Efficient solution technique for solving the Poisson-Boltzmann equation

Creative Commons License

Sayyed-Ahmad A., Tuncay K., Ortoleva P.

JOURNAL OF COMPUTATIONAL CHEMISTRY, cilt.25, sa.8, ss.1068-1074, 2004 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 25 Sayı: 8
  • Basım Tarihi: 2004
  • Doi Numarası: 10.1002/jcc.20039
  • Dergi Adı: JOURNAL OF COMPUTATIONAL CHEMISTRY
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Sayfa Sayıları: ss.1068-1074
  • Anahtar Kelimeler: Poisson-Boltzmann, electrostatics, finite difference method, MULTIGRID SOLUTION, ELEMENT SOLUTION, SOLVENT, MACROMOLECULES, MOLECULES, DYNAMICS, PROTEINS, CHARGE, MODEL, IONS
  • Orta Doğu Teknik Üniversitesi Adresli: Hayır

Özet

The Poisson-Boltzmann (PB) equation has been extensively used to analyze the energetics and structure of proteins and other significant biomolecules immersed in electrolyte media. A new highly efficient approach for solving PB-type equations that allows for the modeling of many-atoms structures such as encountered in cell biology, virology, and nanotechnology is presented. We accomplish these efficiencies by reformulating the elliptic PB equation as the long-time solution of an advection-diffusion equation. An efficient modified, memory optimized, alternating direction implicit scheme is used to integrate the reformulated PB equation. Our approach is demonstrated on protein composites (a polio virus capsid protomer and a pentamer). The approach has great potential for the analysis of supramillion atoms immersed in a host electrolyte. (C) 2004 Wiley Periodicals, Inc.