%0 Journal Article %1 Song_2004_1558 %A Song, Yuhua %A Zhang, Yongjie %A Bajaj, Chandrajit L %A Baker, Nathan A %D 2004 %J Biophys. J. %K , 15345536 Acetylcholine, Acetylcholinesterase, Activation, Adrenergic Adrenergic, Alcohols, 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 Gov't, Hemiterpenes, Humans, Indoles, Ions, Kinetics, Leucine, Ligands, Line, Lymphocyte Mice, Models, Molecular, Multiprotein Muscle Mutation, Myocytes, Newborn, Non-P.H.S., Non-U.S. Norepinephrine, Organophosphorus P.H.S., Piperazines, Prazosin, Protein Proteins, Rats, Receptors, Relationship, Reproducibility Research Results, Simulation, Sites, Sprague-Dawley, Statistical, Stereoisomerism, Study, Subsets, Support, T-Cell, T-Lymphocyte Theoretical, Time Tumor, U.S. alpha-1, alpha-Agonists, alpha-Antagonists, gamma-delta, of ysis, %N 3 %P 1558--1566 %R 10.1529/biophysj.104.041517 %T Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: adaptive finite element analysis. %U http://dx.doi.org/10.1529/biophysj.104.041517 %V 87 %X 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.

@article{Song_2004_1558, 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.}, added-at = {2009-06-03T11:20:58.000+0200}, author = {Song, Yuhua and Zhang, Yongjie and Bajaj, Chandrajit L and Baker, Nathan A}, biburl = {https://www.bibsonomy.org/bibtex/23eab27045a6992f05fd341bcd0ec3ec0/hake}, description = {The whole bibliography file I use.}, doi = {10.1529/biophysj.104.041517}, file = {Song_2004_1558.pdf:Song_2004_1558.pdf:PDF}, interhash = {9998718cb1c3444829f41696ca418c1c}, intrahash = {3eab27045a6992f05fd341bcd0ec3ec0}, journal = {Biophys. J.}, keywords = {, 15345536 Acetylcholine, Acetylcholinesterase, Activation, Adrenergic Adrenergic, Alcohols, 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 Gov't, Hemiterpenes, Humans, Indoles, Ions, Kinetics, Leucine, Ligands, Line, Lymphocyte Mice, Models, Molecular, Multiprotein Muscle Mutation, Myocytes, Newborn, Non-P.H.S., Non-U.S. Norepinephrine, Organophosphorus P.H.S., Piperazines, Prazosin, Protein Proteins, Rats, Receptors, Relationship, Reproducibility Research Results, Simulation, Sites, Sprague-Dawley, Statistical, Stereoisomerism, Study, Subsets, Support, T-Cell, T-Lymphocyte Theoretical, Time Tumor, U.S. alpha-1, alpha-Agonists, alpha-Antagonists, gamma-delta, of ysis,}, month = Sep, number = 3, pages = {1558--1566}, pii = {87/3/1558}, pmid = {15345536}, timestamp = {2009-06-03T11:21:32.000+0200}, title = {Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: adaptive finite element analysis.}, url = {http://dx.doi.org/10.1529/biophysj.104.041517}, volume = 87, year = 2004 }