{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T15:21:05Z","timestamp":1789572065426,"version":"build-2803163510"},"reference-count":62,"publisher":"Biophysical Society of Japan","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BIOPHYSICS"],"published-print":{"date-parts":[[2026]]},"DOI":"10.2142\/biophysico.bppb-v23.0015","type":"journal-article","created":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T22:09:57Z","timestamp":1778278197000},"page":"n\/a","source":"Crossref","is-referenced-by-count":1,"title":["A lattice Monte Carlo model for amyloid fibril formation"],"prefix":"10.2142","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3912-5604","authenticated-orcid":false,"given":"Hisashi","family":"Okumura","sequence":"first","affiliation":[{"name":"Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences"},{"name":"Institute for Molecular Science, National Institutes of Natural Sciences"},{"name":"Graduate Institute for Advanced Studies, SOKENDAI (The Graduate University for Advanced Studies)"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linh Truong","family":"Hoai","sequence":"additional","affiliation":[{"name":"Institute for Molecular Science, National Institutes of Natural Sciences"},{"name":"The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pornthep","family":"Sompornpisut","sequence":"additional","affiliation":[{"name":"The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Satoru G.","family":"Itoh","sequence":"additional","affiliation":[{"name":"Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences"},{"name":"Institute for Molecular Science, National Institutes of Natural Sciences"},{"name":"Graduate Institute for Advanced Studies, SOKENDAI (The Graduate University for Advanced Studies)"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"909","reference":[{"key":"1","doi-asserted-by":"publisher","unstructured":"[1] Chiti, F., Dobson, C. M. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem. 75, 333\u2013366 (2006). https:\/\/doi.org\/10.1146\/annurev.biochem.75.101304.123901","DOI":"10.1146\/annurev.biochem.75.101304.123901"},{"key":"2","doi-asserted-by":"publisher","unstructured":"[2] Chiti, F., Dobson, C. M. Amyloid formation by globular proteins under native conditions. Nat. Chem. Biol. 5, 15\u201322 (2009). https:\/\/doi.org\/10.1038\/nchembio.131","DOI":"10.1038\/nchembio.131"},{"key":"3","doi-asserted-by":"crossref","unstructured":"[3] Almeida, Z. L., Brito, R. M. M. Structure and aggregation mechanisms in amyloids. Molecules 25, 1195 (2020). https:\/\/doi.org\/10.3390\/molecules25051195","DOI":"10.3390\/molecules25051195"},{"key":"4","doi-asserted-by":"crossref","unstructured":"[4] Sengupta, U., Kayed, R. Amyloid \u03b2, tau, and \u03b1-synuclein aggregates in the pathogenesis, prognosis, and therapeutics for neurodegenerative diseases. Prog. Neurobiol. 