See also Google Scholar
Original Research (*: Corresponding author)
Minimal-background chemo-optogenetic dimerization for precise control of cellular signaling
T. Kowada, T. Sato, K. Kasahara, S. Hamaguchi, K. Baba, T. Mashita, M. W. Saifudin, H. Yamamoto, N. Matubayasi, and S. Mizukami*, ChemRxiv:10001881/v1 (2026). [ChemRxiv]
IEPDYN: Integral-equation formalism of population Dynamics
K. Kasahara*, R. Okabe, C. A. Chang, T. Mori, and N. Matubayasi, J. Chem. Phys., 164, 124112-124128 (2026). [Link][arXiv]
Dual effect of cholesterol on interfacial water dynamics in lipid membranes: Interplay between membrane packing and hydration
K. Shikata, K. kasahara, N. M. Watanabe, H. Umakoshi, K. Kim*, and N. Matubayasi, J. Chem. Phys., 163, 245101-245111 (2025). [Link][arXiv]
Ion Transport Analysis of Anion-Exchange Membranes in Various Hydration States: Combining Experiments with Molecular Dynamics Simulation
Y. Nara, K. Kasahara*, K. Yagi, K. Kim, N. Matubayasi, H. Kawakami, and M. Tanaka, ACS Appl. Polym. Mater., 7, 13971-13981 (2025). [Link]
Characterizing the embedded states of a fluorescent probe within a lipid bilayer using molecular dynamics simulations
R. Okabe, N. Ito, Y. Matsubara, N. M. Watanabe, H. Umakoshi, K. Kasahara*, and N. Matubayasi, J. Chem. Phys., 163, 034708-034719 (2025). [Link][arXiv]
Solvent-Environment Dependence of the Excess Chemical Potential and Its Computation Scheme Formulated through Error Minimization
S. Hansen, K. Okita, K. Kasahara, and N. Matubayasi*, J. Chem. Theory Comput., 21, 1064-1077 (2025). [Link]
Flexible framework of computing binding free energy using the energy representation theory of solution
K. Okita, Y. Maruyama, K. Kasahara*, and N. Matubayasi, J. Chem. Phys., 162, 034103-034114 (2025). [Link][arXiv]
A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation
Y. Matsubara, R. Okabe, R. Masayama, N. M. Watanabe, H. Umakoshi, K. Kasahara*, and N. Matuabyasi, J. Chem. Phys., 161, 024108-024122 (2024). [Link][arXiv]
Influence of cholesterol on hydrogen-bond dynamics of water molecules in lipid-bilayer systems at varying temperatures
K. Shikata, K. kasahara, N. M. Watanabe, H. Umakoshi, K. Kim*, and N. Matubayasi, J. Chem. Phys., 161, 015102-015111 (2024). [Link][arXiv]
Solvation dynamics on the diffusion timescale elucidated using energy-represented dynamics theory
K. Okita, N. Ito, N. M. Watanabe, H. Umakoshi, K. Kasahara*, and N. Matubayasi, Phys. Chem. Chem. Phys., 26, 12852-12861 (2024). [Link (Open access)]
Free-energy decomposition of salt effects on the solubilities of small molecules and the role of excluded-volume effects
S. H. Hansen*, D. Lin, K. Kasahara, and N. Matubayasi, Chem. Sci., 15, 477-489 (2024). [Link (Open access)]
Elucidating protein-ligand binding kinetics based on returning probability theory
K. Kasahara*, R. Masayama, K. Okita, and N. Matubayasi, J. Chem. Phys., 159, 134103-134117 (2023). [Link][OUKA repository]
Arylazopyrazole-Based Photoswitchable Inhibitors Selective for Escherichia coli Dihydrofolate Reductase
H. S. Sarkar, T. Mashita, T. Kowada, S. Hamaguchi, T. Sato, K. Kasahara, N. Matubayasi, T. Matsui, S. Mizukami*, ACS Chem. Biol., 18, 340-346 (2023). [Link]
Diffusion theory of molecular liquids in the energy representation and application to solvation dynamics
K. Okita, K. Kasahara*, and N. Matubayasi, J. Chem. Phys., 157, 244505-244518 (2022). [Link][OUKA repository]
Selected as Editor's pick
Crystal Growth of Urea and Its Modulation by Additives as Analyzed by All-Atom MD Simulation and Solution Theory
S. Tanaka, N. Yamamoto, K. Kasahara, Y. Ishii, and N. Matubayasi*, J. Phys. Chem. B, 126, 5274-5290 (2022). [Link]
Modified protein-water interactions in CHARMM36m for thermodynamics and kinetics of proteins in dilute and crowded solutions
D. Matsubara, K. Kasahara, H. Dokainish, H. Oshima, and Y. Sugita*, Molecules, 27, 5726-5743 (2022). [Link (Open access)]
