[DMANET] PhD Position in Computer Science/Cheminformatics

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 10 Design of Multienzyme Cascades Based on Declarative Descriptions: Novel Computational Approaches.

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

We are seeking an excellent and highly motivated individual with either a Master's degree in computer science, applied mathematics, or in chemistry, or a degree from a related field (preferably with a focus on computational methods). The ideal candidate has familiarity with one or more of the following areas: optimization, declarative approaches, algorithmics, graph theory, algorithm engineering, computational chemistry. Proven competences in programming and ease with formal thinking are a necessity.

Project description: Declarative approaches to solve design and optimization problems are well established in computer science - in those, one does not aim at specifying how a solution is implemented, but one rather specifies what an overall goal should be and the solution is then automatically computed. Such approaches have a large potential for computational chemistry, and in particular for the design of multienzyme cascades: conceptually enzymes define formal graph transformation rules, which can be used to computationally expand chemical spaces. The declarative approaches can subsequently be used to identify efficient reaction cascades (i.e. sequences of graph transformation rules). Such multi-enzymatic cascade reactions, i.e., the combination of several enzymatic transformations in one pot, have in chemistry proven to possess considerable advantages compared to classical synthesis. For instance, it is possible to reduce costs, to allow for overall reactions that would otherwise not be possible, and to reduce the concentration of harmful or unstable compounds.

In this project, the PhD candidate will focus on computational and declarative approaches to model and solve multi-enzymatic cascade design problems. Among the chemical aspects to model and optimize for are: allosteric regulation of enzymes, competitive inhibition of the active sites, cofactor recycling, switching between different operation modes, and overall autocatalytic behavior. The candidate will develop such approaches and conduct extensive in-silico testing. We aim to compare and evaluate the computational tools developed in this project against wet-lab data produced in other projects of TACsy. The student will have a 3 month research stay with our industry partner (Fluigent) focusing on microfluidics and lab-on-a-chip technologies.

This PhD project will be a joint effort between the University of Vienna (Christoph Flamm, Austria) and the University of Southern Denmark (Daniel Merkle, Denmark). Additionally, the student will have a three months internship at Fluigent SA (France).

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/1208132

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

**********************************************************
*
* Contributions to be spread via DMANET are submitted to
*
* DMANET@zpr.uni-koeln.de
*
* Replies to a message carried on DMANET should NOT be
* addressed to DMANET but to the original sender. The
* original sender, however, is invited to prepare an
* update of the replies received and to communicate it
* via DMANET.
*
* DISCRETE MATHEMATICS AND ALGORITHMS NETWORK (DMANET)
* http://www.zaik.uni-koeln.de/AFS/publications/dmanet/
*
**********************************************************