214, 102270 (2022). https:\/\/doi.org\/10.1016\/j.pneurobio.2022.102270","DOI":"10.1016\/j.pneurobio.2022.102270"},{"key":"5","doi-asserted-by":"crossref","unstructured":"[5] Nguyen, P. H., Derreumaux, P. Conformational ensemble and polymorphism of the all-atom Alzheimer\u2019s A\u03b237\u201342 amyloid peptide oligomers. J. Phys. Chem. B 117, 5831\u20135840 (2013). https:\/\/doi.org\/10.1021\/jp401563n","DOI":"10.1021\/jp401563n"},{"key":"6","doi-asserted-by":"publisher","unstructured":"[6] Itoh, S. G., Okumura, H. Dimerization process of amyloid-\u03b2 (29\u201342) studied by the hamiltonian replica-permutation molecular dynamics simulations. J. Phys. Chem. B 118, 11428\u201311436 (2014). https:\/\/doi.org\/10.1021\/jp505984e","DOI":"10.1021\/jp505984e"},{"key":"7","doi-asserted-by":"publisher","unstructured":"[7] Itoh, S. G., Okumura, H. Oligomer formation of amyloid-\u03b2 (29\u201342) from its monomers using the hamiltonian replica-permutation molecular dynamics simulation. J. Phys. Chem. B 120, 6555\u20136561 (2016). https:\/\/doi.org\/10.1021\/acs.jpcb.6b03828","DOI":"10.1021\/acs.jpcb.6b03828"},{"key":"8","doi-asserted-by":"publisher","unstructured":"[8] Barz, B., Olubiyi, O. O., Strodel, B. Early amyloid beta-protein aggregation precedes conformational change. Chem. Commun. (Camb.) 50, 5373\u20135375 (2014). https:\/\/doi.org\/10.1039\/c3cc48704k","DOI":"10.1039\/c3cc48704k"},{"key":"9","doi-asserted-by":"crossref","unstructured":"[9] Barz, B., Liao, Q., Strodel, B. Pathways of amyloid-\u03b2 aggregation depend on oligomer shape. J. Am. Chem. Soc. 140, 319\u2013327 (2018). https:\/\/doi.org\/10.1021\/jacs.7b10343","DOI":"10.1021\/jacs.7b10343"},{"key":"10","doi-asserted-by":"crossref","unstructured":"[10] Man, V. H., Nguyen, P. H., Derreumaux, P. High-resolution structures of the amyloid-\u03b2 1\u201342 dimers from the comparison of four atomistic force fields. J. Phys. Chem. B 121, 5977\u20135987 (2017). https:\/\/doi.org\/10.1021\/acs.jpcb.7b04689","DOI":"10.1021\/acs.jpcb.7b04689"},{"key":"11","doi-asserted-by":"crossref","unstructured":"[11] Man, V. H., He, X., Ji, B., Liu, S., Xie, X.-Q., Wang, J. Molecular mechanism and kinetics of amyloid-\u03b242 aggregate formation: A simulation study. ACS Chem. Neurosci. 10, 4643\u20134658 (2019). https:\/\/doi.org\/10.1021\/acschemneuro.9b00473","DOI":"10.1021\/acschemneuro.9b00473"},{"key":"12","doi-asserted-by":"crossref","unstructured":"[12] Nguyen, H. L., Linh, H. Q., Matteini, P., La Penna, G., Li, M. S. Emergence of barrel motif in amyloid-\u03b2 trimer: A computational study. J. Phys. Chem. B 124, 10617\u201310631 (2020). https:\/\/doi.org\/10.1021\/acs.jpcb.0c05508","DOI":"10.1021\/acs.jpcb.0c05508"},{"key":"13","doi-asserted-by":"publisher","unstructured":"[13] Itoh, S. G., Yagi-Utsumi, M., Kato, K., Okumura, H. Key residue for aggregation of amyloid-\u03b2 peptides. ACS Chem. Neurosci. 13, 3139\u20133151 (2022). https:\/\/doi.org\/10.1021\/acschemneuro.2c00358","DOI":"10.1021\/acschemneuro.2c00358"},{"key":"14","doi-asserted-by":"crossref","unstructured":"[14] Khaled, M., R\u00f6nnb\u00e4ck, I., Ilag, L. L., Gr\u00e4slund, A., Strodel, B., \u00d6sterlund, N. A hairpin motif in the amyloid-\u03b2 peptide is important for formation of disease-related oligomers. J. Am. Chem. Soc. 145, 18340\u201318354 (2023). https:\/\/doi.org\/10.1021\/jacs.3c03980","DOI":"10.1021\/jacs.3c03980"},{"key":"15","doi-asserted-by":"crossref","unstructured":"[15] Okumura, H., Itoh, S. G. Molecular dynamics simulations of amyloid-\u03b2 (16\u201322) peptide aggregation at air\u2013water interfaces. J. Chem. Phys. 152, 095101 (2020). https:\/\/doi.org\/10.1063\/1.5131848","DOI":"10.1063\/1.5131848"},{"key":"16","doi-asserted-by":"publisher","unstructured":"[16] Farah, A.