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  <doc>
    <id>6940</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>214107</issue>
    <volume>148</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
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    <title language="eng">MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations</title>
    <abstract language="eng">Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long-timescale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large lengthscales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time- and lengthscales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step towards MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B &lt;--&gt; C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported.</abstract>
    <parentTitle language="eng">Journal of Chemical Physics</parentTitle>
    <identifier type="doi">10.1063/1.5020294</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Manuel Dibak</author>
    <submitter>Paulina Bressel</submitter>
    <author>Mauricio J. del Razo</author>
    <author>David De Sancho</author>
    <author>Christof Schütte</author>
    <author>Frank Noé</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="projects" number="MODAL-MedLab">MODAL-MedLab</collection>
    <collection role="projects" number="MOL-ANALYSIS">MOL-ANALYSIS</collection>
    <collection role="projects" number="MODAL-Gesamt">MODAL-Gesamt</collection>
    <collection role="persons" number="delrazo">del Razo Sarmina, Mauricio</collection>
  </doc>
</export-example>
