First version submitted: 31 March 2015. Submission of split papers: June 7 & June 12. Accepted: 4 Sept. & 26 Dec. 2015. UPDATE: The material in the original manuscript was split in two papers, submitted to different peer-reviewed journals. The editorial decision on the first submission was that the paper was out of scope... Continue »
Submitted: 20 September, 2013. Accepted: 24 October, 2013. This paper presents a study of the effect of solvent-filled cavities and Stern layers in a biomolecular electrostatics solver based on a boundary integral formulation. The tool for this study was the PyGBe code: a solver for biomolecular electrostatics using Python, GPUs and boundary elements. To determine... Continue »
Poster presented at the GPU Technology Conference, March 2013, San Jose, CA.
It presents the PyGBe code (pronounced 'pig-bee'), which solves the linearized Poisson-Boltzmann equation using a boundary element method, BEM. The underlying dense systems are solved using a Krylov-subspace method, accelerated with... Continue »
The PyGBe code solves the linearized Poisson-Boltzmann equation using a boundary-integral formulation. We use a boundary element method with a collocation approach, and solve it via a Krylov-subspace method. To do this efficiently, the matrix-vector multiplications in the Krylov iterations are accelerated with a... Continue »