José Colmenares

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The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic(More)
SUMMARY In this work, we present a CUDA-based GPU implementation of a Poisson-Boltzmann equation solver, in both the linear and non-linear versions, using double precision. A finite difference scheme is adopted and made suitable for the GPU architecture. The resulting code was interfaced with the electrostatics software for biomolecules DelPhi, which is(More)
In this work an implementation of a linearized Poisson-Boltzmann equation solver based on a Finite Differences scheme on the GPU architecture is presented. The algorithm exploits the checkerboard structure of the discretized Laplace operator and follows the footprints of a popular solver called DelPhi, which is widely used in the Computational Biology(More)
A proper and efficient representation of molecular surfaces is an important issue in biophysics from several view points. Molecular surfaces indeed are used for different aims, in particular for visualization, as support tools for biologists, computation, in electrostatics problems involving implicit solvents (e.g. while solving the Poisson-Boltzmann(More)
The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades, the amount of data(More)
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