Nüske, F. and Keller, B. and PérezHernández, G. and Mey, A.S.J.S. and Noé, F. (2014) Variational Approach to Molecular Kinetics. J. Chem. Theory Comput., 10 . pp. 17391752.

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Abstract
The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator) contain the essential information about the molecular thermodynamics and kinetics. This includes the stationary distribution, the metastable states, and statetostate transition rates. Here, we present a variational approach for computing these dominant eigenvalues and eigenvectors. This approach is analogous the variational approach used for computing stationary states in quantum mechanics. A corresponding method of linear variation is formulated. It is shown that the matrices needed for the linear variation method are correlation matrices that can be estimated from simple MD simulations for a given basis set. The method proposed here is thus to first define a basis set able to capture the relevant conformational transitions, then compute the respective correlation matrices, and then to compute their dominant eigenvalues and eigenvectors, thus obtaining the key ingredients of the slow kinetics.
Item Type:  Article 

Subjects:  Physical Sciences Mathematical and Computer Sciences 
Divisions:  Department of Mathematics and Computer Science > Institute of Mathematics > Comp. Molecular Biology 
ID Code:  1388 
Deposited By:  BioComp Admin 
Deposited On:  01 Mar 2014 17:31 
Last Modified:  03 Mar 2017 14:41 
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