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PhD Position in Computer Science/ Cheminformatics

University of Southern Denmark (SDU)
Odense, Fyn (DK)
Closing date
23 Oct 2023

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Job Type
PhD Studentship
Employment - Hours
Full time
Fixed term

We are looking for PhD candidates to join the TACsy (Training Alliance for Computational Systems Chemistry) Marie-Sklodowska-Curie Joint Doctoral Network. This network consists of fifteen (15) highly interlinked PhD projects, of which this particular call is for project DC 3: From formal behavioral specifications of chemical systems to their chemical implementation.

The application deadline is 23 October 2023.

The anticipated start date is 1 January 2024, but flexibility in both directions is possible.

Systems theory defines a chemical reaction system as transformations of abstract entities, i.e. only the stoichiometric relations between the entities are considered. Rule-based approaches on the other hand focus on the rearrangements of chemical bonds and therefore require that the entities have explicit internal structure. This imposes constraints on the stoichiometry and, vice versa, the system level constrains the molecules (entities) given the rules and th e rules given the molecules. The aim of this project is to develop a theory and accompanying algorithms to decide if an abstract system can be instantiated by a concrete "chemistry" defined as a set of molecules and a set of rules. The PhD candidate will study abstract reaction networks with respect to their realizability with concrete chemistry. For example, given a metabolic network is there an alternative chemistry that produces the same stoichiometric network? This type of problem can be formalised in the framework of SMT (Satisfiability Modulo Theory). The PhD project involves the development of a theory and accompanying algorithms to tackle such problems. Applications will lie in the area of the design of enzyme cascades.

We are seeking an excellent and highly motivated individual with an MSc degree in computer science, mathematics, chemistry, computational biology or a related subject. The ideal candidate has familiarity with one or more of the following areas: algorithmics, graph theory, satisfiability problems, discrete optimization. Strong interests in chemistry as well as proven competences in programming and ease with formal thinking are a necessity.

See details about the network as a whole, its scientific content, and the application and selection process here.

Please note that there are two limitations to apply for this programme, as specified in the MSCA regulations. Applicants must:

  • Not be in possession of a PhD degree at the date of recruitment.
  • Meet the Marie-Curie mobility rule (see pages 81-82 here). In TACsy, this means the applicants are not eligible for a specific position if it is true for both host institutions of the position that the applicant for more than 12 of the last 36 months has resided or performed a main activity (work, studies, etc.) in the country of that host institution. The host institutions relevant to this rule are for the present call located in (DC 1: Denmark and Germany), (DC 3: Austria and Germany), (DC 6: Austria and Germany), (DC 12: Austria and Denmark), (DC 13: Austria and Denmark).

These positions are subject to the entry into force of grant agreement no 101072930 by and between the European Research Executive Agency and University of Southern Denmark and thereby funded by the European Union's Horizon Europe Research and Innovation Programme.

Please see the full call, including how to apply, on

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