研究・研究者
研究会・セミナー
演 題 | 「Investigation Conformational Changes of Biological Macromolecules Using Kinetic Network Models」 |
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日 時 | 2016年12月15日(木) 16:00 より 17:00 まで |
講演者 | Prof. Xuhui Huang (香港科技大学 化学科 准教授) |
場 所 | 研究棟201号室 |
概 要 | Simulating biologically relevant timescales at atomic resolution is a challenging task since typical atomistic simulations are at least two orders of magnitude shorter. Markov State Models (MSMs), a kinetic network model, built from molecular dynamics (MD) simulations provide one means of overcoming this gap without sacrificing atomic resolution by extracting long time dynamics from short MD simulations through the coarse graining on the phase space and time. In this talk, I will demonstrate the power of kinetic network models by applying it to simulate the complex conformational changes, that occurs at tens to hundreds of microsecond timescales for a large RNA Polymerase II complex containing nearly half million atoms. Furthermore, I will introduce a new efficient dynamic clustering algorithm for the automatic construction of MSMs for multi-body systems. We have successfully applied this new algorithm to model the protein-ligand recognition and self-assembly of co-polymers. Finally, I will introduce a new algorithm using the projection operator approach to identify optimal kinetic lumping and recover slowest conformational dynamics of complex systems. |
お問合せ先 | 石崎章仁 |