Lorena A. Barba group


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Probing protein orientation near charged surfaces

Figure from our paper on probing protein orientation near charged surfaces.

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 »

Accepted: Biomolecular electrostatics solver using Python and GPUs

Surface charge plot on a lysozyme molecule, obtained using the PyGBe code.

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 »

Validation of the PyGBe code for Poisson-Boltzmann equation

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 »

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