Mots-Clés
Extracellular Matrix (ECM)
Mesoscopic Modeling
Molecular Modeling
Biomolecular Simulations
Biophysics
Description
Mesoscopic Modeling of the Basement Membrane with DURABIN
Background
The extracellular matrix (ECM) is a complex three-dimensional network of macromolecules that
contributes to tissue architecture. Understanding how its organization influences its physical
properties is important for studying many biological and pathological processes. However,
studying the ECM at the molecular scale remains limited by the computational cost of atomistic
simulations. In contrast, a mesoscopic approach can represent large-scale systems while
retaining a description of their structural organization. The MEDyC laboratory is developing
DURABIN1,2, a modeling software designed to construct and analyze mesoscopic
representations of the extracellular matrix. This approach represents different ECM components
as molecular objects that can be assembled into complex three-dimensional architectures. The
developers of DURABIN are also members of the laboratory, providing a favorable environment for
learning and using the software.
This internship aims to build and compare mesoscopic models of the basement membrane using
DURABIN. Different basement membrane compositions, varying the proportions of type IV
collagen, laminins, and proteoglycans, will be generated, analyzed, and compared. This work will
establish the models that will serve as a starting point for studying their mechanical behavior
under compression and stretching as part of a PhD project.
Candidate profile
We are looking for a motivated Master 2 student interested in an interdisciplinary approach and in
the modeling of biological systems. Previous experience in programming (Python, C#, or another
language), molecular modeling (Modeller, AlphaFold), or numerical simulation (CHARMM,
Gromacs, NAMD, etc.) is an advantage, but training will be provided on the tools specific to the
project. This internship is part of a broader research project dedicated to the mesoscopic
modeling of extracellular matrix mechanics under compression and stretching. A PhD position
may be considered following the internship, depending on the candidate’s profile and
performance.
References
(1) Wong, H.; Prévoteau-Jonquet, J.; Baud, S.; Dauchez, M.; Belloy, N. Mesoscopic Rigid Body Modelling of the
Extracellular Matrix Self-Assembly. Journal of Integrative Bioinformatics 2018, 15 (2). https://doi.org/10.1515/jib-2018-
0009
(2) Depenveiller, C.; Wong, H.; Crowet, J. M.; Debelle, L.; Baud, S.; Dauchez, M.; Belloy, N. Challenging Level of Rigid-
Body Approach Involving Numerical Elements (CHLORAINE) Applied to Repeated Elastin Peptides. Journal of Structural
Biology 2023, 215 (3), 107986. https://doi.org/10.1016/j.jsb.2023.107986