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  <doc>
    <id>4257</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
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    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2013-09-27</completedDate>
    <publishedDate>2013-09-27</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Efficient Conformational Analysis by Partition-of-Unity Coupling</title>
    <abstract language="eng">Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely n-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent.</abstract>
    <parentTitle language="eng">Math Chem</parentTitle>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-42570</identifier>
    <author>Alexander Bujotzek</author>
    <submitter>Konstantin Fackeldey</submitter>
    <author>Ole Schütt</author>
    <author>Adam Nielsen</author>
    <author>Konstantin Fackeldey</author>
    <author>Marcus Weber</author>
    <series>
      <title>ZIB-Report</title>
      <number>13-58</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Markov State Models</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Meshfree</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Molecular Simulation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Partition of Unity</value>
    </subject>
    <collection role="ccs" number="G.4">MATHEMATICAL SOFTWARE</collection>
    <collection role="ccs" number="">Markov processes (NEW)</collection>
    <collection role="pacs" number="87.10.-e">General theory and mathematical aspects</collection>
    <collection role="msc" number="60Jxx">Markov processes</collection>
    <collection role="msc" number="92-08">Computational methods</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
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    <collection role="projects" number="MIP_FORMATION">MIP_FORMATION</collection>
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    <collection role="projects" number="Salsa-Klimm">Salsa-Klimm</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/4257/MolPyPUM.pdf</file>
  </doc>
  <doc>
    <id>4658</id>
    <completedYear/>
    <publishedYear>2014</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst>781</pageFirst>
    <pageLast>804</pageLast>
    <pageNumber/>
    <edition/>
    <issue>3</issue>
    <volume>52</volume>
    <type>article</type>
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    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling</title>
    <parentTitle language="eng">Journal of Mathematical Chemistry</parentTitle>
    <identifier type="doi">10.1007/s10910-013-0265-1</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-42570</enrichment>
    <author>Alexander Bujotzek</author>
    <submitter>Adam Nielsen</submitter>
    <author>Ole Schütt</author>
    <author>Adam Nielsen</author>
    <author>Konstantin Fackeldey</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
    <collection role="projects" number="MIP_FORMATION">MIP_FORMATION</collection>
    <collection role="projects" number="NAMPAR">NAMPAR</collection>
    <collection role="projects" number="Salsa-Klimm">Salsa-Klimm</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
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