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.
Пожалуйста, войдите в систему, чтобы принять участие в дискуссии (добавить собственные рецензию, или комментарий)
Цитировать эту публикацию
%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
}