A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation

Matsubara, Yuya; Okabe, Ryo; Masayama, Ren; Watanabe, Nozomi Morishita; Umakoshi, Hiroshi; Kasahara, Kento; Matubayasi, Nobuyuki

doi:https://doi.org/10.1063/5.0214401

A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation

Matsubara, Yuya; Okabe, Ryo; Masayama, Ren et al.

Journal of Chemical Physics, 2024, 161(2), 024108

アクセス数:29件（2025-04-05 00:07 集計）

固定URL: https://hdl.handle.net/11094/97732

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タイトル	A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation
著者	著者名 Matsubara, Yuya
	著者名 Okabe, Ryo
	著者名 Masayama, Ren
	NRID 1000040892683 1000040892683 ORCID 0000-0002-3461-3660 0000-0002-3461-3660 researchmap permalink nozomiwatanabe nozomiwatanabe Scopus Author ID 57190045741 57190045741 著者名 Watanabe, Nozomi Morishita
	NRID 1000020311772 1000020311772 researchmap permalink read0191167 read0191167 Scopus Author ID 6701925853 6701925853 著者名 Umakoshi, Hiroshi
	NRID 1000010824469 1000010824469 ORCID 0000-0001-7138-250X 0000-0001-7138-250X researchmap permalink kasakento kasakento Scopus Author ID 56245700800 56245700800 著者名 Kasahara, Kento
	NRID 1000020281107 1000020281107 ORCID 0000-0001-7176-441X 0000-0001-7176-441X researchmap permalink nbyk_MTBYS nbyk_MTBYS Scopus Author ID 7003410578 7003410578 著者名 Matubayasi, Nobuyuki
内容	Matsubara Y., Okabe R., Masayama R., et al. Journal of Chemical Physics 161, 024108 (2024) https://doi.org/10.1063/5.0214401.
抄録	We propose a theoretical approach to estimate the permeability coefficients of substrates (permeants) for crossing membranes from donor (D) phase to acceptor (A) phase by means of molecular dynamics (MD) simulation. A fundamental aspect of our approach involves reformulating the returning probability (RP) theory, a rigorous bimolecular reaction theory, to describe permeation phenomena. This reformulation relies on the parallelism between permeation and bimolecular reaction processes. In the present method, the permeability coefficient is represented in terms of the thermodynamic and kinetic quantities for the reactive (R) phase that exists within the inner region of a membrane. One can evaluate these quantities using multiple MD trajectories starting from phase R. We apply the RP theory to the permeation of ethanol and methylamine at different concentrations (infinitely dilute and 1 mol % conditions of permeants). Under the 1 mol% condition, the present method yields a larger permeability coefficient for ethanol (0.12 ± 0.01 cm s−1) than for methylamine (0.069 ± 0.006 cm s−1), while the values of the permeability coefficient are satisfactorily close to those obtained from the brute-force MD simulations (0.18 ± 0.03 and 0.052 ± 0.005 cm s−1 for ethanol and methylamine, respectively). Moreover, upon analyzing the thermodynamic and kinetic contributions to the permeability, we clarify that a higher concentration dependency of permeability for ethanol, as compared to methylamine, arises from the sensitive nature of ethanol’s free-energy barrier within the inner region of the membrane against ethanol concentration.
出版者	American Institute of Physics
収録物名	Journal of Chemical Physics
巻(号)	161(2)
ページ	024108
刊行年月	2024-07-14
言語	英語
ハンドルURL	https://hdl.handle.net/11094/97732
PISSN	00219606
eISSN	10897690
関連情報 (isIdenticalTo)	DOI (出版社版) https://doi.org/10.1063/5.0214401
アクセス権	embargoed access
権利情報	This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Matsubara Y., Okabe R., Masayama R., et al. A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation. Journal of Chemical Physics 161, 024108 (2024) and may be found at https://doi.org/10.1063/5.0214401.
権利情報	The full-text file will be made open to the public on 14 July 2025 in accordance with the publisher's policy.
出版タイプ	Version of Record
カテゴリ	学術雑誌論文 Journal Article

資源タイプ	学術雑誌論文
ローカル資源タイプ	学術雑誌論文
DCTERMS.bibliographicCitation	Journal of Chemical Physics. 2024, 161(2), p. 024108
DC.title	A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation
DC.creator	Matsubara, Yuya
	Okabe, Ryo
	Masayama, Ren
	Watanabe, Nozomi Morishita
	Umakoshi, Hiroshi
	Kasahara, Kento
	Matubayasi, Nobuyuki
DC.publisher	American Institute of Physics
DC.language' scheme='DCTERMS.RFC1766	英語
DCTERMS.issued' scheme='DCTERMS.W3CDTF	2024-07-14
DC.identifier	https://doi.org/10.1063/5.0214401
DC.description	Matsubara Y., Okabe R., Masayama R., et al. Journal of Chemical Physics 161, 024108 (2024) https://doi.org/10.1063/5.0214401.
DCTERMS.abstract	We propose a theoretical approach to estimate the permeability coefficients of substrates (permeants) for crossing membranes from donor (D) phase to acceptor (A) phase by means of molecular dynamics (MD) simulation. A fundamental aspect of our approach involves reformulating the returning probability (RP) theory, a rigorous bimolecular reaction theory, to describe permeation phenomena. This reformulation relies on the parallelism between permeation and bimolecular reaction processes. In the present method, the permeability coefficient is represented in terms of the thermodynamic and kinetic quantities for the reactive (R) phase that exists within the inner region of a membrane. One can evaluate these quantities using multiple MD trajectories starting from phase R. We apply the RP theory to the permeation of ethanol and methylamine at different concentrations (infinitely dilute and 1 mol % conditions of permeants). Under the 1 mol% condition, the present method yields a larger permeability coefficient for ethanol (0.12 ± 0.01 cm s−1) than for methylamine (0.069 ± 0.006 cm s−1), while the values of the permeability coefficient are satisfactorily close to those obtained from the brute-force MD simulations (0.18 ± 0.03 and 0.052 ± 0.005 cm s−1 for ethanol and methylamine, respectively). Moreover, upon analyzing the thermodynamic and kinetic contributions to the permeability, we clarify that a higher concentration dependency of permeability for ethanol, as compared to methylamine, arises from the sensitive nature of ethanol’s free-energy barrier within the inner region of the membrane against ethanol concentration.
DC.rights	This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Matsubara Y., Okabe R., Masayama R., et al. A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation. Journal of Chemical Physics 161, 024108 (2024) and may be found at https://doi.org/10.1063/5.0214401.
DC.rights	The full-text file will be made open to the public on 14 July 2025 in accordance with the publisher's policy.
DC.format	97732
citation_title	A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation
citation_author	Matsubara, Yuya
	Okabe, Ryo
	Masayama, Ren
	Watanabe, Nozomi Morishita
	Umakoshi, Hiroshi
	Kasahara, Kento
	Matubayasi, Nobuyuki
citation_publisher	American Institute of Physics
citation_language	英語
citation_date	2024-07-14
citation_journal_title	Journal of Chemical Physics
citation_volume	161
citation_issue	2
citation_firstpage	024108
citation_doi	https://doi.org/10.1063/5.0214401
citation_public_url	https://hdl.handle.net/11094/97732

A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation

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