Explore Slow Dynamics of Proteins Based on Trajectory Map
Prof. Xin Zhou
School of Physical Sciences, University of Chinese Academy of Sciences

Not only the static structure but (slow) dynamics of biological macromolecules are more and more focused on in recent experiments and simulations to understand their functions. As an important tool, current all-atomic molecular dynamics (MD) simulations start to approach to experimental timescales in small proteins, we may further improve the accessed spatial-temporal scales of MD and analyze the generate big data to understand the properties, behavior and functions of   proteins with atomic details. In the talk, we present a scheme to extend MD simulation timescale, and to analyze slow dynamics from simulation data. We first develop an adaptive non-equilibrium simulation method to high efficiently explore conformational space of proteins, which involving many possible important regions separated by high free energy barriers. Ensemble simulations (multiple independent simulations under the same dynamics) started from conformations generated in the non-equilibrium simulation are then applied to detect locally these regions. The ensemble of trajectories is mapped to a high-dimensional space to automatically construct slow variables for only focusing on the conformational change in large time scale. Thus the trajectory map (TM) method splits the MD trajectories into some time-successive segments, each of them covers a conformational region, corresponds to a metastable state in slow dynamics. The slow dynamics in the MD trajectories are described as a kinetic transition network among states.  The network representation in high-dimensional conformational space honestly describes the thermodynamic, kinetic and dynamical properties of the systems and their intrinsic complexity without requiring a priori assumptions about reaction coordinates. 


About the Speaker

周昕, 中国科学院大学物理学院教授, 中国科学院百人计划入选者。2001年中国科学院理论物理研究所博士。2001-2003年日本东京工业大学JSPS Fellow; 2003 - 2005年德国马普高分子研究所Humboldt Fellow; 20052008美国Los Alamos 国家实验室研究助理; 20082011年韩国亚太理论物理中心(APCTP)独立研究组负责人, 韩国蒲项工业大学(POSTECH)物理系兼职教授。2011年至今为中国科学院大学教授。主要从事分子动力学计算机模拟软物质与生物高分子等的平衡态与动力学, 以及纳米材料、低维系统的计算模拟, 和非平衡统计物理理论等方面的研究。在Phys. Rev., J Phys. Chem, J Chem. Phys., Europhys. Lett. 等杂志上发表30多篇研究论文。


2016-06-24 10:00 AM
Room: A203 Meeting Room
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