Hybrid vesicle and reaction-diffusion modeling with STEPS

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. As computational power advances and researchers want to add new realism to their models an important advance in the field of computational biology is to simulate vesicles in a realistic yet efficient manner. We describe a general vesicle modeling tool that has been designed for wide application to a variety of cell models, implemented within our voxel-based approach to modeling reaction-diffusion processes in realistic mesh reconstructions of cell tissue in our software STEPS. The implementation is validated in an extensive test suite, parallel performance demonstrated in a realistic synaptic bouton model, and example models are visualized in a Blender extension module.