COMP 178

1) Although the principles of reaction kinetics apply to biological systems, these systems differ from industrial-scale chemical systems in a fundamental way: they are far from the thermodynamic limit. Using deterministic, ordinary differential equations for simulating the reaction kinetics assumes the absence of thermal, stochastic noise in biomolecular systems. This can indeed be distinctly false. We will explore the limitations of traditional mathematical frameworks and detail the multiscale algorithms we developed to properly capture biological complexity.

2) We will present simulations of antimicrobial peptides in water, in micelles and in lipid bilayers. The simulations provide insight in the molecular phenomena that impact the antimicrobial activity and host toxicity profiles of these peptides. This insight can prove invaluable in engineering novel AMPS with therapeutic potential.