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 |
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Document Type: | Article |
Parent Title (English): | Proceedings in Applied Mathematics & Mechanics |
Volume: | 23 |
Year of first publication: | 2023 |
ArXiv Id: | http://arxiv.org/abs/2307.04439 |
DOI: | https://doi.org/10.1002/pamm.202300264 |