Post-Doctoral Research Visit F/M Modeling subterranean biofilms to improve carbon capture

The Inria center at the University of Bordeaux is one of the nine Inria centers in France and has about twenty research teams.. The Inria centre is a major and recognized player in the field of digital sciences. It is at the heart of a rich R&D and innovation ecosystem: highly innovative SMEs, large industrial groups, competitiveness clusters, research and higher education players, laboratories of excellence, technological research institute...

Within the framework of a partnership between Inria and the IFPEN we study the interaction between microbial communities, lithic media, and carbon dioxyde in deep carbon storage sites. These interactions produce biological phenomena that can be beneficial or detrimental, and can play a key role in the efficiency and reliability of carbon capture storage (CCS).

We are developing a common framework for simulating these phenomena, by coupling two existing codes developed at the IFPEN and Inria. The IFPEN provides codes for phenomenological modeling of chemolithotrophy, in the form of coupled autonomous non-linear dynamic systems, that predict biological effects and transformations. Inria provides codes for mechanistic modeling of metabolic exchanges of very large communities, that predict the potential for biofilm formation and the activation of biological functions.

The principal place of work will be the Inria center at the University of Bordeaux, in the offices of the Pleiade project-team.

Travel between Bordeaux, Toulouse, and Reuil-Malmaison may be necessary from time to time, and expenses will be covered within the limits of rates imposed by the Institute.

Assignments: With the help of David Sherman (Inria) and Arnaud Pujol (IFPEN), the recruited person will couple two existing codes, one for numerical simulation of dynamic systems in chemolithotropy, the other for logical inference of metabolic interaction potential. This coupling will infer inter-species metabolic interactions and realizability of biochemical functions, starting from large collections of taxa identified by sampling or from the literature, and from nutritional environments deduced from geological analyses. The phenomena discovered by this procedure will provide a starting point for numerical simulation and sensitivity analysis. These numerical results, in turn, will provide a means for identifying biological objectives, in particular biofilm formation, that our logical inference system can use to generate sets of minimal microbial communities that meet those objectives.

For a better knowledge of the proposed research subject: scientific references for metabolic modeling are available at https://team.inria.fr/pleiade.

Collaboration : The recruited person will be in contact with experts from the IFPEN in phenomenological modeling in geological environments, and with Inria project-teams concerned with modeling biological systems.

Responsibilities : The person recruited will be responsible for software development and will adopt best practices from the team including continuous integration and reproducibility.

Main activities:

• Develop computer programs for numerical and logical simulation
• Test and modify until validation
• Perform simulations
• Write reports and scientifique articles

Additional activities:

• Present progress of ongoing work to colleagues and partners
• Discuss with scientific collaborators
• Review the scientific literature

Technical skills: A major activity of this work is the development of computer programs for modeling, and the execution of those programs in Kubernetes and HPC environments. The post-doc must be competent in software development. Knowledge of software engineering best practices per se would be a plus but we train these skills for all team members as a matter of routine.

Languages: Candidates must be at ease in scientific English and eager to publish their results in scientific journals. The team uses English and French interchangeably.

Relational skills: Ability to communicate with colleagues from the biological, chemical, and computer sciences will be necessary and a willingness to listen to and learn from these colleagues will be a key to success.

• Subsidized meals
• Partial reimbursement of public transport costs
• Leave: 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.)
• Possibility of teleworking (after 6 months of employment) and flexible organization of working hours
• Professional equipment available (videoconferencing, loan of computer equipment, etc.)
• Social, cultural and sports events and activities
• Access to vocational training
• Social security coverage

The gross monthly salary will be 2788€ (before social security contributions and monthly witholding tax).