PSU Mark
Eberly College of Science Mathematics Department

Meeting Details

For more information about this meeting, contact Qingtian Zhang.

Title:Accurate and Efficient Interface Methods for Implicitly Solvated Biomolecular Simulation
Seminar:Mathematical Biology and Physiology Seminar
Speaker:Weihua Geng, Southern Methodist University
Abstract:
The Poisson-Boltzmann (PB) model is an effective implicit solvent approach for simulating solvated biomolecular systems. By treating the solvent with a mean field approximation and capturing the mobile ions with the Boltzmann distribution, the PB model largely reduces the degree of freedom and computational cost. However, solving the PB equation suffers many numerical difficulties arising from interface jump conditions, complex geometry, charge singularities, and boundary conditions at infinity. In order to overcome these difficulties, two interface methods with different formulation and discretization are investigated. The first approach is the matched interface and boundary (MIB) method. This finite difference meshed method repeatedly uses interface jump conditions to capture the non-smoothness of solutions, adaptively applies local interpolation to characterize the complex geometry, and analytically takes Green's function based decomposition to regularize the singularities of the source terms. By computing a series of benchmark tests, the MIB-PB solver shows a solid 2nd order convergence thus stands out among Cartesian grid based PB solvers. The second approach is the treecode-accelerated boundary integral (TABI) method, which adopts a well-conditioned boundary integral formulation to handle aforementioned difficulties while accelerates the Krylov subspace based iterative methods such as GMRES with Cartesian treecode. This treecode is an O(N*logN) scheme with properties of easy implementation, efficient memory usage, infrequent communication, and straightforward parallelization. In addition, the treecode/boundary integral scheme can be conveniently implemented on GPUs. Numerical tests show 100+ times speed-up on a single GPU card, potentially making it possible to run PB model based molecular dynamics simulation for billions of time-steps.

Room Reservation Information

Room Number:MB216
Date:10 / 24 / 2013
Time:11:00am - 01:00pm