Efficient solution technique for solving the Poisson-Boltzmann equation.
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.
Sayyed-Ahmad
Abdallah
A
Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
Tuncay
Kagan
K
Ortoleva
Peter J
PJ
D000465:Algorithms; D002213:Capsid / Q000737:chemistry; D008962:Models, Theoretical; D016012:Poisson Distribution; D017955:Poliovirus / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity
D011506:Proteins