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Finite Element Modelling of a Cellular Electric Microenvironment
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mFES: A Robust Molecular Finite Element Solver for Electrostatic Energy Computations.

I Sakalli1, J Schöberl2, E W Knapp1

  • 1Freie Universität Berlin , Institute of Chemistry and Biochemistry, Fabeckstr. 36a, Berlin 14195, Germany.

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|November 20, 2015
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Summary
This summary is machine-generated.

We developed a robust finite element (FE) method for calculating electrostatic potentials in large molecules. This adaptive grid approach offers high accuracy and efficiency, outperforming traditional finite difference (FD) methods for complex systems.

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Electrostatics

Background:

  • Calculating electrostatic potentials is crucial for understanding molecular interactions.
  • Traditional finite difference (FD) methods struggle with accuracy and efficiency for large molecular systems.
  • Adaptive grids offer potential for improved computational performance.

Purpose of the Study:

  • To present a robust and efficient method for calculating electrostatic potentials of large molecular systems.
  • To demonstrate the advantages of the finite element (FE) method with adaptive grids over conventional FD methods.
  • To provide a free and accessible computational tool (mFES) for researchers.

Main Methods:

  • Utilized tetrahedral finite elements (FE) for solving the Poisson equation.
  • Employed an adaptive grid strategy with grid points placed on molecular surfaces.
  • Reduced grid point density towards the asymptotic boundary for efficiency.
  • Applied tools to regularize the grid for a stable linear system.
  • Incorporated second-order polynomials as shape functions to enhance accuracy.

Main Results:

  • Achieved high accuracy and efficiency in electrostatic potential calculations for large molecular systems.
  • Demonstrated significant reduction in unknowns and solver execution times compared to FD methods.
  • Showcased the method's advantage for systems too large for conventional FD approaches.
  • Validated the method's utility in pKA and redox potential computations for proteins.

Conclusions:

  • The finite element (FE) method with adaptive grids provides a powerful and accurate approach for electrostatic potential calculations.
  • This method is particularly beneficial for large molecular systems and repeated calculations on the same geometry.
  • The mFES program offers a valuable, free resource for the scientific community.