Bulletin of the American Physical Society
APS March Meeting 2021
Volume 66, Number 1
Monday–Friday, March 15–19, 2021; Virtual; Time Zone: Central Daylight Time, USA
Session P25: Predicting Rare Event Kinetics in Complex Systems with Theory, Simulations and Machine Learning II
3:00 PM–5:48 PM,
Wednesday, March 17, 2021
Sponsoring
Unit:
DCP
Chair: Matteo Salvalaglio, University College London; Andrew Ferguson, University of Chicago
Abstract: P25.00006 : Square Root Approximation of the Infinitesimal Generator for Molecular Systems*
4:24 PM–4:36 PM
Live
Presenter:
Luca Donati
(Freie Univ Berlin)
Authors:
Luca Donati
(Freie Univ Berlin)
Marcus Weber
(Zuse Institute Berlin)
Bettina Keller
(Freie Univ Berlin)
Square Root Approximation (SqRA) is a method to discretize the infinitesimal generator into a transition rate matrix.
Assuming a Voronoi tessellation of the state space, the rate between two adjacent cells is approximated as the product of two terms: the geometric average of the Boltzmann weights of the cells, and the flux of the configurations through the intersecting surface.
The first term is estimated from the potential energy function, while the second depends on the diffusion constant and the grid used for the discretization.
SqRA does not require to integrate the associated stochastic differential equation and it can be useful to study molecular dynamics reducing significantly the computational cost.
We present the underlaying theory of SqRA and the results that demonstrate the computational efficiency and the accuracy of the method.
*This research has been funded by the Deutsche Forschungsgemeinschaft (DFG) and through grant CRC 1114 "Scaling Cascades in Complex Systems", project B05 "Origin of the scaling cascades in protein dynamics"
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