reported mutation in the protease, P108S, may be responsible for milder symptoms observed in COVID-19 patients in Tokyo. Starting from a crystal structure of the SARS-CoV-2 main protease in the dimeric form, we performed triplicate 5.0-μs molecular dynamics simulations of the wild-type and P108S mutant. Our computational results suggest a link between the mutation P108S and dynamics of the catalytic sites in the main protease: The catalytic dyad become considerably inaccessible to substrates in the P108S mutant. Our results also demonstrate the potential of molecular dynamics simulations to complement experimental techniques and other computational methods, such as protein design calculations, which predict effects of mutations based on static crystal structures. Further studies are certainly necessary to quantitively understand the relationships between the P108S mutation and physical properties of the main protease, but the results of our study will immediately inform development of new protease inhibitors.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"215-222"},"PeriodicalIF":0.0,"publicationDate":"2021-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f7/18/18_215.PMC8470906.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39505867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimation of the relative contributions to the electronic energy transfer rates based on Förster theory: The case of C-phycocyanin chromophores.","authors":"Kenji Mishima,&nbsp;Mitsuo Shoji,&nbsp;Yasufumi Umena,&nbsp;Mauro Boero,&nbsp;Yasuteru Shigeta","doi":"10.2142/biophysico.bppb-v18.021","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.021","url":null,"abstract":"<p><p>In the present study, we provide a reformulation of the theory originally proposed by Förster which allows for simple and convenient formulas useful to estimate the relative contributions of transition dipole moments of a donor and acceptor (chemical factors), their orientation factors (intermolecular structural factors), intermolecular center-to-center distances (intermolecular structural factors), spectral overlaps of absorption and emission spectra (photophysical factors), and refractive index (material factor) to the excitation energy transfer (EET) rate constant. To benchmark their validity, we focused on the EET occurring in C-phycocyanin (C-PC) chromophores. To this aim, we resorted to quantum chemistry calculations to get optimized molecular structures of the C-PC chromophores within the density functional theory (DFT) framework. The absorption and emission spectra, as well as transition dipole moments, were computed by using the time-dependent DFT (TDDFT). Our method was applied to several types of C-PCs showing that the EET rates are determined by an interplay of their specific physical, chemical, and geometrical features. These results show that our formulas can become a useful tool for a reliable estimation of the relative contributions of the factors regulating the EET transfer rate.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"196-214"},"PeriodicalIF":0.0,"publicationDate":"2021-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/14/96/18_196.PMC8421246.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39443072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biochemical and crystallographic studies of monomeric and dimeric bovine cytochrome <i>c</i> oxidase.","authors":"Kyoko Shinzawa-Itoh, Kazumasa Muramoto","doi":"10.2142/biophysico.bppb-v18.020","DOIUrl":"10.2142/biophysico.bppb-v18.020","url":null,"abstract":"<p><p>Cytochrome <i>c</i> oxidase (CcO), a terminal oxidase in the respiratory chain, catalyzes the reduction of O₂ to water coupled with the proton pump across the membrane. Mitochondrial CcO exists in monomeric and dimeric forms, and as a monomer as part of the respiratory supercomplex, although the enzymatic reaction proceeds in the CcO monomer. Recent biochemical and crystallographic studies of monomeric and dimeric CcOs have revealed functional and structural differences among them. In solubilized mitochondrial membrane, the monomeric form is dominant, and a small amount of dimer is observed. The activity of the monomeric CcO is higher than that of the dimer, suggesting that the monomer is the active form. In the structure of monomeric CcO, a hydrogen bond network of water molecules is formed at the entrance of the proton transfer K-pathway, and in dimeric CcO, this network is altered by a cholate molecule binding between monomers. The specific binding of the cholate molecule at the dimer interface suggests that the binding of physiological ligands similar in size or shape to cholate could also trigger dimer formation as a physiological standby form. Because the dimer interface also contains weak interactions of nonspecifically bound lipid molecules, hydrophobic interactions between the transmembrane helices, and a Met-Met interaction between the extramembrane regions, these interactions could support the stabilization of the standby form. Structural analyses also suggest that hydrophobic interactions of cardiolipins bound to the trans-membrane surface of CcO are involved in forming the supercomplex.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"186-195"},"PeriodicalIF":0.0,"publicationDate":"2021-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/48/43/18_186.PMC8390318.