{"id":1721,"date":"2024-04-18T14:44:35","date_gmt":"2024-04-18T05:44:35","guid":{"rendered":"https:\/\/www.ifs.tohoku.ac.jp\/eng\/?page_id=1721"},"modified":"2024-04-30T10:50:41","modified_gmt":"2024-04-30T01:50:41","slug":"bfsl","status":"publish","type":"page","link":"https:\/\/www.ifs.tohoku.ac.jp\/eng\/research\/dv_nfrd\/bfsl\/","title":{"rendered":"Biomolecular Flow Systems Laboratory"},"content":{"rendered":"<div class=\"research\">\r\n<div class=\"header\">\r\n<div class=\"wrapper\">\r\n<div class=\"clearfix\"><ul class=\"breadcrumb\">\n<li><a href=\"\/jpn\/\">TOP<\/a><\/li>\n<li><a href=\"https:\/\/www.ifs.tohoku.ac.jp\/eng\/research\/\">Research<\/a><\/li>\n<li><a href=\"https:\/\/www.ifs.tohoku.ac.jp\/eng\/research\/dv_nfrd\/\">Nanoscale Flow Research Division<\/a><\/li>\n<li>Biomolecular Flow Systems Laboratory<li>\n<\/ul><\/div>\r\n<h2>Nanoscale Flow Research Division<\/h2>\r\n<h3>Biomolecular Flow Systems Laboratory<\/h3>\r\n<div class=\"clearfix\">\r\n<ul class=\"professor\">\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/professor\/takashitokumasu.jpeg\" \/>\r\n<p><span>Concurrent Professor<\/span>Takashi Tokumasu<\/p>\r\n<\/li>\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/professor\/takuyamabuchi_v2.jpg\" \/>\r\n<p><span>Associate Professor<\/span>Takuya Mabuchi<\/p>\r\n<\/li>\r\n<\/ul>\r\n<\/div>\r\n<div class=\"clearfix\">\r\n<ul class=\"sdgs\">\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/sdgs_icon_e\/sdgs-02.jpg\" \/><\/li>\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/sdgs_icon_e\/sdgs-03.jpg\" \/><\/li>\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/sdgs_icon_e\/sdgs-06.jpg\" \/><\/li>\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/sdgs_icon_e\/sdgs-07.jpg\" \/><\/li>\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/sdgs_icon_e\/sdgs-09.jpg\" \/><\/li>\r\n<\/ul>\r\n<\/div>\r\n<div class=\"clearfix\">\r\n<div class=\"labo\"><a href=\"https:\/\/mabuchigroup.jp\/en\/\" target=\"_blank\" rel=\"noopener\">Enter the Lab Page<\/a><\/div>\r\n<\/div>\r\n<\/div>\r\n<\/div>\r\n<div class=\"gray\">\r\n<div class=\"wrapper\">The research involves theoretical and computer simulation studies of biomolecular systems. Current research activities span both development of new computational methods and theoretical characterization of proton transport and protein phase behavior in biomolecular systems at multiple length scales. For example, to probe complex transport phenomena of protons, a reactive model has been developed within the simplicity of the theoretical framework of classical molecular dynamics (MD) simulations. Proton transport through complex structure such as transmembrane ion channels are one of our research interests. Protein phase behavior (i.e, aggregation, self-assembly, and liquid\u2013liquid phase separation) in aqueous solutions are also of our research interest. Computational studies can assist in the challenge of designing the artificial ion channels. Our research is thus often carried out in close collaboration with leading experimentalists and is integrated in a feedback loop with experiments.<\/div>\r\n<\/div>\r\n<div class=\"contents\">\r\n<div class=\"wrapper\">\r\n<h4>Reactive transport mechanisms of protons in nanopores<\/h4>\r\n<div>Transport of protons (H<sup>+<\/sup>) and hydroxide ions (OH<sup>&#8211;<\/sup>) requires consideration of a complex mechanism involving chemical reactions with water molecules, known as the Grotthuss mechanism, unlike other ions. Additionally, these ions move through water hydrogen bonding networks that are significantly influenced by confined pore structures, making them difficult to understand experimentally. Therefore, in this study, we utilize reactive molecular dynamics simulations based on quantum chemical calculations to elucidate the correlation between water domain structures and ion conduction mechanisms. <br \/><br \/><br \/>Proton transport via Grotthuss mechanism<\/div>\r\n<iframe loading=\"lazy\" width=\"360\" height=\"203\" src=\"https:\/\/www.youtube.com\/embed\/EkQ7yhMzGm0?si=TH2pJoviHRlpkDQ-?rel=0\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen=\"allowfullscreen\"><\/iframe>\r\n<div class=\"clearfix\">\r\n<ul class=\"sdgs\">\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/sdgs_icon_e\/sdgs-09.jpg\" \/><\/li>\r\n<\/ul>\r\n<\/div>\r\n<\/div>\r\n<\/div>\r\n<div class=\"contents\">\r\n<div class=\"wrapper\">\r\n<h4>Development of artificial ion channels with selective permeability<\/h4>\r\n<div>We aim to construct artificial ion channels with selective permeability using DNA nanotechnology. This technique allows for precise design of the channel structure by engineering DNA base sequences, offering a high degree of flexibility in fabrication design. Through molecular simulations, we investigate not only the transport mechanisms of small molecules within DNA nanopores but also the stability and dynamics of membrane-spanning DNA nanopores to lipid bilayers (liposomes). This research has the potential to establish various engineering applications, ranging from the treatment of intractable diseases related to ion channels to enhancing substance storage and developing environmental remediation materials.