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  <doc>
    <id>1030</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation>Zuse-Institut Berlin</creatingCorporation>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2007-11-07</completedDate>
    <publishedDate>2007-11-07</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Classical hybrid Monte-Carlo simulations of the interconversion of hexabromocyclododecane</title>
    <abstract language="eng">In this paper, we investigate the interconversion processes of the major flame retardant -- 1,2,5,6,9,10-hexabromocyclododecane (HBCD) -- by the means of statistical thermodynamics based on classical force-fields. Three ideas will be presented. First, the application of classical hybrid Monte-Carlo simulations for quantum mechanical processes will be justified. Second, the problem of insufficient convergence properties of hybrid Monte-Carlo methods for the generation of low temperature canonical ensembles will be solved by an interpolation approach. Furthermore, it will be shown how free energy differences can be used for a rate matrix computation. The results of our numerical simulations will be compared to experimental results.</abstract>
    <identifier type="serial">07-31</identifier>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="opus3-id">1059</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-10308</identifier>
    <enrichment key="SourceTitle">A substantially revised version appeared under the title "Classical hybrid Monte-Carlo simulation of the interconversion of hexabromocyclododecane stereoisomers" in: Journal of Molecular Simulation, 34(7):727 - 736, June 2008</enrichment>
    <author>Marcus Weber</author>
    <submitter>unknown unknown</submitter>
    <author>Roland Becker</author>
    <author>Robert Köppen</author>
    <author>Vedat Durmaz</author>
    <series>
      <title>ZIB-Report</title>
      <number>07-31</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Markov process</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>molecular dynamics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>rate matrix</value>
    </subject>
    <collection role="ddc" number="510">Mathematik</collection>
    <collection role="msc" number="80A17">Thermodynamics of continua [See also 74A15]</collection>
    <collection role="msc" number="82-08">Computational methods</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="durmaz">Durmaz, Vedat</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/1030/ZR_07_31.pdf</file>
  </doc>
  <doc>
    <id>2448</id>
    <completedYear>2008</completedYear>
    <publishedYear>2008</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>727</pageFirst>
    <pageLast>736</pageLast>
    <pageNumber/>
    <edition/>
    <issue>7</issue>
    <volume>34</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Classical hybrid Monte-Carlo simulations of the interconversion of hexabromocyclododecane</title>
    <parentTitle language="eng">Journal of Molecular Simulation</parentTitle>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-10308</enrichment>
    <author>Marcus Weber</author>
    <author>Roland Becker</author>
    <author>Robert Köppen</author>
    <author>Vedat Durmaz</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="durmaz">Durmaz, Vedat</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
  <doc>
    <id>2645</id>
    <completedYear>2012</completedYear>
    <publishedYear>2012</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>2399</pageFirst>
    <pageLast>2408</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>18</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">How to Simulate Affinities for Host-Guest Systems Lacking Binding Mode Information: application to the liquid chromatographic separation of hexabromocyclododecane stereoisomers</title>
    <parentTitle language="eng">Journal of Molecular Modeling</parentTitle>
    <identifier type="doi">10.1007/s00894-011-1239-5</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Vedat Durmaz</author>
    <author>Marcus Weber</author>
    <author>Roland Becker</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="durmaz">Durmaz, Vedat</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BAM-Becker">BAM-Becker</collection>
    <collection role="projects" number="BAM-glycosidases">BAM-glycosidases</collection>
    <collection role="projects" number="BB3R">BB3R</collection>
    <collection role="projects" number="TransRisk">TransRisk</collection>
  </doc>
  <doc>
    <id>2628</id>
    <completedYear>2009</completedYear>
    <publishedYear>2009</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>910</pageFirst>
    <pageLast>913</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>70</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">HBCD stereoisimers: Thermal interconversion and enantiospecific trace analysis in biota</title>
    <parentTitle language="eng">Organohalogen Compounds</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Robert Köppen</author>
    <author>Roland Becker</author>
    <author>Marcus Weber</author>
    <author>Vedat Durmaz</author>
    <author>Irene Nehls</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="durmaz">Durmaz, Vedat</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
  <doc>
    <id>2631</id>
    <completedYear>2009</completedYear>
    <publishedYear>2009</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>247</pageFirst>
    <pageLast>252</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>71</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Predictive Identification of Pentabromocyclododecane (PBCD) Isomers with high Binding Affinity to hTTR</title>
    <parentTitle language="eng">Organohalogen Compounds</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Marcus Weber</author>
    <author>Vedat Durmaz</author>
    <author>Roland Becker</author>
    <author>Susanne Esslinger</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="durmaz">Durmaz, Vedat</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
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