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arXiv · 2307.04439

Efficient Estimation of Transition Rates as Functions of pH

Luca Donati·Marcus Weber
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Abstract

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.

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Luca Donati, Marcus Weber. 2023-07-10. Efficient Estimation of Transition Rates as Functions of pH. https://arxiv.org/abs/2307.04439

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