Fast Solution of the Linearized Poisson-Boltzmann Equation with nonaffine Parametrized Boundary Conditions Using the Reduced Basis Method
This work provides a proof-of-concept for accelerating electrostatic calculations in biomolecular modeling, which is important for structural biology but remains incremental due to the simplified PBE version used.
The authors apply the reduced basis method (RBM) to the linearized Poisson-Boltzmann equation, reducing the model order from 2×10^6 to 6 with 10^{-9} accuracy and achieving a 7,600-fold speedup in computational time.
The Poisson-Boltzmann equation (PBE) is a nonlinear elliptic PDE that arises in biomolecular modeling and is a fundamental tool for structural biology. It is used to calculate electrostatic potentials around an ensemble of fixed charges immersed in an ionic solution. Efficient numerical computation of the PBE yields a high number of degrees of freedom in the resultant algebraic system of equations. Coupled with the fact that in most cases the PBE requires to be solved multiple times for a large number of system configurations, this poses great computational challenges to conventional numerical techniques. To accelerate such computations, we here present the reduced basis method (RBM) which greatly reduces this computational complexity by constructing a reduced order model of typically low dimension. In this study, we employ a simple version of the PBE for proof of concept and discretize the linearized PBE (LPBE) with a centered finite difference scheme. The resultant linear system is solved by the aggregation-based algebraic multigrid method at different samples of ionic strength on a three-dimensional Cartesian grid. The discretized LPBE, which we call the high-fidelity full order model (FOM), yields solution as accurate as other LPBE solvers. We then apply the RBM to FOM. The discrete empirical interpolation method (DEIM) is applied to the Dirichlet boundary conditions which are nonaffine with the parameter, to reduce the complexity of the reduced order model (ROM). From the numerical results, we notice that the RBM reduces the model order from $\mathcal{N} = 2\times 10^{6}$ to $N = 6$ at an accuracy of $10^{-9}$ and reduces computational time by a factor of approximately $7,600$. DEIM, on the other hand, is also used in the offline-online phase of solving the ROM for different values of parameters which provides a speed-up of $20$ for a single iteration of the greedy algorithm.