2022-05502 - Post-Doctoral Research Visit F/M Particle-based computer simulations in a virtual liver model to evaluate replacement of histology by Magnetic-resonance-based technologies
Le descriptif de l’offre ci-dessous est en Anglais

Type de contrat : CDD

Contrat renouvelable : Oui

Niveau de diplôme exigé : Thèse ou équivalent

Fonction : Post-Doctorant

Contexte et atouts du poste

The location of the position is INRIA Saclay-Ile de France. The selected candidate should perform the project outlined below in close collaboration with the research team SIMBIOTX, and our medical collaborators at Hopital Beaujon and perhaps other clinical partners.

Researchers from SIMBIOTX have developed over decades computational models of multicellular systems with applications in systems biology and systems medicine of multi-cell systems in liver (e.g. Hoehme et. al., PNAS, 2010; Schliess et. al., Hepatology, 2014; Drasdo et. al., J. Hepat. 2014; Hammad et. al., Arch. Toxicol. 2014; Ghallab et. al., J. Hepat. 2016; Aubert et. al. J Biomech 2017 & CMAME 2017; Hoehme et. al., Bull. Math. Biol. 2018; Ghallab et. al., Hepatology 2018; Van Liedekerke et. al., Biomechanics and Modeling in Mechanobiology, 2020) and in in vitro experimental settings (Van Liedekerke et. al., Plos Comput. Biol. 2019 and refs. therein). The models span a wide range of submodels, including tissue organisation models representing each individual cell in time and space, molecular processes inside each cell, as well as models of flow and transport in the tissue (Vartak et. al., Hepatology, 2021, Boissier et. al. International Journal for Numerical Methods in Biomedical Engineering, 37(2), e3422, 2020). 

These models are now being integrated into a mathematical virtual liver model that should be used for medical hypothesis testing.

Within the project STEDI-NASH the objective is to establish a model that can – guided by medical data – help to test whether and in how far histopathological information can be inferred from Magnetic resonance data.

The objective is to develop models and implement them to test this hypothesis in silico, guided by the experimental data from experimental and clinical collaborators.

The implementation will be done inside a novel tissue simulation code that is modular and maintained inside the team, which will help and guide in coding.

Regular visits of the collaborator within Paris region and occasional visits of other partners may be necessary.

Mission confiée

Assignements:

With the help of team members of SIMBIOTX, the recruited person will co-develop and implement model extensions permitting to simulate the diffusion of quasi-particles in a piece of a virtual liver tissue.

The model should contain steps as (1) particle-based simulation of a single or several randomly moving quasi-particles; (2) conversion of the movement into a signal similar as those obtained by MRI-spectroscopy.

The particle movement should occur in a virtual (digital) liver subunit (called lobule). Such a virtual liver lobule in healthy liver is sketched in Van Liedekerke et. al., Biomechanics and Modeling in Mechanobiology, 19, pages 189–220 (2020); Van Liedekerke et. al., Plos Comput Biol 15(3), e1006273 (2019);

More information on request from: dirk.drasdo@inria.fr.

Collaboration :

In a first step, the recruited person will work with several coworkers inside and of SIMBIOTX to discuss the possible model realization and learn about the software tool.

Responsibilities :

The candidate is responsible for pursuing and maintaining the contact between team and our clinical and medical collaborators, mostly at Hopital Beaujon, partially at Univ. Mannheim and IfADo, Dortmund.

 

Principales activités

Main activities (5 maximum) :

  • Co-development of model for diffusing quasi-particles in realistic virtual liver lobule structures and other microscopic structures used to calibrate the model.
  • Implementation of model on the computer
  • Running simulations on the computer
  • Maintaining regular interactions with medical/clinical collaborators
  • Writing reports / papers. 

Additional activities (3 maximum) :

  •  coordination of data-and information exchange with experimental and clinical partners.

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
  • C++ advanced level

Languages : English (main communication language), reasonable French (preferred by clinical partners)

Relational skills :

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

Other valued appreciated :

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 (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

Rémunération

2746 €/month gross salary