<br \/><br \/><br \/>Molecular simulations of membrane-spanning DNA nanopore<\/div>\r\n<iframe loading=\"lazy\" width=\"360\" height=\"203\" src=\"https:\/\/www.youtube.com\/embed\/lVEp-ydVPdg?si=mmCs6Xr0klZVzdN5?rel=0\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen=\"allowfullscreen\"><\/iframe><br \/><br \/><br \/>Liposome formation using coarse-grained molecular simulations<br \/><iframe loading=\"lazy\" width=\"360\" height=\"203\" src=\"https:\/\/www.youtube.com\/embed\/GZyl6OLJos0?si=_0LLWgxte-ovnOWO?rel=0\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen=\"allowfullscreen\"><\/iframe>\r\n<div class=\"clearfix\">\r\n<ul class=\"sdgs\">\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/sdgs_icon_e\/sdgs-03.jpg\" \/><\/li>\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/sdgs_icon_e\/sdgs-06.jpg\" \/><\/li>\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/sdgs_icon_e\/sdgs-07.jpg\" \/><\/li>\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/sdgs_icon_e\/sdgs-09.jpg\" \/><\/li>\r\n<\/ul>\r\n<\/div>\r\n<\/div>\r\n<\/div>\r\n<div class=\"contents\">\r\n<div class=\"wrapper\">\r\n<h4>Liquid-liquid phase separation using artificial polypeptides<\/h4>\r\n<div>Biomolecules such as proteins and RNA are known to undergo liquid-liquid phase separation, forming liquid droplets or gel-like structures within cells through self-assembly. It is believed that cells regulate various life phenomena such as transcription, translation, and signal transduction by converting biomolecules into liquid droplets. We focus on theoretically designing artificial coacervates using artificial proteins, such as elastin-like polypeptides (ELPs), to encapsulate specific molecules into liquid droplets. This research is closely linked to material selection, separation, and concentration technologies, with broad applications across industries. For example, enzyme concentration could enhance activity, leading to applications in long-term food preservation and the efficient synthesis of pharmaceutical proteins.<br \/><br \/><br \/>Elastin-like polypeptides (ELP) coacervate formation<br \/><iframe loading=\"lazy\" width=\"360\" height=\"203\" src=\"https:\/\/www.youtube.com\/embed\/ZUmHVRmw3wU?si=fToGBdT6W0EnSPpw?rel=0\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen=\"allowfullscreen\"><\/iframe><br \/><br \/><br \/>RNA partitioning in the ELP coacervate<br \/><iframe loading=\"lazy\" width=\"360\" height=\"203\" src=\"https:\/\/www.youtube.com\/embed\/5NBIebQO1Yc?si=3hdNXxT9RJHbDbIz?rel=0\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen=\"allowfullscreen\"><\/iframe>\r\n<div class=\"clearfix\">\r\n<ul class=\"sdgs\">\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/sdgs_icon_e\/sdgs-02.jpg\" \/><\/li>\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/sdgs_icon_e\/sdgs-03.jpg\" \/><\/li>\r\n<li><img decoding=\"async\" src=\"\/jpn\/wp-content\/themes\/ifs\/images\/research\/sdgs_icon_e\/sdgs-09.jpg\" \/><\/li>\r\n<\/ul>\r\n<br \/><br \/><br \/><br \/><br \/><br \/><br \/><\/div>\r\n<\/div>\r\n<\/div>\r\n<div class=\"footer clearfix\">\r\n<div class=\"wrapper\">\r\n<div class=\"labo\"><a href=\"https:\/\/mabuchigroup.jp\/en\/\" target=\"_blank\" rel=\"noopener\">Enter the Lab Page<\/a><\/div>\r\n<\/div>\r\n<\/div>\r\n<\/div>\r\n<\/div>","protected":false},"excerpt":{"rendered":"Nanoscale Flow Research Division Biomolecular Flow Systems Laboratory Concurrent ProfessorTakashi Tokumasu Associate ProfessorTakuya Mabuchi Enter the Lab Page The research involves theoretical and computer simulation studies of biomolecular systems. Current research activities span both development of new computational methods and theoretical characterization of proton transport and protein phase behavior in biomolecular systems at multiple length [&hellip;]","protected":false},"author":1,"featured_media":0,"parent":80,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-1721","page","type-page","status-publish","hentry"],"acf":[],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/www.ifs.tohoku.ac.jp\/eng\/wp-json\/wp\/v2\/pages\/1721","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ifs.tohoku.ac.jp\/eng\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ifs.tohoku.ac.jp\/eng\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ifs.tohoku.ac.jp\/eng\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ifs.tohoku.ac.jp\/eng\/wp-json\/wp\/v2\/comments?post=1721"}],"version-history":[{"count":13,"href":"https:\/\/www.ifs.tohoku.ac.jp\/eng\/wp-json\/wp\/v2\/pages\/1721\/revisions"}],"predecessor-version":[{"id":1785,"href":"https:\/\/www.ifs.tohoku.ac.jp\/eng\/wp-json\/wp\/v2\/pages\/1721\/revisions\/1785"}],"up":[{"embeddable":true,"href":"https:\/\/www.ifs.tohoku.ac.jp\/eng\/wp-json\/wp\/v2\/pages\/80"}],"wp:attachment":[{"href":"https:\/\/www.ifs.tohoku.ac.jp\/eng\/wp-json\/wp\/v2\/media?parent=1721"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}