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  <doc>
    <id>742</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
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    <completedDate>2003-07-02</completedDate>
    <publishedDate>2003-07-02</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Molecular Conformation Dynamics and Computational Drug Design</title>
    <abstract language="eng">The paper surveys recent progress in the mathematical modelling and simulation of essential molecular dynamics. Particular emphasis is put on computational drug design wherein time scales of $msec$ up to $min$ play the dominant role. Classical long-term molecular dynamics computations, however, would run into ill-conditioned initial value problems already after time spans of only $psec=10^{-12} sec$. Therefore, in order to obtain results for times of pharmaceutical interest, a combined deterministic-stochastic model is needed. The concept advocated in this paper is the direct identification of metastable conformations together with their life times and their transition patterns. It can be interpreted as a {\em transfer operator} approach corresponding to some underlying hybrid Monte Carlo process, wherein short-term trajectories enter. Once this operator has been discretized, which is a hard problem of its own, a stochastic matrix arises. This matrix is then treated by {\em Perron cluster analysis}, a recently developed cluster analysis method involving the numerical solution of an eigenproblem for a Perron cluster of eigenvalues. In order to avoid the 'curse of dimension', the construction of appropriate boxes for the spatial discretization of the Markov operator requires careful consideration. As a biomolecular example we present a rather recent SARS protease inhibitor.</abstract>
    <identifier type="serial">03-20</identifier>
    <identifier type="opus3-id">743</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-7427</identifier>
    <enrichment key="SourceTitle">Appeared in: J. M. Hill, R. Moore (eds.) Applied Mathematics Entering the 21st Century. Proc. ICIAM 2003, Sydney, Australia, 2004, pp. 91-119 (2004)</enrichment>
    <author>Peter Deuflhard</author>
    <author>Christof Schütte</author>
    <series>
      <title>ZIB-Report</title>
      <number>03-20</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>conformation dynamics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Monte Carlo methods</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>transfer operations</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Hamiltonian dynamics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Smoluchowski dynamics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>metastable sets</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Perron cluster an</value>
    </subject>
    <collection role="ddc" number="000">Informatik, Informationswissenschaft, allgemeine Werke</collection>
    <collection role="msc" number="65C05">Monte Carlo methods</collection>
    <collection role="msc" number="65C40">Computational Markov chains</collection>
    <collection role="msc" number="65P10">Hamiltonian systems including symplectic integrators</collection>
    <collection role="institutes" number="">ZIB Allgemein</collection>
    <collection role="persons" number="deuflhard">Deuflhard, Peter</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/742/ZR-03-20.ps</file>
    <file>https://opus4.kobv.de/opus4-zib/files/742/ZR-03-20.pdf</file>
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