PhD Position in Computer Science/Cheminformatics

We are looking for a PhD candidate 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 3: From formal behavioral specifications of chemical systems to their chemical implementation. 

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 the 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 problems 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 a 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.

This PhD project is a joint degree between Leipzig University (Peter Stadler) and University of Vienna (Christoph Flamm). Additionally, the student will have a three months research visit at TU Vienna (Thomas Gärtner) and a research training in entrepreneurship.

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.

All candidates will be expected to:

• Have potential for conducting outstanding research, as demonstrated by scientific accomplishments (in particular quality of thesis, but also publications, code repositories, conference presentations, outreach activities, etc.).
• Be interested in working in a multidisciplinary and international research environment.
• Have excellent communication skills in English, verbally as well as in scientific writing.
• Be willing to undertake international research stays, internships, and travels.

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

All positions are fully funded, with very competitive salaries. More information on funding from the MSCA programme can be found here (beginning on page 78). Please note that a country correction coefficient (page 109) applies to the living allowance in order to ensure equal treatment and purchasing power parity for all researchers. Salary rules apply to the doctoral candidates hosted in the European Union and will change depending on the host institution.

The TACsy project wishes our staff to reflect the diversity of society and thus welcome