Abstract
As described previously, continuum models, such as the Smoluchowski
equation, offer a scalable framework for studying diffusion in biomolecular
systems. This work presents new developments in the efficient solution
of the continuum diffusion equation. Specifically, we present 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 boundary
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 of mouse acetylcholinesterase. The
results show good agreement with experiment and help to define optimal
reactive boundary conditions.
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- acetylcholine,
- acetylcholinesterase,
- activation,
- adrenergic
- adrenergic,
- alcohols,
- alpha-1,
- alpha-agonists,
- alpha-antagonists,
- anal,
- animals,
- antigen,
- antigens,
- binding
- binding,
- cardiac,
- cell
- cells,
- chemical,
- comparative
- complexes,
- compounds,
- computer
- conformation,
- crystallization,
- crystallography,
- cultured,
- diffusion,
- dioxanes,
- dose-response
- drug,
- element
- enlargement,
- factors,
- finite
- gamma-delta,
- gov't,
- hemiterpenes,
- humans,
- indoles,
- ions,
- kinetics,
- leucine,
- ligands,
- line,
- lymphocyte
- mice,
- models,
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