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Published on: September 30, 2014
Bridging Eulerian and Lagrangian Poisson-Boltzmann solvers by ESES.
Sheik Ahmed Ullah1, Xin Yang2, Ben Jones3
1Model Risk, Regions Bank, Birmingham, Alabama, USA.
Journal of Computational Chemistry
|October 13, 2023
Summary
This study validates the Eulerian Solvent Excluded Surface (ESES) software for biomolecular electrostatic analysis. ESES enables accurate comparisons of Poisson-Boltzmann (PB) solvers and validates a key PB model property.
Area of Science:
- Computational chemistry
- Biophysics
- Molecular modeling
Background:
- The Poisson-Boltzmann (PB) model is essential for analyzing biomolecular solvation.
- Accurate numerical solutions depend on molecular surface generation.
- Eulerian and Lagrangian mesh-based solvers exist for PB models.
Purpose of the Study:
- To investigate the Eulerian Solvent Excluded Surface (ESES) software for generating surface representations.
- To enable numerical validation and comparison of Eulerian and Lagrangian PB solvers.
- To numerically validate a source-target symmetric property of the linearized PB model.
Main Methods:
- Utilized ESES software to generate conjugated Eulerian and Lagrangian surface representations.
- Employed ESES-associated PB solvers, including MIBPB (Eulerian) and TABI-PB (Lagrangian).
- Performed numerical validation and comparison of different PB solver types.
Main Results:
- ESES software effectively renders both Eulerian and Lagrangian surface representations.
- Facilitated accurate numerical validation and comparison of Eulerian and Lagrangian PB solvers.
- Successfully validated the source-target symmetric property of the linearized PB model.
Conclusions:
- ESES software is a valuable tool for assessing PB solver accuracy and efficiency.
- The study confirms the utility of ESES in comparing diverse PB numerical approaches.
- Numerical validation of the linearized PB model's symmetric property is achieved.
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