A GPU-accelerated Direct-sum Boundary Integral Poisson-Boltzmann Solver

In this paper, we present a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov subspace based linear algebraic solver such as the GMRES. The molecular surfaces are discretized with flat triangles and centroid collocation. To speed up our method, we take advantage of the parallel nature of the boundary integral formulation and parallelize the schemes within CUDA shared memory architecture on GPU. The schemes use only $11N+6N_c$ size-of-double device memory for a biomolecule with $N$ triangular surface elements and $N_c$ partial charges. Numerical tests of these schemes show well-maintained accuracy and fast convergence. The GPU implementation using one GPU card (Nvidia Tesla M2070) achieves 120-150X speed-up to the implementation using one CPU (Intel L5640 2.27GHz). With our approach, solving PB equations on well-discretized molecular surfaces with up to 300,000 boundary elements will take less than about 10 minutes, hence our approach is particularly suitable for fast electrostatics computations on small to medium biomolecules

The self-consistent quantum-electrostatic problem in strongly non-linear regime

The self-consistent quantum-electrostatic (also known as Poisson-Schr\"odinger) problem is notoriously difficult in situations where the density of states varies rapidly with energy. At low temperatures, these fluctuations make the problem highly non-linear which renders iterative schemes deeply unstable. We present a stable algorithm that provides a solution to this problem with controlled accuracy. The technique is intrinsically convergent including in highly non-linear regimes. We illustrate our approach with (i) a calculation of the compressible and incompressible stripes in the integer quantum Hall regime and (ii) a calculation of the differential conductance of a quantum point contact geometry. Our technique provides a viable route for the predictive modeling of the transport properties of quantum nanoelectronics devices.Comment: 28 pages. 14 figures. Added solution to a potential failure mode of the algorith