pSpatiocyte

pSpatiocyte simulates three-dimensional diffusion and reaction processes on a hexagonal close-packed (HCP) lattice to model intracellular molecular dynamics including diffusion-limited reactions and volume exclusion due to molecular crowding.

Key Features:

• Lattice-Based Simulation: Captures individual diffusing molecules on an HCP lattice with explicit particle representation, supporting diffusion-limited reactions and volume exclusion from molecular crowding.
• Parallelization: Implements specialized coordinate systems, parallelized event schedulers, and Gillespie’s direct method for efficient simulation of large or crowded intracellular compartments.
• Performance: Achieves up to 74% parallel efficiency and a speedup of 7686 times with 663552 cores compared to 64 cores in fine lattice discretization scenarios, maintaining at least 60% efficiency across up to 663552 cores.

Scientific Applications:

• Intracellular Dynamics: Constructs physically accurate models integrating experimental data on intracellular molecular distributions and simulates complex reaction networks such as the MAPK system dual phosphorylation-dephosphorylation cycle.

Methodology:

pSpatiocyte employs simultaneous simulation using mass action kinetics, Gillespie Next-Reaction, Gillespie’s direct method, and lattice-based particle diffusion and reaction algorithms.