Paper Citing NAMD - Abstract
Gill, J. P.; Shaw, K. M.; Rountree, B. L.; Kehl, C. E.; Chiel, H. J.
Simulating Kinetic Processes in Time and Space on a Lattice
MATHEMATICAL MODELLING OF NATURAL PHENOMENA, 6:159-197, 2011
We have developed a chemical kinetics simulation that can be used as both an educational and research tool. The simulator is designed as an accessible, open-source project that can be run on a laptop with a student-friendly interface. The application can potentially be scaled to run in parallel for large simulations. The simulation has been successfully used in a classroom setting for teaching basic electrochemical properties. We have shown that this can be used for simulating fundamental molecular and chemical processes and even simplified models of predator-prey interactions. By giving the simulated entities spatial extent in the lattice, the particles do not interpenetrate, and clusters of particles can spatially exclude one another. Our simulation demonstrates that spatial inhomogeneity leads to different results than those that are obtained by using standard ordinary differential equation models, as previously reported.
