PhD Position in Computer Science/Cheminformatics

Application deadline: 21 May 2025 at 23:59 hours local Danish time
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.

Salary, working conditions, application process, etc.

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 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.

The position is co-funded by the EU and the University of Vienna. While the project can guarantee the EU-funded salary as proposed for the first 18 months - until the end of the project - any continuation beyond this period will follow the rules, regulations, and salary framework applicable under Austrian national employment law. The holder of the scholarship is not allowed to have other paid employment during the three-year period. Additional funding may be possible, depending on the local supervisor and in accordance with the regular PhD time in the country of origin.

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 have 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 Austria and Germany.

Contact Information
For further information please contact Daniel Merkle, tel.: 45 6550 2322, e-mail: daniel@imada.sdu.dk
Application deadline: 21 May 2025 at 23:59 hours local Danish time
The anticipated start date is August, 2025, but flexibility in both directions is possible.

Application, salary etc.
Applications must be in English and must include the following:

• A research proposal/description of your approach to the project in question (max one page excluding references) should be attached under the “Project description” option.
• A letter stating your specific interest, motivation and qualifications for the project. (max. two pages) should be attached under the "Application form" option.
• Detailed CV, including personal contact information of two or three references, should be attached under the “CV” option.
• Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes/grades. This should be collated into one document and attached under the “Certificates” option.
• At least two signed reference letters, combined into one file and attached under the “References” option. Should your referees wish to send their letters directly to us, please have them sent to ebak@sdu.dk and mention your name and the title of the position in the subject line. And please note that these also need to reach us before the deadline.

Applications must be submitted electronically using the link "Apply online". Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read “How to apply” before you apply.

Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.

Details on the selection process can be found here. Please note that the recruitment team reserves the right to conduct a second interview. Shortlisting may be used in the assessment process.

The successful applicant will be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). Please check links for more information on salary (only available in Danish) and taxation.

The successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).

Further information about the PhD-study can be found at the homepage of the University.

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

Application must be in English and made in the form of a Declaration of Interest including the following:

• A letter stating your specific interest, motivation, and qualifications for the project in question (max. two pages) .
• Detailed CV, including personal contact information.
• Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes/grades

Shortlisting may be used in the assessment process. Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.

Applications will be assessed by an expert assessor/committee. Applicants will be informed of their assessment by the university.

Applications should be sent electronically via the link "Apply now". The faculty expects applicants to read the information "How to apply: FAQ" before applying. Please note that the application documents should be in pdf-format and attached as three documents: motivation letter, CV and the remaining documents.

We recommend that as an international applicant you take the time to visit Work in Denmark where you will find information and facts about moving to, working and living in Denmark, as well as the International Staff Office at SDU.

Placering: Odense, Denmark