Donati, L. and Heida, M. and Weber, M. and Keller, B. (2018) Estimation of the infinitesimal generator by squareroot approximation. Journal of Physics: Condensed Matter, 30 (42). p. 425201. ISSN 09538984, ESSN: 1361648X

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Official URL: https://doi:10.1088/1361648X/aadfc8
Abstract
For the analysis of molecular processes, the estimation of timescales, i.e., transition rates, is very important. Estimating the transition rates between molecular conformations is  from a mathematical point of view  an invariant subspace projection problem. A certain infinitesimal generator acting on function space is projected to a lowdimensional rate matrix. This projection can be performed in two steps. First, the infinitesimal generator is discretized, then the invariant subspace is approximated and used for the subspace projection. In our approach, the discretization will be based on a Voronoi tessellation of the conformational space. We will show that the discretized infinitesimal generator can simply be approximated by the geometric average of the Boltzmann weights of the Voronoi cells. Thus, there is a direct correlation between the potential energy surface of molecular structures and the transition rates of conformational changes. We present results for a 2ddiffusion process and Alanine dipeptide.
Item Type:  Article 

Additional Information:  SFB 1114 Preprint 08/2017 im WIAS (2416) 
Subjects:  Mathematical and Computer Sciences > Mathematics > Applied Mathematics 
Divisions:  Department of Mathematics and Computer Science > Institute of Mathematics 
ID Code:  2167 
Deposited By:  Silvia Hoemke 
Deposited On:  19 Dec 2017 13:30 
Last Modified:  22 Feb 2022 17:29 
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