ArticleBiophysical journal2004
Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: adaptive finite element analysis.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT).PLoS computational biology · 2018Article
- Improvements to the APBS biomolecular solvation software suite.Protein science : a publication of the Protein Society · 2018Article
- Hybrid finite element and Brownian dynamics method for charged particles.The Journal of chemical physics · 2016Article
- Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics.BMC biophysics · 2015Article
- Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes.Molecular based mathematical biology · 2013Article
- Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction.Computational science & discovery · 2012Article
- Differential geometry based solvation model II: Lagrangian formulation.Journal of mathematical biology · 2011Article
- MIBPB: a software package for electrostatic analysis.Journal of computational chemistry · 2011Article
- Differential geometry based solvation model I: Eulerian formulation.Journal of computational physics · 2010Article
- Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions.Journal of computational physics · 2010Article
- Finite element analysis of drug electrostatic diffusion: inhibition rate studies in N1 neuraminidase.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2009Article
- Diffusional channeling in the sulfate-activating complex: combined continuum modeling and coarse-grained brownian dynamics studies.Biophysical journal · 2008Article
- Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations.Biophysical journal · 2007Article
- Quality Meshing of Implicit Solvation Models of Biomolecular Structures.Computer aided geometric design · 2006Article
- Adaptive and Quality Quadrilateral/Hexahedral Meshing from Volumetric Data.Computer methods in applied mechanics and engineering · 2006Article
- Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods.Biophysical journal · 2005Article
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Authors and funding
4 authors.
Funding
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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