文档介绍：该【聚类分析与生物分子动力学 】是由【zhilebei】上传分享，文档一共【45】页，该文档可以免费在线阅读，需要了解更多关于【聚类分析与生物分子动力学 】的内容，可以使用淘豆网的站内搜索功能，选择自己适合的文档，以下文字是截取该文章内的部分文字，如需要获得完整电子版，请下载此文档到您的设备，方便您编辑和打印。摘 要
分子动力学仿真数据特点
聚类分析
合作伙伴
Stanford University
Chemistry/Biophysics
Vijay Pande
Xuhui Huang
Greg Bowman
Sergio Bacallado
Computer Science
Leo Guibas
Jian sun
Mathematics
Gunnar Carlsson
Yuan Yao
Michael Lesnick
Gurjeet Singh
Guibas-Carlsson-Pande Collaboration
Chemistry/Biophysics
Vijay Pande
Xuhui Huang
Greg Bowman
Sergio Bacallado
Computer Science
Leo Guibas
Jian sun
Mathematics
Gunnar Carlsson
Yuan Yao
Michael Lesnick
Gurjeet Singh
Massive Datasets
Topological
and Geometric Algorithms
Design and Implementation
Biology
生物分子动力系统仿真
Shirts and Pande, Science, 290, 1903 , 2000
生物问题: Conformational Changes
Illustrations by David Goodsell
Protein Folding
Understanding Conformational Changes at Atomic Resolution is Difficult Experimentally
X-ray
structures are static snapshots
Computer simulations may complement experiments!
NMR
can provide dynamics, but difficult for large systems
Provide information of an order parameter
Single Molecule FRET
Atomistic Simulations
Experiments
Solution:
Use short simulations to predict long timescale dynamics
Key Challenge: Timescale Gap
Conformational Dynamics: Nearly Uncoupled Markov Chains
Figure Courtesy John Chodera
Each Markov chain corresponds to a meta-stable state
Zwanzig, J. Stat. Phys. 1983
Chodera. et. al. J. Chem. Phys. 2007
Noé. . J. Chem. Phys. 2007
Huang . 2009, Hummer, Shuttle....
Markov State Models (MSMs)
Define transition probabilities between states
The configuration space is decomposed into non-overlapping states
The time is coarse-grained in
We can extract long time dynamics from MSMs built from short simulations
How to construct MSMs?
Dataset: Multiple trajectories with a lot of conformations.
time
Conformation
Trajectory
Trajectory 1
Trajectory 2
Trajectory 3