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39409368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure of a retinal chromophore of dark-adapted middle rhodopsin as studied by solid-state nuclear magnetic resonance spectroscopy.","authors":"Izuru Kawamura,&nbsp;Hayato Seki,&nbsp;Seiya Tajima,&nbsp;Yoshiteru Makino,&nbsp;Arisu Shigeta,&nbsp;Takashi Okitsu,&nbsp;Akimori Wada,&nbsp;Akira Naito,&nbsp;Yuki Sudo","doi":"10.2142/biophysico.bppb-v18.019","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.019","url":null,"abstract":"<p><p>Middle rhodopsin (MR) found from the archaeon <i>Haloquadratum walsbyi</i> is evolutionarily located between two different types of rhodopsins, bacteriorhodopsin (BR) and sensory rhodopsin II (SRII). Some isomers of the chromophore retinal and the photochemical reaction of MR are markedly different from those of BR and SRII. In this study, to obtain the structural information regarding its active center (i.e., retinal), we subjected MR embedded in lipid bilayers to solid-state magic-angle spinning nuclear magnetic resonance (NMR) spectroscopy. The analysis of the isotropic ¹³C chemical shifts of the retinal chromophore revealed the presence of three types of retinal configurations of dark-adapted MR: (13-<i>trans</i>, 15-<i>anti</i> (all-<i>trans</i>)), (13-<i>cis</i>, 15-<i>syn</i>), and 11-<i>cis</i> isomers. The higher field resonance of the 20-C methyl carbon in the all-<i>trans</i> retinal suggested that Trp182 in MR has an orientation that is different from that in other microbial rhodopsins, owing to the changes in steric hindrance associated with the 20-C methyl group in retinal. ¹³Cζ signals of Tyr185 in MR for all-<i>trans</i> and 13-<i>cis</i>, 15-<i>syn</i> isomers were discretely observed, representing the difference in the hydrogen bond strength of Tyr185. Further, ¹⁵N NMR analysis of the protonated Schiff base corresponding to the all-<i>trans</i> and 13-<i>cis</i>, 15-<i>syn</i> isomers in MR showed a strong electrostatic interaction with the counter ion. Therefore, the resulting structural information exhibited the property of stable retinal conformations of dark-adapted MR.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"177-185"},"PeriodicalIF":0.0,"publicationDate":"2021-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/81/90/18_177.PMC8354847.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39347188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural basis for Ca²⁺-dependent catalysis of a cutinase-like enzyme and its engineering: application to enzymatic PET depolymerization.","authors":"Masayuki Oda","doi":"10.2142/biophysico.bppb-v18.018","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.018","url":null,"abstract":"<p><p>A cutinase-like enzyme from <i>Saccharomonospora viridis</i> AHK190, Cut190, can depolymerize polyethylene terephthalate (PET). As high activity at approximately 70°C is required for PET depolymerization, structure-based protein engineering of Cut190 was carried out. Crystal structure information of the Cut190 mutants was used for protein engineering and for evaluating the molecular basis of activity and thermal stability. A variety of biophysical methods were employed to unveil the mechanisms underlying the unique features of Cut190, which included the regulation of its activity and thermal stability by Ca²⁺. Ca²⁺ association and dissociation can change the enzyme conformation to regulate catalytic activity. Weak metal-ion binding would be required for the naïve conformational change of Cut190, while maintaining its fluctuation, to \"switch\" the enzyme on and off. The activity of Cut190 is regulated by the weak Ca²⁺ binding to the specific site, Site 1, while thermal stability is mainly regulated by binding to another Site 2, where a disulfide bond could be introduced to increase the stability. Recent results on the structure-activity relationship of engineered Cut190 are reviewed, including the application for PET depolymerization by enzymes.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"168-176"},"PeriodicalIF":0.0,"publicationDate":"2021-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/59/8e/18_168.PMC8326265.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39306744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Limitations of the ABEGO-based backbone design: ambiguity between αα-corner and αα-hairpin.","authors":"Koya Sakuma","doi":"10.2142/biophysico.bppb-v18.017","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.017","url":null,"abstract":"<p><p>ABEGO is a coarse-grained representation for poly-peptide backbone dihedral angles. The Ramachandran map is divided into four segments denoted as A, B, E, and G to represent the local conformation of poly-peptide chains in the character strings. Although the ABEGO representation is widely used in backbone building simulation for de novo protein design, it cannot capture minor differences in backbone dihedral angles, which potentially leads to ambiguity between two structurally distinct fragments. Here, I show a nontrivial example of two local motifs that could not be distinguished by their ABEGO representations. I found that two well-known local motifs αα-hairpins and αα-corners are both represented as