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- Title
Vesicle and reaction-diffusion hybrid modeling with STEPS.
- Authors
Hepburn, Iain; Lallouette, Jules; Chen, Weiliang; Gallimore, Andrew R.; Nagasawa-Soeda, Sarah Y.; De Schutter, Erik
- Abstract
Vesicles carry out many essential functions within cells through the processes of endocytosis, exocytosis, and passive and active transport. This includes transporting and delivering molecules between different parts of the cell, and storing and releasing neurotransmitters in neurons. To date, computational simulation of these key biological players has been rather limited and has not advanced at the same pace as other aspects of cell modeling, restricting the realism of computational models. We describe a general vesicle modeling tool that has been designed for wide application to a variety of cell models, implemented within our software STochastic Engine for Pathway Simulation (STEPS), a stochastic reaction-diffusion simulator that supports realistic reconstructions of cell tissue in tetrahedral meshes. The implementation is validated in an extensive test suite, parallel performance is demonstrated in a realistic synaptic bouton model, and example models are visualized in a Blender extension module. A computational study describing a parallel extension to software "STochastic Engine for Pathway Simulation" that simulates vesicles and their interactions with the cellular environment, including endocytosis, docking, fusion and active transport.
- Subjects
ACTIVE biological transport; BIOLOGICAL transport; CELL physiology; ENDOCYTOSIS; EXOCYTOSIS; POLYMERSOMES
- Publication
Communications Biology, 2024, Vol 7, Issue 1, p1
- ISSN
2399-3642
- Publication type
Article
- DOI
10.1038/s42003-024-06276-5