Estimation of the infinitesimal generator by square-root approximation

  title={Estimation of the infinitesimal generator by square-root approximation},
  author={Luca Donati and Martin Heida and Bettina G. Keller and Marcus Weber},
  journal={Journal of Physics: Condensed Matter},
In recent years, for the analysis of molecular processes, the estimation of time-scales and transition rates has become fundamental. Estimating the transition rates between molecular conformations is—from a mathematical point of view—an invariant subspace projection problem. We present a method to project the infinitesimal generator acting on function space to a low-dimensional rate matrix. This projection can be performed in two steps. First, we discretize the conformational space in a Voronoi… 

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