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  <doc>
    <id>9158</id>
    <completedYear/>
    <publishedYear>2023</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>23</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2023-10-04</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Efficient Estimation of Transition Rates as Functions of pH</title>
    <abstract language="eng">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.</abstract>
    <parentTitle language="eng">Proceedings in Applied Mathematics &amp; Mechanics</parentTitle>
    <identifier type="arxiv">2307.04439</identifier>
    <identifier type="doi">10.1002/pamm.202300264</identifier>
    <enrichment key="opus.source">publish</enrichment>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="SubmissionStatus">epub ahead of print</enrichment>
    <author>Luca Donati</author>
    <submitter>Luca Donati</submitter>
    <author>Marcus Weber</author>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="institutes" number="MSoCP">Modeling and Simulation of Complex Processes</collection>
    <collection role="projects" number="MathPlusAA1-15">MathPlusAA1-15</collection>
    <collection role="persons" number="donati">Donati, Luca</collection>
  </doc>
</export-example>