-I., Itoh, S. G., Okumura, H. Molecular dynamics simulations of amyloid-\u03b2 (29\u201342) aggregation in bulk water and at the air\u2013water interface. Biophys. Physicobiol. 22, e220033 (2025). https:\/\/doi.org\/10.2142\/biophysico.bppb-v22.0033","DOI":"10.2142\/biophysico.bppb-v22.0033"},{"key":"17","doi-asserted-by":"publisher","unstructured":"[17] Rodriguez, R. A., Chen, L. Y., Plascencia-Villa, G., Perry, G. Thermodynamics of amyloid-\u03b2 fibril elongation: Atomistic details of the transition state. ACS Chem. Neurosci. 9, 783\u2013789 (2018). https:\/\/doi.org\/10.1021\/acschemneuro.7b00409","DOI":"10.1021\/acschemneuro.7b00409"},{"key":"18","doi-asserted-by":"crossref","unstructured":"[18] Okumura, H., Itoh, S. G. Structural and fluctuational difference between two ends of A\u03b2 amyloid fibril: MD simulations predict only one end has open conformations. Sci. Rep. 6, 38422 (2016). https:\/\/doi.org\/10.1038\/srep38422","DOI":"10.1038\/srep38422"},{"key":"19","doi-asserted-by":"publisher","unstructured":"[19] Okumura, H., Itoh, S. G. Amyloid fibril disruption by ultrasonic cavitation: Nonequilibrium molecular dynamics simulations. J. Am. Chem. Soc. 136, 10549\u201310552 (2014). https:\/\/doi.org\/10.1021\/ja502749f","DOI":"10.1021\/ja502749f"},{"key":"20","doi-asserted-by":"crossref","unstructured":"[20] Hoang Viet, M., Derreumaux, P., Nguyen, P. H. Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils. J. Chem. Phys. 145, 174113 (2016). https:\/\/doi.org\/10.1063\/1.4966263","DOI":"10.1063\/1.4966263"},{"key":"21","doi-asserted-by":"crossref","unstructured":"[21] Hoang Viet, M., Derreumaux, P., Li, M. S., Roland, C., Sagui, C., Nguyen, P. H. Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study. J. Chem. Phys. 143, 155101 (2015). https:\/\/doi.org\/10.1063\/1.4933207","DOI":"10.1063\/1.4933207"},{"key":"22","doi-asserted-by":"publisher","unstructured":"[22] Okumura, H., Itoh, S. G., Nakamura, K., Kawasaki, T. Role of water molecules and helix structure stabilization in the laser-induced disruption of amyloid fibrils observed by nonequilibrium molecular dynamics simulations. J. Phys. Chem. B 125, 4964\u20134976 (2021). https:\/\/doi.org\/10.1021\/acs.jpcb.0c11491","DOI":"10.1021\/acs.jpcb.0c11491"},{"key":"23","doi-asserted-by":"crossref","unstructured":"[23] Okumura, H., Itoh, S. G., Zen, H., Nakamura, K. Dissociation process of polyalanine aggregates by free electron laser irradiation. PLoS One 18, e0291093 (2023). https:\/\/doi.org\/10.1371\/journal.pone.0291093","DOI":"10.1371\/journal.pone.0291093"},{"key":"24","doi-asserted-by":"crossref","unstructured":"[24] Bieschke, J., Russ, J., Friedrich, R. P., Ehrnhoefer, D. E., Wobst, H., Neugebauer, K., et al. EGCG remodels mature \u03b1-synuclein and amyloid-\u03b2 fibrils and reduces cellular toxicity. Proc. Natl. Acad. Sci. U.S.A. 107, 7710\u20137715 (2010). https:\/\/doi.org\/doi:10.1073\/pnas.0910723107","DOI":"10.1073\/pnas.0910723107"},{"key":"25","doi-asserted-by":"crossref","unstructured":"[25] Zhang, T., Zhang, J., Derreumaux, P., Mu, Y. Molecular mechanism of the inhibition of EGCG on the Alzheimer Abeta(1\u201342) dimer. J. Phys. Chem. B 117, 3993\u20134002 (2013). https:\/\/doi.org\/10.1021\/jp312573y","DOI":"10.1021\/jp312573y"},{"key":"26","doi-asserted-by":"publisher","unstructured":"[26] Doytchinova, I., Atanasova, M., Salamanova, E., Ivanov, S., Dimitrov, I. Curcumin inhibits the primary nucleation of amyloid-beta peptide: A molecular dynamics study. Biomolecules 10, 1323 (2020). https:\/\/doi.org\/10.3390\/biom10091323","DOI":"10.3390\/biom10091323"},{"key":"27","doi-asserted-by":"crossref","unstructured":"[27] Sukumaran, S. D., Faraj, F. L., Lee, V. S., Othman, R., Buckle, M. J. C. 2-Aryl-3-(arylideneamino)-1,2-dihydroquinazoline-4 (3H)-ones as inhibitors of cholinesterases and self-induced \u03b2-amyloid (A\u03b2) aggregation: Biological evaluations and mechanistic insights from molecular dynamics simulations. RSC Adv. 8, 7818\u20137831 (2018). https:\/\/doi.org\/10.1039\/C7RA11872D","DOI":"10.1039\/C7RA11872D"},{"key":"28","doi-asserted-by":"crossref","unstructured":"[28] Ngoc, L. L. N., Itoh, S. G., Sompornpisut, P., Okumura, H. Replica-permutation molecular dynamics simulations of an amyloid-\u03b2 (16\u201322) peptide and polyphenols. Chem. Phys. Lett. 758, 137913 (2020). https:\/\/doi.org\/10.1016\/j.cplett.2020.137913","DOI":"10.1016\/j.cplett.2020.137913"},{"key":"29","doi-asserted-by":"publisher","unstructured":"[29] Fukuhara, D., Itoh, S. G., Okumura, H. Inhibition of amyloid-\u03b2 (16\u201322) aggregation by polyphenols using replica permutation with solute tempering molecular dynamics simulation. Biophys. Physicobiol. 20, e200045 (2023). https:\/\/doi.org\/10.2142\/biophysico.bppb-v20.0045","DOI":"10.2142\/biophysico.bppb-v20.0045"},{"key":"30","doi-asserted-by":"crossref","unstructured":"[30] Nguyen, P. H., Derreumaux, P. Structures of the intrinsically disordered A\u03b2, tau and \u03b1-synuclein proteins in aqueous solution from computer simulations. Biophys. Chem. 264, 106421 (2020). https:\/\/doi.org\/10.1016\/j.bpc.2020.106421","DOI":"10.1016\/j.bpc.2020.106421"},{"key":"31","doi-asserted-by":"publisher","unstructured":"[31] Itoh, S. G., Okumura, H. Promotion and inhibition of amyloid-\u03b2 peptide aggregation: Molecular dynamics studies. Int. J. Mol. Sci. 22, 1859 (2021). https:\/\/doi.org\/10.3390\/ijms22041859","DOI":"10.3390\/ijms22041859"},{"key":"32","doi-asserted-by":"publisher","unstructured":"[32] Nguyen, P. H., Ramamoorthy, A., Sahoo, B. R., Zheng, J., Faller, P., Straub, J. E., et al. Amyloid oligomers: A joint experimental\/computational perspective on alzheimer\u2019s disease, parkinson\u2019s disease, type II diabetes, and amyotrophic lateral sclerosis. Chem. Rev. 121, 2545\u20132647 (2021). https:\/\/doi.org\/10.1021\/acs.chemrev.0c01122","DOI":"10.1021\/acs.chemrev.0c01122"},{"key":"33","doi-asserted-by":"publisher","unstructured":"[33] Okumura, H., Itoh, S. G. Molecular dynamics simulation studies on the aggregation of amyloid-\u03b2 peptides and their disaggregation by ultrasonic wave and infrared laser irradiation. Molecules 27, 2483 (2022). https:\/\/doi.org\/10.3390\/molecules27082483","DOI":"10.3390\/molecules27082483"},{"key":"34","doi-asserted-by":"publisher","unstructured":"[34] Tachi, Y., Itoh, S. G., Okumura, H. Molecular dynamics simulations of amyloid-\u03b2 peptides in heterogeneous environments. Biophys. Physicobiol. 