Abstract

We present a new style of molecular dynamics and self-assembly simulation, the Lattice Polymer Automaton [LPA]. In the LPA all interactions, including electromagnetic forces, are decomposed and communicated via propagating particles, "photons". The monomer-monomer bond forces, the molecular excluded volume forces, the longer range intermolecular forces, and the polymer-solvent interactions may all be modeled with propagating particles. The LPA approach differs significantly from both of the standard approaches, Monte Carlo lattice methods and Molecular Dynamics simulations. On the one hand, the LPA provides more realism than Monte Carlo methods, because it produces a time series of configurations of a single molecule, rather than a set of causally unrelated samples from a distribution of configurations. The LPA can therefore be used directly to study dynamical properties; one can in fact watch polymers move in real time. On the other hand, the LPA is fully discrete, and therefore much ...

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