α-GBB-α and thus indistinguishable in the ABEGO representation, although they show distinct arrangements of the flanking α-helices. I also found that α-GBB-α motifs caused a loss of efficiency in the ABEGO-based fragment-assembly simulations for de novo protein backbone design. Nevertheless, I was able to design amino-acid sequences that were predicted to fold into the target topologies that contained these α-GBB-α motifs, which suggests such topologies that are difficult to build by ABEGO-based simulations are designable once the backbone structures are modeled by some means. The finding that certain local motifs bottleneck the ABEGO-based fragment-assembly simulations for construction of backbone structures suggests that finer representations of backbone torsion angles are required for efficiently generating diverse topologies containing such indistinguishable local motifs.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"159-167"},"PeriodicalIF":0.0,"publicationDate":"2021-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1b/58/18_159.PMC8214924.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39045146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Glycine insertion modulates the fluorescence properties of <i>Aequorea victoria</i> green fluorescent protein and its variants in their ambient environment.","authors":"Takamitsu J Morikawa,&nbsp;Masayoshi Nishiyama,&nbsp;Keiko Yoshizawa,&nbsp;Hideaki Fujita,&nbsp;Tomonobu M Watanabe","doi":"10.2142/biophysico.bppb-v18.016","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.016","url":null,"abstract":"<p><p>The green fluorescent protein (GFP) derived from Pacific Ocean jellyfish is an essential tool in biology. GFP-solvent interactions can modulate the fluorescent property of GFP. We previously reported that glycine insertion is an effective mutation in the yellow variant of GFP, yellow fluorescent protein (YFP). Glycine insertion into one of the β-strands comprising the barrel structure distorts its structure, allowing water molecules to invade near the chromophore, enhancing hydrostatic pressure or solution hydrophobicity sensitivity. However, the underlying mechanism of how glycine insertion imparts environmental sensitivity to YFP has not been elucidated yet. To unveil the relationship between fluorescence and β-strand distortion, we investigated the effects of glycine insertion on the dependence of the optical properties of GFP variants named enhanced-GFP (eGFP) and its yellow (eYFP) and cyan (eCFP) variants with respect to pH, temperature, pressure, and hydrophobicity. Our results showed that the quantum yield decreased depending on the number of inserted glycines in all variants, and the dependence on pH, temperature, pressure, and hydrophobicity was altered, indicating the invasion of water molecules into the β-barrel. Peak shifts in the emission spectrum were observed in glycine-inserted eGFP, suggesting a change of the electric state in the excited chromophore. A comparative investigation of the spectral shift among variants under different conditions demonstrated that glycine insertion rearranged the hydrogen bond network between His148 and the chromophore. The present results provide important insights for further understanding the fluorescence mechanism in GFPs and suggest that glycine insertion could be a potent approach for investigating the relationship between water molecules and the intra-protein chromophore.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"145-158"},"PeriodicalIF":0.0,"publicationDate":"2021-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f9/50/18_145.PMC8214926.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39045145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transfer entropy dependent on distance among agents in quantifying leader-follower relationships.","authors":"Udoy S Basak, Sulimon Sattari, Motaleb Hossain, Kazuki Horikawa, Tamiki Komatsuzaki","doi":"10.2142/biophysico.bppb-v18.015","DOIUrl":"10.2142/biophysico.bppb-v18.015","url":null,"abstract":"<p><p>Synchronized movement of (both unicellular and multicellular) systems can be observed almost everywhere. Understanding of how organisms are regulated to synchronized behavior is one of the challenging issues in the field of collective motion. It is hypothesized that one or a few agents in a group regulate(s) the dynamics of the whole collective, known as leader(s). The identification of the leader (influential) agent(s) is very crucial. This article reviews different mathematical models that represent different types of leadership. We focus on the improvement of the leader-follower classification problem. It was found using a simulation model that the use of interaction domain information significantly improves the leader-follower classification ability using both linear schemes and information-theoretic schemes for quantifying influence. This article also reviews different schemes that can be used to identify the interaction domain using the motion data of agents.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"131-144"},"PeriodicalIF":0.0,"publicationDate":"2021-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/cf/0f/18_131.PMC8214925.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39045144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}