Affiliations: Project CyberCell™, Institute for Biomolecular
Design, 3-67, Medical Sciences Bldg, University of Alberta, Edmonton, Alberta,
Canada, T6G 2H7
Abstract: A framework is presented that captures the discrete and
probabilistic nature of molecular transport and reaction kinetics found in a
living cell as well as formally representing the spatial distribution of these
phenomena. This particle or agent-based approach is computationally robust and
complements established methods. Namely it provides a higher level of spatial
resolution than formulations based on ordinary differential equations (ODE)
while offering significant advantages in computational efficiency over
molecular dynamics (MD). Using this framework, a model cell membrane has been
constructed with discrete particle agents that respond to local component
interactions that resemble flocking or herding behavioural cues in animals.
Results from simulation experiments are presented where this model cell
exhibits many of the characteristic behaviours associated with its biological
counterpart such as lateral diffusion, response to osmotic pressure gradients,
membrane growth and cell division. Lateral diffusion rates and estimates for
the membrane modulus of elasticity derived from these simple experiments fall
well within a biologically relevant range of values. More importantly, these
estimates were obtained by applying a simple qualitative tuning of the model
membrane. Membrane growth was simulated by injecting precursor molecules into
the proto-cell at different rates and produced a variety of morphologies
ranging from a single large cell to a cluster of cells. The computational
scalability of this methodology has been tested and results from benchmarking
experiments indicate that real-time simulation of a complete bacterial cell
will be possible within 10 years.
