<?xml version="1.0" encoding="utf-8"?>
<TEI xmlns="http://www.tei-c.org/ns/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:hal="http://hal.archives-ouvertes.fr/" xmlns:gml="http://www.opengis.net/gml/3.3/" xmlns:gmlce="http://www.opengis.net/gml/3.3/ce" version="1.1" xsi:schemaLocation="http://www.tei-c.org/ns/1.0 http://api.archives-ouvertes.fr/documents/aofr-sword.xsd">
  <teiHeader>
    <fileDesc>
      <titleStmt>
        <title>HAL TEI export of hal-02920023</title>
      </titleStmt>
      <publicationStmt>
        <distributor>CCSD</distributor>
        <availability status="restricted">
          <licence target="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 - Universal</licence>
        </availability>
        <date when="2026-04-29T08:13:30+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Rewriting Theory for the Life Sciences</title>
            <title xml:lang="en" type="sub">A Unifying Theory of CTMC Semantics</title>
            <author role="aut">
              <persName>
                <forename type="first">Nicolas</forename>
                <surname>Behr</surname>
              </persName>
              <email type="md5">02bf7b483853896e18cd92cb049bd3be</email>
              <email type="domain">irif.fr</email>
              <ptr type="url" target="http://nicolasbehr.com"/>
              <idno type="idhal" notation="string">nicolas-behr</idno>
              <idno type="idhal" notation="numeric">1087401</idno>
              <idno type="halauthorid" notation="string">1101698-1087401</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-8738-5040</idno>
              <affiliation ref="#struct-1005016"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Jean</forename>
                <surname>Krivine</surname>
              </persName>
              <email type="md5">0a7d224b25e70a62be4c29ac86aeb375</email>
              <email type="domain">irif.fr</email>
              <idno type="idhal" notation="string">jkrivine</idno>
              <idno type="idhal" notation="numeric">114</idno>
              <idno type="halauthorid" notation="string">15018-114</idno>
              <idno type="IDREF">https://www.idref.fr/114283311</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-7261-7462</idno>
              <affiliation ref="#struct-1005016"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Jean</forename>
                <surname>Krivine</surname>
              </persName>
              <email type="md5">0a7d224b25e70a62be4c29ac86aeb375</email>
              <email type="domain">irif.fr</email>
            </editor>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2020-12-18 16:48:35</date>
              <date type="whenWritten">2020-05-10</date>
              <date type="whenModified">2025-12-19 10:22:02</date>
              <date type="whenReleased">2021-01-06 11:38:06</date>
              <date type="whenProduced">2020-06-25</date>
              <date type="whenEndEmbargoed">2020-12-18</date>
              <ref type="file" target="https://hal.science/hal-02920023v1/document">
                <date notBefore="2020-12-18"/>
              </ref>
              <ref type="file" subtype="author" n="1" target="https://hal.science/hal-02920023v1/file/2003.09395.pdf" id="file-3082675-2697979">
                <date notBefore="2020-12-18"/>
              </ref>
              <ref type="externalLink" target="https://link.springer.com/content/pdf/10.1007%2F978-3-030-51372-6_11.pdf"/>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="111579">
                <persName>
                  <forename>Jean</forename>
                  <surname>Krivine</surname>
                </persName>
                <email type="md5">0a7d224b25e70a62be4c29ac86aeb375</email>
                <email type="domain">irif.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-02920023</idno>
            <idno type="halUri">https://hal.science/hal-02920023</idno>
            <idno type="halBibtex">behr:hal-02920023</idno>
            <idno type="halRefHtml">&lt;i&gt;International Conference on Graph Transformation 2020&lt;/i&gt;, Jun 2020, Bergen, Norway. pp.185-202, &lt;a target="_blank" href="https://dx.doi.org/10.1007/978-3-030-51372-6_11"&gt;&amp;#x27E8;10.1007/978-3-030-51372-6_11&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">International Conference on Graph Transformation 2020, Jun 2020, Bergen, Norway. pp.185-202, &amp;#x27E8;10.1007/978-3-030-51372-6_11&amp;#x27E9;</idno>
            <availability status="restricted">
              <licence target="https://about.hal.science/hal-authorisation-v1/">HAL Authorization<ref corresp="#file-3082675-2697979"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="TDS-MACS">Réseau de recherche en Théorie des Systèmes Distribués, Modélisation, Analyse et Contrôle des Systèmes</idno>
            <idno type="stamp" n="UNIV-PARIS">Université Paris Cité</idno>
            <idno type="stamp" n="UNIVERSITE-PARIS" corresp="UNIV-PARIS">Université Paris Cité</idno>
            <idno type="stamp" n="UP-SCIENCES">Université Paris Cité - Faculté des Sciences</idno>
            <idno type="stamp" n="IRIF">Institut de Recherche en Informatique Fondamentale</idno>
          </seriesStmt>
          <notesStmt>
            <note type="audience" n="2">International</note>
            <note type="invited" n="0">No</note>
            <note type="popular" n="0">No</note>
            <note type="peer" n="1">Yes</note>
            <note type="proceedings" n="1">Yes</note>
          </notesStmt>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">Rewriting Theory for the Life Sciences</title>
                <title xml:lang="en" type="sub">A Unifying Theory of CTMC Semantics</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Nicolas</forename>
                    <surname>Behr</surname>
                  </persName>
                  <email type="md5">02bf7b483853896e18cd92cb049bd3be</email>
                  <email type="domain">irif.fr</email>
                  <ptr type="url" target="http://nicolasbehr.com"/>
                  <idno type="idhal" notation="string">nicolas-behr</idno>
                  <idno type="idhal" notation="numeric">1087401</idno>
