Document Detail


Exploring a charge-central strategy in the solution of Poisson's equation for biomolecular applications.
MedLine Citation:
PMID:  23147243     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Continuum solvent treatments based on the Poisson-Boltzmann equation have been widely accepted for energetic analysis of biomolecular systems. In these approaches, the molecular solute is treated as a low dielectric region and the solvent is treated as a high dielectric continuum. The existence of a sharp dielectric jump at the solute-solvent interface poses a challenge to model the solvation energetics accurately with such a simple mathematical model. In this study, we explored and evaluated a strategy based on the "induced surface charge" to eliminate the dielectric jump within the finite-difference discretization scheme. In addition to the use of the induced surface charges in solving the equation, the second-order accurate immersed interface method is also incorporated to discretize the equation. The resultant linear system is solved with the GMRES algorithm to explicitly impose the flux conservation condition across the solvent-solute interface. The new strategy was evaluated on both analytical and realistic biomolecular systems. The numerical tests demonstrate the feasibility of utilizing induced surface charge in the finite-difference solution of the Poisson-Boltzmann equation. The analysis data further show that the strategy is consistent with theory and the classical finite-difference method on the tested systems. Limitations of the current implementations and further improvements are also analyzed and discussed to fully bring out its potential of achieving higher numerical accuracy.
Authors:
Xingping Liu; Changhao Wang; Jun Wang; Zhilin Li; Hongkai Zhao; Ray Luo
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2012-11-13
Journal Detail:
Title:  Physical chemistry chemical physics : PCCP     Volume:  15     ISSN:  1463-9084     ISO Abbreviation:  Phys Chem Chem Phys     Publication Date:  2013 Jan 
Date Detail:
Created Date:  2012-12-11     Completed Date:  2013-05-13     Revised Date:  2014-01-16    
Medline Journal Info:
Nlm Unique ID:  100888160     Medline TA:  Phys Chem Chem Phys     Country:  England    
Other Details:
Languages:  eng     Pagination:  129-41     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Computer Simulation
Models, Chemical
Models, Molecular
Proteins / chemistry*
Small Molecule Libraries / chemistry*
Solvents
Static Electricity
Thermodynamics
Grant Support
ID/Acronym/Agency:
R01 GM093040/GM/NIGMS NIH HHS; R01 GM096195/GM/NIGMS NIH HHS; R01GM093040/GM/NIGMS NIH HHS; R01GM79383/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Proteins; 0/Small Molecule Libraries; 0/Solvents
Comments/Corrections

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