19, e190010 (2022). https:\/\/doi.org\/10.2142\/biophysico.bppb-v19.0010","DOI":"10.2142\/biophysico.bppb-v19.0010"},{"key":"35","doi-asserted-by":"crossref","unstructured":"[35] Strodel, B. Amyloid aggregation simulations: Challenges, advances and perspectives. Curr. Opin. Struct. Biol. 67, 145\u2013152 (2021). https:\/\/doi.org\/10.1016\/j.sbi.2020.10.019","DOI":"10.1016\/j.sbi.2020.10.019"},{"key":"36","doi-asserted-by":"publisher","unstructured":"[36] Okumura, H. Perspective for molecular dynamics simulation studies of amyloid-\u03b2 aggregates. J. Phys. Chem. B 127, 10931\u201310940 (2023). https:\/\/doi.org\/10.1021\/acs.jpcb.3c06051","DOI":"10.1021\/acs.jpcb.3c06051"},{"key":"37","doi-asserted-by":"crossref","unstructured":"[37] Roy, R., Paul, S. Illustrating the effect of small molecules derived from natural resources on amyloid peptides. J. Phys. Chem. B 127, 600\u2013615 (2023). https:\/\/doi.org\/10.1021\/acs.jpcb.2c07607","DOI":"10.1021\/acs.jpcb.2c07607"},{"key":"38","doi-asserted-by":"publisher","unstructured":"[38] Okumura, H., Yonezawa, F. Liquid\u2013vapor coexistence curves of several interatomic model potentials. J. Chem. Phys. 113, 9162\u20139168 (2000). https:\/\/doi.org\/10.1063\/1.1320828","DOI":"10.1063\/1.1320828"},{"key":"39","doi-asserted-by":"publisher","unstructured":"[39] Okumura, H., Okamoto, Y. Liquid\u2013gas phase transitions studied by multibaric\u2013Multithermal Monte Carlo simulations. J. Phys. Soc. Jpn. 73, 3304\u20133311 (2004). https:\/\/doi.org\/10.1143\/jpsj.73.3304","DOI":"10.1143\/JPSJ.73.3304"},{"key":"40","doi-asserted-by":"publisher","unstructured":"[40] Lee, T. D., Yang, C. N. Statistical theory of equations of state and phase transitions. II. Lattice gas and ising model. Phys. Rev. 87, 410\u2013419 (1952). https:\/\/doi.org\/10.1103\/PhysRev.87.410","DOI":"10.1103\/PhysRev.87.410"},{"key":"41","doi-asserted-by":"crossref","unstructured":"[41] de Gennes, P. G. Exponents for the excluded volume problem as derived by the Wilson method. Phys. Lett. A 38, 339\u2013340 (1972). https:\/\/doi.org\/10.1016\/0375-9601(72)90149-1","DOI":"10.1016\/0375-9601(72)90149-1"},{"key":"42","doi-asserted-by":"crossref","unstructured":"[42] Kremer, K., Binder, K. Monte Carlo simulation of lattice models for macromolecules. Computer Physics Reports 7, 259\u2013310 (1988). https:\/\/doi.org\/10.1016\/0167-7977(88)90015-9","DOI":"10.1016\/0167-7977(88)90015-9"},{"key":"43","doi-asserted-by":"publisher","unstructured":"[43] G\u014c, N., Abe, H. Noninteracting local-structure model of folding and unfolding transition in globular proteins. I. Formulation. Biopolymers 20, 991\u20131011 (1981). https:\/\/doi.org\/10.1002\/bip.1981.360200511","DOI":"10.1002\/bip.1981.360200511"},{"key":"44","doi-asserted-by":"publisher","unstructured":"[44] Abe, H., G\u014c, N. Noninteracting local-structure model of folding and unfolding transition in globular proteins. II. Application to two-dimensional lattice proteins. Biopolymers 20, 1013\u20131031 (1981). https:\/\/doi.org\/10.1002\/bip.1981.360200512","DOI":"10.1002\/bip.1981.360200512"},{"key":"45","doi-asserted-by":"publisher","unstructured":"[45] Yagi-Utsumi, M., Kanaoka, Y., Miyajima, S., Itoh, S. G., Yanagisawa, K., Okumura, H., et al. Single-molecule kinetic observation of antibody interactions with growing amyloid \u03b2 fibrils. J. Am. Chem. Soc. 146, 31518\u201331528 (2024). https:\/\/doi.org\/10.1021\/jacs.4c08841","DOI":"10.1021\/jacs.4c08841"},{"key":"46","doi-asserted-by":"crossref","unstructured":"[46] Kundu, D., Prerna, K., Chaurasia, R., Bharty, M. K., Dubey, V. K. Advances in protein misfolding, amyloidosis and its correlation with human diseases. 