September 27 – October 2 , 2015, Dagstuhl Seminar 15402

Self-assembly and Self-organization in Computer Science and Biology


Vincent Danos (University of Edinburgh, GB)
Heinz Koeppl (TU Darmstadt, DE)

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Dagstuhl Report, Volume 5, Issue 9 Dagstuhl Report
Aims & Scope
List of Participants
Dagstuhl Seminar Schedule [pdf]


The Seminar brought together researchers from molecular biology, molecular modeling and theoretical computer scientists with interest in formal models of molecular computation and self-organization. Molecular biology provides a rich substrate to implement molecular computation and complex self-assembly algorithms. The Seminar featured several talks on DNA-assembly systems, that to-date represents the most advanced molecular substrate for self-assembly. The increase in the achieveable complexity of such molecular structures asks for a formal description and analysis of those systems using methods from theoretical computer science. The Seminar was successful in identifying common problem statements and in establishing a common scientific language. Apart from self-assembly, the broader term self-organization was mostly represented by research on swarming or self-propelled particle (SPP) models. The common feature of SPP systems and self-assembly is the emergence of global structures through local interaction rules (self-assembled structure vs swarms or flocks). One contribution also featured the combination of swarming and self-assembly system in terms of nucleation studies. Moreover, novel methodological overlap between simulation algorithms for molecular self-assembly and simulation algorithms for SPP systems were identified and elaborated during the workshop.

The seminar was structured as a regular workshop with morning and afternoon sessions but plenty of time was allocated for discussions after each talk. For the first such Dagstuhl Seminar no working groups were defined. For follow-up Seminars on the same topic we aim to additionally define working groups that may also deliver preliminary research results and initiation of new collaborations.

Although the workshop was very interdisciplinary we were able to arrange the presentations into sessions of a coherent theme. The feedback of participants was extremely positive, stating that they could really profit from the technical discussions that accompanied every presentation and that were performed in the free time. Correspondingly, several new collaborations across disciplines were initiated at the seminar.

Summary text license
  Creative Commons BY 3.0 Unported license
  Vincent Danos and Heinz Koeppl


  • Data Structures / Algorithms / Complexity
  • Modelling / Simulation
  • Networks


  • Self-assembly
  • Self-organization
  • Self-* systems
  • Concurrency
  • Graph-rewriting grammars Topics: Modelling/simulation


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