Refine
Year of publication
Language
- English (1103) (remove)
Keywords
- optimal control (27)
- stability (14)
- integer programming (11)
- Stochastic programming (9)
- finite elements (9)
- mixed integer programming (9)
- Hamiltonian matrix (8)
- finite element method (8)
- model reduction (8)
- state constraints (8)
The key to molecular conformation dynamics is the direct identification of metastable conformations, which are almost invariant sets of molecular dynamical systems. Once some reversible Markov operator has been discretized, a generalized symmetric stochastic matrix arises. This matrix can be treated by Perron cluster analysis, a rather recent method involving a Perron cluster eigenproblem. The paper presents an improved Perron cluster analysis algorithm, which is more robust than earlier suggestions. Numerical examples are included.