Post-Doctoral Research Visit F/M Mathematical modeling of tissue morphogenesis, repair and ageing

Le descriptif de l'offre ci-dessous est en Anglais

Type de contrat : CDD

Niveau de diplôme exigé : Thèse ou équivalent

Fonction : Post-Doctorant

Contexte et atouts du poste

This post-doctoral position is in the frame of the ANR project ENERGENCE headed by D. Peurichard (Inria Paris, MUSCLEES team) and our biological partners at RESTORE, Toulouse. The long lasting collaboration between the two partners led to the development of mathematical models for adipose tissue development and morphogenesis [Peurichard et al, JTB, 2017], [Chassonery et al, RSOS, 2024] and was extended to study AT reconstruction abilities after injury [Peurichard et al, JTB, 2019]. In both studies, it proved to be an invaluable tool to highlight the key role of mechanical interactions in AT, and enabled to identify a new therapeutic target to induce regeneration in scarring tissues, validated in-vivo [Pacary et al, Nat Reg Med, 2024]. Therefore, these models represent an important proof-of concept that mechanical interactions could be a major driver of tissue architectures. However, in their present state the developed models do not take into account energy exchanges/metabolism, as biological phenomena (cell growth, insemination, matrix crosslinking) are prescribed by some growth laws not linked to external energy arrivals nor to mechanical constraints. The goal of this project is therefore to take a step further and introduce metabolic considerations into the mechanical model to reach a complete model for tissue architecture emergence, enabling to study the role of mecano-chemical feedback loops in tissue equilibria, repair and ageing.

The post-doctoral candidate will develop and analyze agent-based models (ABM) to explore and determine the complex feedback loops between energy intakes and local growth laws, and study how the tissue architecture evolves as a result of changes in energy fluxes, modelling cafeteria diet and food deprivation. The parameters of the constructed ABM will be calibrated on experimental measurements at RESTORE and the model results will be systematically confronted to experimental data from the litterature and generated by our biological partners.

The post-doctoral fellow will be located at LJLL, Sorbonne University, with regular visits to the RESTORE lab in Toulouse. Travel expenses will be covered by the projects.

Mission confiée

The recruited person will use the 2D and 3D spatial models developed in the team -featuring mechanical interactions between adipocyte cells and cross-linked fibers- as a starting point [Peurichard et al, JTB, 2017], and implement new rules to account for nutrient- and mechanically-limited growth laws. This task will be highly interactive, since the choice of a convenient model is both critical and the very first key point. It will be performed via constant interactions with the biological partner. This step will validate the choice of growth laws and energetical feedback loops, and may lead to an adaptation of the model hypothesis.

The recruited person will perform numerical simulations to study the new behaviors / tissue architectures that emerge from the new model, and the influence of these newly defined feedback loops between energy and mechanics in the equilibrium structures. The fine-tuning and validation of the newly developed model will rely on a quantitative comparison with experimental images generated at the RESTORE lab. The complete model will be analyzed by a systematic sensitivity analysis of the free model parameters to better understand how they control model outputs described by a set of quantifiers. With the help of D. Peurichard and informaticians at the RESTORE lab, the candidate will develop new unsupervised sensitivity analysis tools at the intersection between machine learning and ABM.

Depending on the first results and on the software competences of the recruited person, a user-friendly interface will be developed based on the ABM, to be transferred to the RESTORE lab and used to explore how the AT architecture is modified by the amplitude, frequency and length of energy intake modifications.

More information on request from:

Principales activités

Main activities:

• Bibliographic work
• Development of agent-based models and numerical implementation of the models (python, C++, Fortran90 ...)
• Analysis of the models (sensitivity analysis combining classical and machine learning tools)
• Development of image processing tools and appropriate quantifiers for confrontation model/ data
• Maintaining regular interactions with biological collaborators
• Writing reports/papers

Additional activities (according to the candidate preference) :

• Development of a user-friendly software and transfer to the biologist lab

Compétences

Technical skills and level required :

• Knowledge in mechanics, stochastic processes and / or in statistical physics
• Knowledge in mathematical model building and implementation on the computer
• Basic knowledge in numerics, ready to read and understand the necessary algorithms
• Programming language (Fortran90, C++ and / or python) advanced level

Relational skills :

• Good interpersonal skills
• Good communications skills
• Reasonable presentations skills

Avantages

• 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 and flexible organization of working hours
• Professional equipment available (videoconferencing, loan of computer equipment, etc.)
• Social, cultural and sports events and activities
• Health insurance as from May 2025

Informations générales

• Thème/Domaine : Modélisation et commande pour le vivant

Biologie et santé, Sciences de la vie et de la terre (BAP A)
- Ville : Paris
- Centre Inria : Centre Inria de Paris
- Date de prise de fonction souhaitée :
- Durée de contrat : 1 an, 1 mois
- Date limite pour postuler :

Attention: Les candidatures doivent être déposées en ligne sur le site Inria. Le traitement des candidatures adressées par d'autres canaux n'est pas garanti.

Consignes pour postuler

Sécurité défense :

Ce poste est susceptible d'être affecté dans une zone à régime restrictif (ZRR), telle que définie dans le décret n° relatif à la protection du potentiel scientifique et technique de la nation (PPST). L'autorisation d'accès à une zone est délivrée par le chef d'établissement, après avis ministériel favorable, tel que défini dans l'arrêté du 03 juillet 2012, relatif à la PPST. Un avis ministériel défavorable pour un poste affecté dans une ZRR aurait pour conséquence l'annulation du recrutement.

Politique de recrutement :

Dans le cadre de sa politique diversité, tous les postes Inria sont accessibles aux personnes en situation de handicap.

Contacts

• Équipe Inria : MUSCLEES
• Recruteur :

Peurichard Diane /

L'essentiel pour réussir

The candidate should hold a PhD in applied mathematics, physics or other relevant fields. We are looking for a highly motivated candidate with a strong background in mathematical modelling, computational physics / numerics, in particular if in the fields of classical mechanics, bio-physics, soft matter or granular matter, and a deep interest in biological applications. Proven experience in a programming language (Fortran90, C++ and / or python) is required. The ideal candidates are able to work effectively as part of a team, but also to develop and pursue independent ideas. Experience in modelling and applications in biology is highly recommended and collaboration with other people, best cross-disciplinary will be highly appreciated. Previous experience with academic environment and software is an advantage.

A propos d'Inria

Inria est l'institut national de recherche dédié aux sciences et technologies du numérique. Il emploie 2600 personnes. Ses 215 équipes-projets agiles, en général communes avec des partenaires académiques, impliquent plus de 3900 scientifiques pour relever les défis du numérique, souvent à l'interface d'autres disciplines. L'institut fait appel à de nombreux talents dans plus d'une quarantaine de métiers différents. 900 personnels d'appui à la recherche et à l'innovation contribuent à faire émerger et grandir des projets scientifiques ou entrepreneuriaux qui impactent le monde. Inria travaille avec de nombreuses entreprises et a accompagné la création de plus de 200 start-up. L'institut s'efforce ainsi de répondre aux enjeux de la transformation numérique de la science, de la société et de l'économie.

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