Mesoscopic Rigid Body Modelling of the Extracellular Matrix Self-Assembly

Autor: Jessica Prevoteau-Jonquet, Stéphanie Baud, Nicolas Belloy, Manuel Dauchez, Hua Wong
Přispěvatelé: Plateau Technique de Modélisation Moléculaire Multi-échelle (P3M), Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS)
Jazyk: angličtina
Rok vydání: 2018
Předmět:
0301 basic medicine
rigid bodies
Computer science
[SDV]Life Sciences [q-bio]
Models
Biological
Extracellular matrix
User-Computer Interface
03 medical and health sciences
Imaging
Three-Dimensional
Humans
Computer Simulation
[INFO]Computer Science [cs]
Physics engine
Research Articles
ComputingMilieux_MISCELLANEOUS
Haptic technology
Flexibility (engineering)
Mesoscopic physics
030102 biochemistry & molecular biology
interactive simulation
Proteins
General Medicine
Rigid body dynamics
Rigid body
[INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation
Extracellular Matrix
[SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Biophysics
030104 developmental biology
Sandbox (computer security)
virtual reality
Biological system
Heparan Sulfate Proteoglycans
Software
TP248.13-248.65
Biotechnology
Zdroj: Journal of Integrative Bioinformatics, Vol 15, Iss 2, Pp 690-1 (2018)
Journal of Integrative Bioinformatics
Journal of Integrative Bioinformatics, Informationsmanagement in der Biotechnologie e.V. (IMBio e.V.), 2018, ⟨10.1515/jib-2018-0009⟩
ISSN: 1613-4516
DOI: 10.1515/jib-2018-0009⟩
Popis: The extracellular matrix (ECM) plays an important role in supporting tissues and organs. It even has a functional role in morphogenesis and differentiation by acting as a source of active molecules (matrikines). Many diseases are linked to dysfunction of ECM components and fragments or changes in their structures. As such it is a prime target for drugs. Because of technological limitations for observations at mesoscopic scales, the precise structural organisation of the ECM is not well-known, with sparse or fuzzy experimental observables. Based on the Unity3D game and physics engines, along with rigid body dynamics, we propose a virtual sandbox to model large biological molecules as dynamic chains of rigid bodies interacting together to gain insight into ECM components behaviour in the mesoscopic range. We have preliminary results showing how parameters such as fibre flexibility or the nature and number of interactions between molecules can induce different structures in the basement membrane. Using the Unity3D game engine and virtual reality headset coupled with haptic controllers, we immerse the user inside the corresponding simulation. Untrained users are able to navigate a complex virtual sandbox crowded with large biomolecules models in a matter of seconds.
Databáze: OpenAIRE
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