Constructing a Memory Kernel of the Returning Probability to Efficiently Describe Molecular Binding Processes
K. Kasahara*, R. Masayama, Y. Matsubara, and N. Matubayasi, Chem. Lett., 51, 823-827 (2022). [Link]
Solvation in nitration of benzene and the valence electronic structure of the Wheland intermediate
K. Nakatani, S. Teshigawara, Y. Tanahashi, K. Kasahara, M. Higashi, and H. Sato*, Phys. Chem. Chem. Phys., 24, 16453-16461 (2022). [Link]
Atomistic description of molecular binding processes based on returning probability theory
K. Kasahara*, R. Masayama, K. Okita, and N. Matubayasi, J. Chem. Phys., 155, 204503-204517 (2021). [Link][OUKA repository]
Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems
J. Jung, K. Kasahara, C. Kobayashi, H. Oshima, T. Mori, and Y. Sugita*, J. Chem. Theory and Comput., 17, 5312-5321 (2021). [Link (Open access)]
New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems
J. Jung, C. Kobayashi, K. Kasahara, C. Tan, A. Kuroda, K. Minami, S. Ishiduki and T. Nishiki, H. Inoue, Y. Ishikawa, M. Feig, and Y. Sugita*, J. Comput. Chem., 42, 231-241 (2021). [Link (Open access)]
Reduced efficacy of a Src kinase inhibitor in crowded protein solution
K. Kasahara, S. Re, G. Nawrocki, H. Oshima, C. Mishima-Tsumagari, Y. Miyata-Yabuki, M. Kukimoto-Niino, I. Yu, M. Shirouzu, M. Feig, and Y. Sugita*, Nat. Commun., 12, 4099 (8 page) (2021). [Link (Open access)]
Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape
S. Re, H. Oshima, K. Kasahara, M. Kamiya, and Y. Sugita*, Proc. Natl. Acad. Sci., 116, 18404-18409 (2019). [Link (Open access)]
Time-dependent pair distribution functions based on Smoluchowski equation and application to an electrolyte solution
K. Kasahara* and H. Sato, J. Comput. Chem., 39, 1491-1497 (2018). [Link]
Solvation structure of LiClO4/ethylene carbonate solution near a graphite electrode in lithium-ion batteries: 3D-RISM study
K. Kasahara and H. Sato*, Chem. Lett., 47, 311-314 (2018). [Link]
Theoretical Study of the Solvation Effect on the Reductive Reaction of Vinylene Carbonate in the Electrolyte Solution of Lithium Ion Batteries
K. Kasahara, H. Nakano, and H. Sato*, J. Phys. Chem. B, 121, 5293-5299 (2017). [Link]
A theory of diffusion controlled reactions in polyatomic molecule system
K. Kasahara, and H. Sato*, J. Chem. Phys., 145, 194502-194507 (2016). [Link]
Solvent structure of ionic liquid with carbon dioxide
K. Kikui, S. Hayaki, K. Kido, D. Yokogawa, K. Kasahara, Y. Matsumura, H. Sato*, and S. Sakaki, J. Mol. Liq., 217, 12-16 (2016). [Link]
A molecular level study of selective cation capture by a host–guest mechanism for 25,26,27,28-tetramethoxycalix[4]arene in MClO4 solution (M = Na, K)
K. Kido, K. Kasahara, H. Sato*, and S. Sakaki, Mol. Simul., 41, 881-891 (2015). [Link]
A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein-Zernike self-consistent field approach
K. Kido*, K. Kasahara, D. Yokogawa, and H. Sato, J. Chem. Phys., 143, 014103-014111 (2015).
Development of three-dimensional site-site Smoluchowski-Vlasov equation and application to electrolyte solutions
K. Kasahara and H. Sato*, J. Chem. Phys., 140, 244110-244116 (2014). [Link]
Review (*: Corresponding author)
Dynamics theory for molecular liquids based on an interaction site model
K. Kasahara* and H. Sato*, Phys. Chem. Chem. Phys. (Perspective), 19, 27917-27929 (2017). [Link]
日本語の解説記事 (Japanese only)
膜透過現象を記述する分子論
笠原健人*, 松林伸幸, 溶液化学研究会誌, 6, 21-30 (2024). [Link]
凝縮系のダイナミクスを解析するためのエネルギー表示理論の開発
笠原健人*, 沖田和也, 松林伸幸, 理論化学会誌「フロンティア」，5, 90-98 (2023).
分子会合過程に対する理論的アプローチ
笠原健人*, 化学と工業, 76-4, 244-245 (2023).
溶液統計力学と分子動力学に基づく分子会合過程の理論的解析
笠原健人*, 溶液化学研究会誌, 3, 3-11 (2023). [Link]
分子動力学シミュレーション法の基礎
笠原健人*, 溶液化学研究会誌, 1, 22-30 (2022). [Link]
博士論文紹介「分子性液体における拡散と溶媒和の積分方程式理論」
笠原健人*, アンサンブル, 22, 81-86 (2020). [Link (Open access)]