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Efficient Estimation of Transition Rates as Functions of pH

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  • Extracting the kinetic properties of a system whose dynamics depend on the pH of the environment with which it exchanges energy and atoms requires sampling the Grand Canonical Ensemble. As an alternative, we present a novel strategy that requires simulating only the most recurrent Canonical Ensembles that compose the Grand Canonical Ensemble. The simulations are used to estimate the Gran Canonical distribution for a specific pH value by reweighting and to construct the transition rate matrix by discretizing the Fokker-Planck equation by Square Root Approximation and robust Perron Cluster Cluster Analysis. As an application, we have studied the tripeptide Ala-Asp-Ala.
Author:Luca DonatiORCiD, Marcus WeberORCiD
Document Type:Article
Parent Title (English):Proceedings in Applied Mathematics & Mechanics
Year of first publication:2023
ArXiv Id:http://arxiv.org/abs/2307.04439
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