3 Biotech 10, 193 (2020). https:\/\/doi.org\/10.1007\/s13205-020-2166-x","DOI":"10.1007\/s13205-020-2166-x"},{"key":"47","doi-asserted-by":"crossref","unstructured":"[47] Abelein, A., Abrahams, J. P., Danielsson, J., Gr\u00e4slund, A., Jarvet, J., Luo, J., et al. The hairpin conformation of the amyloid-\u03b2 peptide is an important structural motif along the aggregation pathway. J. Biol. Inorg. Chem. 19, 623\u2013634 (2014). https:\/\/doi.org\/10.1007\/s00775-014-1131-8","DOI":"10.1007\/s00775-014-1131-8"},{"key":"48","doi-asserted-by":"crossref","unstructured":"[48] Maity, S., Hashemi, M., Lyubchenko, Y. L. Nano-assembly of amyloid \u03b2 peptide: Role of the hairpin fold. Sci. Rep. 7, 2344 (2017). https:\/\/doi.org\/10.1038\/s41598-017-02454-0","DOI":"10.1038\/s41598-017-02454-0"},{"key":"49","doi-asserted-by":"crossref","unstructured":"[49] Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., Teller, E. Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087\u20131092 (1953). https:\/\/doi.org\/10.1063\/1.1699114","DOI":"10.1063\/1.1699114"},{"key":"50","doi-asserted-by":"crossref","unstructured":"[50] Yagi-Utsumi, M., Yanaka, S., Burton-Smith, R. N., Song, C., Ganser, C., Yamazaki, C., et al. Microgravity-assisted exploration of the conformational space of amyloid \u03b2 affected by Tottori-type familial mutation D7N. ACS Chem. Neurosci. 16, 2682\u20132690 (2025). https:\/\/doi.org\/10.1021\/acschemneuro.5c00217","DOI":"10.1021\/acschemneuro.5c00217"},{"key":"51","doi-asserted-by":"publisher","unstructured":"[51] Knowles, T. P., Waudby, C. A., Devlin, G. L., Cohen, S. I., Aguzzi, A., Vendruscolo, M., et al. An analytical solution to the kinetics of breakable filament assembly. Science 326, 1533\u20131537 (2009). https:\/\/doi.org\/10.1126\/science.1178250","DOI":"10.1126\/science.1178250"},{"key":"52","doi-asserted-by":"publisher","unstructured":"[52] Knowles, T. P. J., Vendruscolo, M., Dobson, C. M. The amyloid state and its association with protein misfolding diseases. Nat. Rev. Mol. Cell Biol. 15, 384\u2013396 (2014). https:\/\/doi.org\/10.1038\/nrm3810","DOI":"10.1038\/nrm3810"},{"key":"53","doi-asserted-by":"crossref","unstructured":"[53] Hukushima, K., Nemoto, K. Exchange Monte Carlo method and application to spin glass simulations. J. Phys. Soc. Jpn. 65, 1604\u20131608 (1996). https:\/\/doi.org\/10.1143\/Jpsj.65.1604","DOI":"10.1143\/JPSJ.65.1604"},{"key":"54","doi-asserted-by":"publisher","unstructured":"[54] Sugita, Y., Okamoto, Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314, 141\u2013151 (1999). https:\/\/doi.org\/10.1016\/S0009-2614(99)01123-9","DOI":"10.1016\/S0009-2614(99)01123-9"},{"key":"55","doi-asserted-by":"publisher","unstructured":"[55] Itoh, S. G., Okumura, H. Replica-permutation method with the suwa\u2013todo algorithm beyond the replica-exchange method. J. Chem. Theory Comput. 