Nonlocal Electrostatics in Spherical Geometries Using Eigenfunction Expansions of Boundary-Integral Operators.

Jaydeep P Bardhan, Matthew G Knepley, Peter Brune
Author Information
  1. Jaydeep P Bardhan: Dept. of Mechanical and Industrial Engineering, Northeastern University, Boston MA 02115.
  2. Matthew G Knepley: Computation Institute, University of Chicago, Chicago IL 60637.
  3. Peter Brune: Google Inc., Mountain View CA 94041.

Abstract

In this paper, we present an exact, infinite-series solution to Lorentz nonlocal continuum electrostatics for an arbitrary charge distribution in a spherical solute. Our approach relies on two key steps: (1) re-formulating the PDE problem using boundary-integral equations, and (2) diagonalizing the boundary-integral operators using the fact that their eigenfunctions are the surface spherical harmonics. To introduce this uncommon approach for calculations in separable geometries, we first re-derive Kirkwood's classic results for a protein surrounded concentrically by a pure-water ion-exclusion (Stern) layer and then a dilute electrolyte, which is modeled with the linearized Poisson-Boltzmann equation. The eigenfunction-expansion approach provides a computationally efficient way to test some implications of nonlocal models, including estimating the reasonable range of the nonlocal length-scale parameter λ. Our results suggest that nonlocal solvent response may help to reduce the need for very high dielectric constants in calculating pH-dependent protein behavior, though more sophisticated nonlocal models are needed to resolve this question in full. An open-source MATLAB implementation of our approach is freely available online.

References

  1. J Chem Phys. 2011 Sep 28;135(12):124107 [PMID: 21974512]
  2. Biopolymers. 1986 Nov;25(11):2097-119 [PMID: 3790703]
  3. J Chem Phys. 2004 Mar 1;120(9):4457-66 [PMID: 15268613]
  4. Biophys J. 1997 Oct;73(4):1830-41 [PMID: 9336178]
  5. Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10037-41 [PMID: 11517324]
  6. Proteins. 2001 Sep 1;44(4):400-17 [PMID: 11484218]
  7. J Phys Chem B. 2008 Jan 24;112(3):938-46 [PMID: 18171044]
  8. Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11145-50 [PMID: 10500144]
  9. J Phys Chem B. 2008 Jul 31;112(30):9020-41 [PMID: 18593145]
  10. J Chem Phys. 2012 Sep 28;137(12):124101 [PMID: 23020318]
  11. J Chem Phys. 2011 Sep 14;135(10):104113 [PMID: 21932882]
  12. J Chem Phys. 2010 Feb 14;132(6):064101 [PMID: 20151727]
  13. J Mol Biol. 1982 Jun 5;157(4):671-9 [PMID: 6288964]
  14. Bioinformatics. 2007 Jan 15;23(2):e99-103 [PMID: 17237112]
  15. J Mech Behav Mater. 2013 Dec;22(5-6):169-184 [PMID: 25505358]
  16. Biopolymers. 2007 Oct 5-15;87(2-3):149-64 [PMID: 17626298]
  17. J Comput Chem. 2009 Jan 15;30(1):132-53 [PMID: 18567005]
  18. Biophys J. 2004 Sep;87(3):1544-57 [PMID: 15345535]
  19. Biophys Chem. 1999 Apr 5;78(1-2):1-20 [PMID: 17030302]
  20. Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Aug;82(2 Pt 1):021915 [PMID: 20866845]
  21. Phys Rev Lett. 2004 Sep 3;93(10):108104 [PMID: 15447456]
  22. Biophys J. 2008 Dec 15;95(12):5587-605 [PMID: 18820239]
  23. Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11146-51 [PMID: 18678891]
  24. Biophys Chem. 1999 Apr 5;78(1-2):89-96 [PMID: 17030305]
  25. J Chem Phys. 2005 Mar 1;122(9):094511 [PMID: 15836154]
  26. J Phys Chem B. 2012 Aug 16;116(32):9776-83 [PMID: 22762271]
  27. J Chem Phys. 2006 Mar 28;124(12):124902 [PMID: 16599720]
  28. Proc Natl Acad Sci U S A. 2006 Dec 19;103(51):19314-9 [PMID: 17148613]
  29. Biophys J. 1998 Apr;74(4):1744-53 [PMID: 9545037]

Grants

  1. R21 GM102642/NIGMS NIH HHS

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