[DMANET] PhD Position in Computer Science/Cheminformatics/Applied Mathematics

We are looking for PhD candidates to join the TACsy (Training Alliance for Computational Systems Chemistry) Marie-Skłodowska-Curie Joint Doctoral Network. This network consists of fifteen (15) highly interlinked PhD projects, of which this particular call is for project DC 6 Dynamical systems theory for generative chemistries.

The application deadline is May 2, 2023. The anticipated start date is September 1, 2023, but flexibility in both directions is possible.

This PhD project involves the development of theory, algorithms, and software, as well as participation in applications studies in collaboration with scientists and potentially industry from the consortium. The ideal candidate is familiar with one or more of the following areas: algorithmics, graph theory, simulation, dynamical systems, discrete structures/algebra, stochastic systems, complex systems, discrete optimization, theoretical chemistry, theoretical biology, coarse-graining. Strong interests in chemistry as well as proven competences in programming and ease with formal thinking are a necessity.

The goal of this PhD project is to develop novel theoretical concepts and software implementations to describe the dynamics of rule-based chemistries at multiple scales and from multiple perspectives. This includes the development of a stochastic simulation engine for rule-based reaction systems specified in the double pushout formalism, alongside with a novel framework to analyze stochastic trajectories in dynamically changing spaces. Departing from an algebraic approach like chemical organization theory (https://link.springer.com/article/10.1007/s11538-006-9130-8) we will harness in particular those systems in which through the interaction of their components, novel components are generated, which effectively changes the state space these components live in. This should open up a novel perspective on highly diverse molecular systems, including instances of chemical evolution, polymer formation, enzymatic synthesis design, lipidomics, prebiotic chemistries, or multifunctional phase-separated protein complexes in biological cells.

If you are a highly motivated individual with a Master's degree in either computer science, mathematics, physics, or computational sciences/biology being interested alongside the aforementioned themes, then we invite you to apply for this exciting PhD position in our team!

This PhD project will be a joint effort between the University of Jena (Peter Dittrich) and the University of Vienna (Christiph Flamm). Additionally, the student will have a research stay at Harvard Medical School (Walter Fontana).

The TACsy consortium encompasses 11 partners across six countries in Europe and North America, including both academic institutions and industrial partners. The consortium consists of world-class scientists with competences spanning chemistry, biochemistry, computer science, and machine learning. All fifteen doctoral candidates will work with two research groups, and will obtain a degree from both host institutions, and complete research stays either at world-leading industry partners or at prestigious non-European academic partners:

      University of Southern Denmark (DK)
      University of Vienna (AT)
      Leipzig University (DE)
      Friedrich-Schiller-University Jena (DE)
      TU Vienna (AT)
      The University of Sheffield (UK)
      European Molecular Biology Laboratory (EMBL)
      BASF SE (DE)
      Fluigent SA (FR)
      Thermo Fisher Scientific GMBH (DE)
      Harvard Medical School (US)

The candidates will all be part of a strong joint PhD training programme, with a focus on career development, application writing, communication skills, and community building through scientific summer schools.

TACsy wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background. We are searching for a diverse group of candidates with very different backgrounds and qualities, who inspire and motivate each other. We want every talent to feel at home in our organisations and to have the same career opportunities. The position of working hours is flexible in order to accommodate individual needs and allow for the best possible work-life balance for each candidate.

* More details on TACsy and the projects: https://tacsy.eu/

* Application instructions and application form:
https://www.sdu.dk/en/service/ledige_stillinger/1208134

* For questions, please contact project leader Daniel Merkle, tel.:
+45 6550 2322, e-mail: daniel@imada.sdu.dk.

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