PhD student Christopher Cooper
Christopher Cooper was a visiting student at University of Bristol, UK, for eight months, funded by Prof. Barba's EC grant Scientific Computing Advanced Training, SCAT. He started PhD studies at Boston University in Spring 2010 and his PhD research involved boundary element method solutions to problems of biomolecular electrostatics, using GPU hardware.
Chris graduated in May 2015 and became a faculty member in the Department of Mechanical Engineering at Universidad Técnica Federico Santa María, in Valparaíso, Chile (where both he and Prof. Barba did their undergraduate studies).
- "Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the PyGBe code", Christopher D. Cooper, Lorena A. Barba. Comput. Phys. Comm., 202:23-32 (May 2016). 10.1016/j.cpc.2015.12.019 // Preprint arXiv:1506.03745 // Code repository // manuscript repository // figshare: grid convergence, spherical surfaces // figshare: grid convergence on protein GB1
Accepted 26 Dec. 2015
- "Probing protein orientation near charged nanosurfaces for simulation-assisted biosensor design", Christopher D. Cooper, Natalia C. Clementi, Lorena A. Barba. J. Chem. Phys., 143:124709 (September 2015). 10.1063/1.4931113 // Preprint arXiv:1503.08150v4 // code repository // manuscript repository // figshare: orientation of protein GB1 // figshare: orientation of immunoglobulin G // figshare: grid convergence, immunoglobulin G
Version 3 of the preprint is the version submitted to a journal, after the original manuscript was split in two. Version 4 is the post peer-review revision.
- "A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. Comput. Phys. Comm., 185(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 // figshare: convergence with sphere // figshare: lysozyme // figshare: trypsin-BPTI complex // figshare: peptide-RNA complex // code repository //
Published online 4 November, 2013.
- "Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods", Christopher D. Cooper, L. A. Barba. (25 January 2013). 10.6084/m9.figshare.154331 // Code repository
Technical Report published on figshare under CC-BY-NC-SA.
- "Efficient boundary element method on Python using GPUs", Christopher D. Cooper, L. A. Barba. World Congress on Computational Mechanics (WCCM) (8–13 July 2012), Sao Paulo, Brazil.
- GPU Computing Spotlight: "Open, Reproducible Computational Chemistry with Python and CUDA," by Brad Nemire (Oct. 2015)