The Scripps Research Institute
General Agent Based Modeling in LAMMPS
The simulation of complex chains of chemical reactions that make life possible cannot be run with traditional molecular dynamics software. At the coarse grained level such simulations have been out of reach to scientists without writing thousands of lines of custom code. In this talk I will define a general language to describe the behavior of simple "agents" which can make decisions in response to collisions (or other changes in their local environment). When connected together, such agents can make intelligent decisions of arbitrary complexity, typically with just a few lines of code. Together with "fix bond/react" and MOLTEMPLATE, this new LAMMPS feature will enable biologists, chemists, and physicists to test hypothesis and simulate the emergent behavior of active matter in physics and in complex living systems. A variety of examples of processes in biology, chemistry, and physics will be shown.