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<export-example>
  <doc>
    <id>7770</id>
    <completedYear/>
    <publishedYear>2019</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber>77</pageNumber>
    <edition/>
    <issue/>
    <volume/>
    <type>masterthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>2019-08-05</thesisDateAccepted>
    <title language="eng">Hybrid Models and Simulations of Reaction-Diffusion Processes</title>
    <abstract language="eng">In this thesis,we are interested in multiscale models for particle-based reaction diffusion (PBRD) simulations,where&#13;
we focus on coupling particle-based simulations to macroscopic chemical reservoirs. These reservoirs are given by a mean concentration of chemical species that can vary in time and space. We model these reservoirs as reaction-diffusion partial differential equations (PDEs). The goal of this work is to achieve a mathematically consistent coupling between the PBRD simulations and the reaction-diffusion PDEs.</abstract>
    <author>Margarita Kostré</author>
    <submitter>Natasa Djurdjevac Conrad</submitter>
    <advisor>Frank Noe</advisor>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="projects" number="SFB1114-C3">SFB1114-C3</collection>
    <collection role="persons" number="kostre">Kostre, Margarita</collection>
    <collection role="projects" number="MathPlusAA1-1">MathPlusAA1-1</collection>
    <collection role="projects" number="MathPlus - AA6">MathPlus - AA6</collection>
    <thesisPublisher>Zuse Institute Berlin (ZIB)</thesisPublisher>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
  </doc>
  <doc>
    <id>9827</id>
    <completedYear/>
    <publishedYear>2024</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Exploration of Particle Swarm Optimisation Algorithm with Divergent Parameters</title>
    <parentTitle language="eng">Natural Computing</parentTitle>
    <enrichment key="PeerReviewed">no</enrichment>
    <enrichment key="SubmissionStatus">under review</enrichment>
    <enrichment key="opus.source">publish</enrichment>
    <author>Margarita Kostré</author>
    <submitter>Ekaterina Engel</submitter>
    <author>Natasa Djurdjevac Conrad</author>
    <author>Christof Schütte</author>
    <author>Vikram Sunkara</author>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="persons" number="natasa.conrad">Conrad, Natasa</collection>
    <collection role="persons" number="sunkara">Sunkara, Vikram</collection>
    <collection role="persons" number="kostre">Kostre, Margarita</collection>
    <collection role="institutes" number="MSoCP">Modeling and Simulation of Complex Processes</collection>
    <collection role="projects" number="MathPlusEF45-1">MathPlusEF45-1</collection>
  </doc>
  <doc>
    <id>9931</id>
    <completedYear>2025</completedYear>
    <publishedYear>2025</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>14</issue>
    <volume>58</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Open reaction-diffusion systems: bridging probabilistic theory and simulations across scales</title>
    <abstract language="eng">Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual particle/agent level, and in realistic applications, they often display interaction with their environment through energy or material exchange with a reservoir. This requires intricate mathematical considerations, especially in the case of material exchange since the varying number of particles/agents results in ``on-the-fly'' modification of the system dimension. In this work, we first overview the probabilistic description of reaction-diffusion processes at the particle level, which readily handles varying number of particles. We then extend this model to consistently incorporate interactions with macroscopic material reservoirs. Based on the resulting expressions, we bridge the probabilistic description with macroscopic concentration-based descriptions for linear and nonlinear reaction-diffusion systems, as well as for an archetypal open reaction-diffusion system. Using these mathematical bridges across scales, we finally develop numerical schemes for open reaction-diffusion systems, which we implement in two illustrative examples. This work establishes a methodological workflow to bridge particle-based probabilistic descriptions with macroscopic concentration-based descriptions of reaction-diffusion in open settings, laying the foundations for a multiscale theoretical framework upon which to construct theory and simulation schemes that are consistent across scales.</abstract>
    <parentTitle language="eng">Journal of Physics A: Mathematical and Theoretical</parentTitle>
    <identifier type="doi">10.1088/1751-8121/adc520</identifier>
    <enrichment key="opus.source">publish</enrichment>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Mauricio del Razo</author>
    <submitter>Mauricio del Razo</submitter>
    <author>Margarita Kostré</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="kostre">Kostre, Margarita</collection>
    <collection role="institutes" number="MSoCP">Modeling and Simulation of Complex Processes</collection>
    <collection role="persons" number="delrazo">del Razo Sarmina, Mauricio</collection>
    <collection role="projects" number="DFG-OpenMultiscaleBiochem">DFG-OpenMultiscaleBiochem</collection>
  </doc>
  <doc>
    <id>8658</id>
    <completedYear>2022</completedYear>
    <publishedYear>2022</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber>18</pageNumber>
    <edition/>
    <issue/>
    <volume>7</volume>
    <type>article</type>
    <publisherName>Springer Nature</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2022-08-02</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Understanding the Romanization Spreading on Historical Interregional Networks in Northern Tunisia</title>
