| 1. |
Ryo Akiyama, Masahiko Annaka, Daisuke Kohda, Hiroyuki Kubota, Yusuke Maeda, Nobuaki Matsumori, Daisuke Mizuno, Norio Yoshida, Biophysics at Kyushu University, Biophysical Reviews, 10.1007/s12551-020-00643-2, 2020.01. |
| 2. |
Hisashi Okumura, Masahiro Higashi, Yuichiro Yoshida, Hirofumi Sato, Ryo Akiyama, Theoretical approaches for dynamical ordering of biomolecular systems, Elsevier, 10.1016/j.bbagen.2017.10.001, BBA (Biochimica et Biophysica Acta) - General Subjects 1862 (2018) 212–228 (査読あり), 2018.02, Background Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies. Scope of review We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified. Major conclusions The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function. General significance These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. This article is part of a Special Issue entitled “Biophysical Exploration of Dynamical Ordering of Biomolecular Systems” edited by Dr. Koichi Kato.. |
| 3. |
Ken Tokunaga, Takuya Furumi, and Ryo Akiyama, Conversion process of chemical reaction into mechanical work through solvation change, AIP Conf. Proc. (NONEQUILIBRIUM STATISTICAL PHYSICS TODAY: Proceedings of the 11th Granada Seminar on Computational and Statistical Physics), Vol.1332, 299 (2011), 2011.04. |
| 4. |
Ryo Akiyama, Ryo Sakata, and Yuji Ide, Reentrant behavior of effective attraction between like-charged macroions immersed in electrolyte solution, AIP Conf. Proc. (NONEQUILIBRIUM STATISTICAL PHYSICS TODAY: Proceedings of the 11th Granada Seminar on Computational and Statistical Physics), Vol.1332, 265 (2011), 2011.04. |
| 5. |
The Asakura-Oosawa Model and the Difference of Thermodynamic Property between under Isobaric Condition and under Isochoric Condition. |
| 6. |
The Young Person's Guide to the Asakura-Oosawa Theory. |
| 7. |
Calorimetry and Macromolecular Interaction Arising from Translational Motion of Solvent Molecules. |
| 8. |
Integral Equation Theory, Depletion Interaction, Potential of Mean force. |
| 9. |
Vibrational Echoes and Simulations of Proteins.. |
