Yuhua Song, Yongjie Zhang, Chandrajit L. Bajaj, Nathan A. Baker Continuum diffusion reaction rate calculations of wild type and mutant mouse acetylcholinesterase: adaptive finite element analysis As described previously (Song and others 2003), continuum models such as the Smoluchowski equation offer a scalable framework for studying diffusion in biomolecular systems. This paper presents new developments in the efficient solution of continuum diffusion equation. Specifically, we present new methods for adaptively refining finite element solutions of the Smoluchowski equation based on a posteriori error estimates. We also describe new, molecular-surface-based models, for diffusional reaction criteria and compare results obtained from these models with the traditional spherical criteria. The new methods are validated by comparison of the calculated reaction rates with experimental values for wild type and mutant forms mouse acetylcholinesterase (mAChE). The results show good agreement with experiment and help to define optimal reactive boundary conditions.