PhD position (M/F): Contingent dynamics in unbounded chemical networks: towards the emergence of prebiotic Darwinian processes

Job Description

Thesis Subject

Context :
From the standpoint of evolutionary biology, understanding the origin of life amounts to understanding how natural selection may arise in a non-biological world governed by purely physico-chemical processes (1). Meeting this goal requires an explicit articulation of evolutionary theory with physics and chemistry. Yet the problem remains challenging, since the basic ingredients of evolutionary thinking – populations of self-replicating objects displaying heritable variation – are still to be fully formulated in a prebiotic framework (2, 3). One promising approach relies on mathematical modelling: simulating open systems that obey the fundamental laws of thermodynamics and tracking dynamical behaviours that could be interpreted as emerging Darwinian processes.
In this context, our team has developed a first model, focusing primarily on the behaviour of autocatalytic cycles within predefined and bounded chemical networks connecting fixed sets of chemical objects through fixed sets of reactions (4). Ongoing projects in our group now investigate how autocatalytic cycles may interact in complex ways, akin to ecological relationships, potentially generating a broad diversity of steady states and paving the way to incipient Darwinian dynamics. While this framework helps clarifying important first principles, it may also overlook a critical property of the real world, where life has actually emerged: the immense diversity of possible chemical objects – especially macromolecules or supramolecular assemblies – produced by contingent trajectories representing only a minute fraction of the virtually infinite space of possibilities.
PhD project :
The goal of the proposed PhD is to overcome these limitations by designing and exploring a new modelling approach, in which only chemical rules are initially specified, generating unbounded chemical networks expanding gradually and stochastically in an infinite chemical space. Preliminary developments suggest that explicitly considering a finite number of discrete particles will be an effective way to implement this framework: in this context, chance effects will naturally come into play, and only a subset of all possible trajectories will be explored. In these simulations, concentration vectors will change dynamically through a combination of deterministic and stochastic processes, producing dynamics that may be only partly repeatable. Given the crucial role of chance in biological evolution, we expect this new modelling scheme will bring us closer to understanding how natural selection should be conceived beyond the standard biological context. Practically, the software will be developed as part of our existing EmergeNS platform (https://github.com/deniskup/EmergeNS), a C++ program integrating an efficient command-line interface and a user-friendly graphical environment with advanced visualisation features.
Required skills :
We are looking for a highly motivated person interested in interdisciplinary approaches, with strong skills in computational or mathematical modelling and a clear interest in evolutionary biology.
References :
1. S. Charlat, L'évolution sans gêne - Aux origines de nos origines (Editions du Seuil, 2025).
2. S. Charlat, et al., Natural Selection beyond Life? A Workshop Report. Life 11, 1051 (2021).
3. S. Charlat, T. Heams, O. Rivoire, “Is Natural Selection Physical?” in Evolutionary Thinking Across Disciplines, Synthese Library., A. Du Crest, et al., Eds. (Springer International Publishing, 2023), pp. 287–296.
4. T. Kosc, D. Kuperberg, E. Rajon, S. Charlat, Thermodynamic consistency of autocatalytic cycles. Proc. Natl. Acad. Sci. U.S.A. 122 (2025).
5. D. Kuperberg et al., EmergeNS software. (2024). GitHub.

Your Work Environment

The recruited person will join the Laboratoire de Biométrie et Biologie Evolutive (LBBE) located on the LyonTech la Doua university campus in Villeurbanne (https://lbbe.univ-lyon1.fr). The LBBE is a laboratory of the University of Lyon 1, the CNRS and VetAgroSup. About 200 people participate in the unit's research activities by combining mathematical and computational modeling with questions in evolutionary ecology, genomics and health. It will benefit from the laboratory's IT infrastructure necessary for the realization of the project (cluster of 1600 cores).
The research will be carried out within a dynamic group, including recently recruited PhD students and postdoctoral researchers, currently working on ecological-like relationships between autocatalytic sets and on the multistability of chemical networks – two directions that will help interpret the results of the PhD.
The PhD is part of the ANR-funded EmergeNS project (started early 2026), which involves groups at LIP (Laboratoire de l'Informatique du Parallélisme, with Denis Kuperberg, ENS Lyon), LBBE (Laboratoire de Biométrie et Biologie Évolutive, with Etienne Rajon, University of Lyon), and PIMIT (Processus Infectieux en Milieu Insulaire Tropical, Reunion Island, with Sylvain Charlat, CNRS). The strong links between partners ensure a stimulating and truly interdisciplinary environment, bridging mathematics, physics, ecology and evolutionary biology. The PhD will take place at the LBBE, and benefit from on-site infrastructures (e.g. a ~1600-CPUs cluster).
Our added benefits:
• A stimulating working environment alongside research staff
• Professional support with in-house training at the laboratory
• The option to work from home
• A staff canteen offering lunch at an attractive price.
• Partial reimbursement of travel costs (75%)
+ a sustainable mobility allowance of up to €300 per year
• A site accessible by public transport (Tram T1 + T4 + bus)
• 44 days' annual leave / RTT per year
• Supplementary social security cover

Compensation and benefits

Compensation

2300 € gross monthly

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

The research professions