    <abstract language="eng">Spreading processes are important drivers of change in social systems. To understand the mechanisms of spreading it is fundamental to have information about the underlying contact network and the dynamical parameters of the process. However, in many real-wold examples, this information is not known and needs to be inferred from data. State-of-the-art spreading inference methods have mostly been applied to modern social systems, as they rely on availability of very detailed data. In this paper we study the inference challenges for historical spreading processes, for which only very fragmented information is available. To&#13;
cope with this problem, we extend existing network models by formulating a model on a mesoscale with temporal spreading rate. Furthermore, we formulate the respective parameter inference problem for the extended model. We apply our approach to the romanization process of Northern Tunisia, a scarce dataset, and study properties of the inferred time-evolving interregional networks. As a result, we show that (1) optimal solutions consist of very different network structures and spreading rate functions; and that (2) these diverse solutions produce very similar spreading patterns. Finally, we discuss how inferred dominant interregional connections are related to available archaeological traces. Historical networks resulting from our approach can help understanding complex processes of cultural&#13;
change in ancient times.</abstract>
    <parentTitle language="eng">Applied Network Science</parentTitle>
    <identifier type="doi">10.1007/s41109-022-00492-w</identifier>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-86764</enrichment>
    <enrichment key="AcceptedDate">18.07.2022</enrichment>
    <enrichment key="PeerReviewed">yes</enrichment>
    <submitter>Margarita Kostre</submitter>
    <author>Margarita Kostré</author>
    <author>Vikram Sunkara</author>
    <author>Christof Schütte</author>
    <author>Natasa Djurdjevac Conrad</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>mesoscale spreading process</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>network inference</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>time-evolving network</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>romanization spreading</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>scarce data</value>
    </subject>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="persons" number="natasa.conrad">Conrad, Natasa</collection>
    <collection role="persons" number="sunkara">Sunkara, Vikram</collection>
    <collection role="persons" number="kostre">Kostre, Margarita</collection>
    <collection role="institutes" number="MSoCP">Modeling and Simulation of Complex Processes</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <collection role="projects" number="MathPlusEF5-2">MathPlusEF5-2</collection>
  </doc>
  <doc>
    <id>8676</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2022-05-11</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Understanding the Romanization Spreading on Historical Interregional Networks in Northern Tunisia</title>
    <abstract language="eng">Spreading processes are important drivers of change in social systems. To understand the mechanisms of spreading it is fundamental to have information about the underlying contact network and the dynamical parameters of the process.&#13;
	However, in many real-wold examples, this information is not known and needs to be inferred from data. State-of-the-art spreading inference methods have mostly been applied to modern social systems, as they rely on availability of very detailed data. In this paper we study the inference challenges for historical spreading processes, for which only very fragmented information is available. To cope with this problem, we extend existing network models by formulating a model on a mesoscale with temporal spreading rate. Furthermore, we formulate the respective parameter inference problem for the extended model. We apply our approach to the romanization process of Northern Tunisia, a scarce dataset, and study properties of the inferred time-evolving interregional networks. As a result, we show that (1) optimal solutions consist of very different network structures and spreading rate functions; and that (2) these diverse solutions produce very similar spreading patterns. Finally, we discuss how inferred dominant interregional connections are related to available archaeological traces. Historical networks resulting from our approach can help understanding complex processes of cultural change in ancient times.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-86764</identifier>
    <author>Margarita Kostré</author>
    <submitter>Margarita Kostre</submitter>
    <author>Vikram Sunkara</author>
    <author>Christof Schütte</author>
    <author>Nataša Djurdjevac Conrad</author>
    <series>
      <title>ZIB-Report</title>
      <number>22-10</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>mesoscale spreading process, network inference, time-evolving network, romanization spreading, scarce data</value>
    </subject>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="persons" number="natasa.conrad">Conrad, Natasa</collection>
    <collection role="persons" number="sunkara">Sunkara, Vikram</collection>
    <collection role="persons" number="kostre">Kostre, Margarita</collection>
    <collection role="institutes" number="MSoCP">Modeling and Simulation of Complex Processes</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <collection role="projects" number="MathPlusEF5-2">MathPlusEF5-2</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/8676/ZIBReportKostre.pdf</file>
  </doc>
</export-example>
