Publications

Refereed journal publications

V. Ramm, J. H. Chaudhry, and C. D. Cooper. Efficient mesh refinement for the Poisson‐Boltzmann equation with boundary elements. Journal of Computational Chemistry 42 (12) (2021): 855-869

M. Martínez, C. D. Cooper, A. B. Poma, and H. V. Guzman. Free Energies of the Disassembly of Viral Capsids from a Multiscale Molecular Simulation Approach. Journal of chemical information and modeling 60 (2) (2019): 974-981

N. C. Clementi, C.D. Cooper, and L. A. Barba. Computational nanoplasmonics in the quasistatic limit for biosensing applications. Physical Review E 100 (6) (2019): 063305

C. D. Cooper. A Boundary‐Integral Approach for the Poisson–Boltzmann Equation with Polarizable Force Fields. Journal of computational chemistry 40 (18) (2019): 1680-1692

A. Molavi Tabrizi, S. Goossens, A. Mehdizadeh Rahimi, C. D. Cooper, M. G. Knepley, and J. P. Bardhan. Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson–Boltzmann Solvent. Journal of Chemical Theory and Computation 13 (6) (2017): 2897-2914

C. D. Cooper, N. C. Clementi, G. Forsyth, and L. A. Barba. PyGBe: Python, GPUs and Boundary elements for biomolecular electrostatics. Journal of Open Source Software. 1 (2016):43. 10.21105/joss.00043

C. D. Cooper and L. A. Barba. Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the PyGBe code. Comput. Phys. Commun. 202 (2016): 23-32. arxiv:1506.03745

C. D. Cooper, N. C. Clementi and L. A. Barba. Probing protein orientation near charged nanosurfaces for simulation-assisted biosensor design. J. Chem. Phys. 143 12 (2015): 124709. arXiv:1503.08150

C. D. Cooper, J. P. Bardhan, L. A. Barba. A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers. Comput. Phys. Commun. 185 3 (2014): 720-729. arXiv:1309.4018