9, 570\u2013581 (2013). https:\/\/doi.org\/10.1021\/ct3007919","DOI":"10.1021\/ct3007919"},{"key":"56","doi-asserted-by":"crossref","unstructured":"[56] Itoh, S. G., Okumura, H. Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-\u03b2 (29\u201342) peptides. J. Comput. Chem. 34, 2493\u20132497 (2013). https:\/\/doi.org\/10.1002\/jcc.23402","DOI":"10.1002\/jcc.23402"},{"key":"57","doi-asserted-by":"publisher","unstructured":"[57] Yamauchi, M., Okumura, H. Development of isothermal-isobaric replica-permutation method for molecular dynamics and Monte Carlo simulations and its application to reveal temperature and pressure dependence of folded, misfolded, and unfolded states of chignolin. J. Chem. Phys. 147, 184107 (2017). https:\/\/doi.org\/10.1063\/1.4996431","DOI":"10.1063\/1.4996431"},{"key":"58","doi-asserted-by":"crossref","unstructured":"[58] Okumura, H., Itoh, S. G. Transformation of a design peptide between the \u03b1-helix and \u03b2-hairpin structures using a helix-strand replica-exchange molecular dynamics simulation. Phys. Chem. Chem. Phys. 15, 13852\u201313861 (2013). https:\/\/doi.org\/10.1039\/c3cp44443k","DOI":"10.1039\/c3cp44443k"},{"key":"59","doi-asserted-by":"crossref","unstructured":"[59] Morinaga, A., Hasegawa, K., Nomura, R., Ookoshi, T., Ozawa, D., Goto, Y., et al. Critical role of interfaces and agitation on the nucleation of A\u03b2 amyloid fibrils at low concentrations of A\u03b2 monomers. Biochim. Biophys. Acta 1804,986\u2013995 (2010). https:\/\/doi.org\/10.1016\/j.bbapap.2010.01.012","DOI":"10.1016\/j.bbapap.2010.01.012"},{"key":"60","doi-asserted-by":"crossref","unstructured":"[60] Fantini, J., Yahi, N. Molecular insights into amyloid regulation by membrane cholesterol and sphingolipids: Common mechanisms in neurodegenerative diseases. Expert Rev. Mol. Med. 12, e27 (2010). https:\/\/doi.org\/10.1017\/S1462399410001602","DOI":"10.1017\/S1462399410001602"},{"key":"61","doi-asserted-by":"publisher","unstructured":"[61] Saito, T., Ishiyama, T., Sakono, M., Itoh, S. G., Okumura, H. Oligomerization mechanism of amyloid-\u03b2 peptides at hydrophobic interfaces revealed by molecular dynamics simulations. J. Phys. Chem. B 129, 6794\u20136804 (2025). https:\/\/doi.org\/10.1021\/acs.jpcb.5c01837","DOI":"10.1021\/acs.jpcb.5c01837"},{"key":"62","doi-asserted-by":"publisher","unstructured":"[62] Otawa, M., Itoh, S. G., Okumura, H. Nonequilibrium molecular dynamics method to generate poiseuille-like flow between lipid bilayers. J. Chem. Theory Comput. 20, 10199\u201310208 (2024). https:\/\/doi.org\/10.1021\/acs.jctc.4c00750","DOI":"10.1021\/acs.jctc.4c00750"}],"container-title":["Biophysics and Physicobiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.jstage.jst.go.jp\/article\/biophysico\/23\/2\/23_e230015\/_pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,13]],"date-time":"2026-06-13T03:36:49Z","timestamp":1781321809000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.jstage.jst.go.jp\/article\/biophysico\/23\/2\/23_e230015\/_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":62,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026]]}},"URL":"https:\/\/doi.org\/10.2142\/biophysico.bppb-v23.0015","relation":{},"ISSN":["2189-4779"],"issn-type":[{"value":"2189-4779","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026]]},"article-number":"e230015"}}