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Efficient and Stable Method to Solve Poisson–Boltzmann Equation with Steep Gradients

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Computational Electrostatics for Biological Applications

Abstract

This work describes a method to solve Poisson–Boltzmann Equation (PBE) with steep gradients when common methods of solving non-linear equations do not converge or work inefficiently. This is particularly the case for relatively large boundary conditions leading to rapid changes of the solution in a narrow interval. The method uses adaptive step in the region of abrupt change of the solution and adopts invertible mapping algorithm to transform the original PBE into a form with a smooth profile which ensures convergency and stability of the solution. The numerical tests demonstrate the advantages of the method compared to usual successive iteration methods, in which the solution is gradually approached by iterations from small values.

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References

  1. Wall FT, Berkowitz J (1957) Numerical solution to the Poisson-Boltzmann equation for spherical polyelectrolyte molecules. J Chem Phys 26(1):114–122

    Article  CAS  Google Scholar 

  2. Lu BZ, Zhou YC, Holst MJ, McCammon JA (2008) Recent progress in numerical methods for the Poisson-Boltzmann equation in biophysical applications. Commun Comput Phys 5(3): 973–1009

    Google Scholar 

  3. Klapper I, Hagstrom R, Fine R, Sharp K, Honig B (1986) Focusing of electric fields in the active site of CU-ZN superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins 1(1):47–59

    Article  CAS  PubMed  Google Scholar 

  4. Gilson MK, Honig B (1988) Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins 4(1):7–18

    Article  CAS  PubMed  Google Scholar 

  5. Nicholls A, Honig B (1991) A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J Comput Chem 12(4):435–445

    Article  CAS  Google Scholar 

  6. Thames FC, Thompson JF, Mastin CW, Walker RL (1977) Numerical solutions for viscous and potential flow about arbitrary two-dimensional bodies using body-fitted coordinate systems. J Comput Phys 24(3):245–273

    Google Scholar 

  7. Kakuda K, Tosaka N (1990) The generalized boundary element approach to Burgers’ equation. Int J Numer Methods Eng 29(2):245–261

    Article  Google Scholar 

  8. Zhang DS, Wei GW, Kouri DJ, Hoffman DK (1997) Burgers equation with high Reynolds number. Phys Fluids 9(6):1853

    Article  CAS  Google Scholar 

  9. Wei G, Zhang D, Kouri D, Hoffman D (1998) Distributed approximating functional approach to Burgers’ equation in one and two space dimensions. Comput Phys Commun 111(1–3):93109

    Google Scholar 

  10. Hoffman DK, Nayar N, Sharafeddin OA, Kouri DJ (1991) Analytic banded approximation for the discretized free propagator. J Phys Chem 95(21):8299–8305

    Article  CAS  Google Scholar 

  11. Hoffman DK, Kouri DJ (1992) Distributed approximating function theory: a general, fully quantal approach to wave propagation. J Phys Chem 96(3):1179–1184

    Article  CAS  Google Scholar 

  12. Huang B, Baulin VA (2013) IPEC solver: numerical simulation tool to study inter-polyelectrolyte complexation. Comput Phys Commun 184(9):2221–2229

    Article  CAS  Google Scholar 

  13. Baulin VA, Trizac E (2012) Self-assembly of spherical interpolyelectrolyte complexes from oppositely charged polymers. Soft Matter 8(25):6755–6766

    Article  CAS  Google Scholar 

  14. Trizac E, Tellez G (2006) Onsager-Manning-Oosawa condensation phenomenon and the effect of salt. Phys Rev Lett 96(3):038302

    Google Scholar 

  15. Gear CW (1971) Numerical initial value problems in ordinary differential equations. Prentice-Hall, Englewood Cliffs

    Google Scholar 

  16. Kelley CT (2003) Solving nonlinear equations with Newton’s method. Society for Industrial and Applied Mathematics, Philadelphia

    Book  Google Scholar 

  17. Press WH (2007) Numerical recipes: the art of scientific computing. Cambridge University Press, Cambridge

    Google Scholar 

Download references

Acknowledgments

Authors thanks Prof G. Wei from Department of Mathematics, Michigan State University. BH thanks NFS grant No.11001257 for computer equipment.

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Correspondence to Vladimir A. Baulin .

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Huang, B., Baulin, V.A. (2015). Efficient and Stable Method to Solve Poisson–Boltzmann Equation with Steep Gradients. In: Rocchia, W., Spagnuolo, M. (eds) Computational Electrostatics for Biological Applications. Springer, Cham. https://doi.org/10.1007/978-3-319-12211-3_5

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