                  <idno type="halauthorid" notation="string">1101698-1087401</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-8738-5040</idno>
                  <affiliation ref="#struct-1005016"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Jean</forename>
                    <surname>Krivine</surname>
                  </persName>
                  <email type="md5">0a7d224b25e70a62be4c29ac86aeb375</email>
                  <email type="domain">irif.fr</email>
                  <idno type="idhal" notation="string">jkrivine</idno>
                  <idno type="idhal" notation="numeric">114</idno>
                  <idno type="halauthorid" notation="string">15018-114</idno>
                  <idno type="IDREF">https://www.idref.fr/114283311</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-7261-7462</idno>
                  <affiliation ref="#struct-1005016"/>
                </author>
              </analytic>
              <monogr>
                <title level="m">Proceedings of the International Conference on Graph Transformation. ICGT 2020</title>
                <meeting>
                  <title>International Conference on Graph Transformation 2020</title>
                  <date type="start">2020-06-25</date>
                  <settlement>Bergen</settlement>
                  <country key="NO">Norway</country>
                </meeting>
                <imprint>
                  <publisher>LNCS</publisher>
                  <biblScope unit="serie">Proceedings of the International Conference on Graph Transformation. ICGT 2020</biblScope>
                  <biblScope unit="volume">12150</biblScope>
                  <biblScope unit="pp">185-202</biblScope>
                  <date type="datePub">2020-05-10</date>
                </imprint>
              </monogr>
              <idno type="doi">10.1007/978-3-030-51372-6_11</idno>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <keywords scheme="author">
                <term xml:lang="en">Double-Pushout rewriting</term>
                <term xml:lang="en">Sesqui-pushout rewriting</term>
                <term xml:lang="en">rule algebra</term>
                <term xml:lang="en">stochastic mechanics</term>
                <term xml:lang="en">biochemistry</term>
                <term xml:lang="en">organic chemistry</term>
              </keywords>
              <classCode scheme="https://dl.acm.org/ccs" n="ACM2012.G.1.5.0"/>
              <classCode scheme="https://dl.acm.org/ccs" n="ACM2012.G.1.0.6"/>
              <classCode scheme="halDomain" n="info.info-mo">Computer Science [cs]/Modeling and Simulation</classCode>
              <classCode scheme="halDomain" n="info.info-bi">Computer Science [cs]/Bioinformatics [q-bio.QM]</classCode>
              <classCode scheme="halDomain" n="info.info-fl">Computer Science [cs]/Formal Languages and Automata Theory [cs.FL]</classCode>
              <classCode scheme="halTypology" n="COMM">Conference papers</classCode>
              <classCode scheme="halOldTypology" n="COMM">Conference papers</classCode>
              <classCode scheme="halTreeTypology" n="COMM">Conference papers</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>The Kappa biochemistry and the MØD organo-chemistry frameworks are amongst the most intensely developed applications of rewriting theoretical methods in the life sciences to date. A typical feature of these types of rewriting theories is the necessity to implement certain structural constraints on the objects to be rewritten (a protein is empirically found to have a certain signature of sites, a carbon atom can form at most four bonds,. . .). In this paper, we contribute to the theoretical foundations of these types of rewriting theory a number of conceptual and technical developments that permit to implement a universal theory of continuous-time Markov chains (CTMCs) for stochastic rewriting systems. Our core mathematical concepts are a novel rule algebra construction for the relevant setting of rewriting rules with conditions, both in Double-and in Sesqui-Pushout semantics, augmented by a suitable stochastic mechanics formalism extension that permits to derive dynamical evolution equations for pattern-counting statistics.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="laboratory" xml:id="struct-1005016" status="VALID">
          <idno type="IdRef">193993007</idno>
          <idno type="RNSR">201621976X</idno>
          <idno type="ROR">https://ror.org/02krdtz55</idno>
          <idno type="Wikidata">Q51783269</idno>
          <orgName>Institut de Recherche en Informatique Fondamentale</orgName>
          <orgName type="acronym">IRIF (UMR_8243)</orgName>
          <date type="start">2020-01-01</date>
          <desc>
            <address>
              <addrLine>Université Paris CitéBâtiment Sophie Germain, Case courrier 70148 Place Aurélie Nemours75205 Paris Cedex 13</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.irif.fr/</ref>
          </desc>
          <listRelation>
            <relation name="UMR8243" active="#struct-441569" type="direct"/>
            <relation name="UMR_8243" active="#struct-557826" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-441569" status="VALID">
          <idno type="IdRef">02636817X</idno>
          <idno type="ISNI">0000000122597504</idno>
          <idno type="ROR">https://ror.org/02feahw73</idno>
          <orgName>Centre National de la Recherche Scientifique</orgName>
          <orgName type="acronym">CNRS</orgName>
          <date type="start">1939-10-19</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.cnrs.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-557826" status="VALID">
          <idno type="IdRef">236453505</idno>
          <idno type="ISNI">0000 0004 7885 7602</idno>
          <idno type="ROR">https://ror.org/05f82e368</idno>
          <orgName>Université Paris Cité</orgName>
          <orgName type="acronym">UPCité</orgName>
          <date type="start">2020-01-01</date>
          <desc>
            <address>
              <addrLine>85 boulevard Saint-Germain75006 Paris</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://u-paris.fr/</ref>
          </desc>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>