References

• Barnes, J. and Hut, P. (1986), “A hierarchical O(N log N) force-calculation algorithm,” Nature, 324: 446–449, doi: 10.1038/324446a0
• Yoon, B.J. and Lenhoff, A.M. (1990), “A boundary element method for molecular electrostatics with electrolyte effects,” Journal of Computational Chemistry, 11(9): 1080–1086, doi: 10.1002/jcc.540110911.

Papers published using PyGBe

• Cooper, C.D, Bardhan, J.P. and Barba, L.A. (2014), “A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers,” Computer Physics Communications, 185(3): 720–729, doi: 10.1016/j.cpc.2013.10.028, arxiv:1309.4018
• Cooper, C.D and Barba, L.A. (2016), “Poisson–Boltzmann model for protein–surface electrostatic interactions and grid-convergence study using the PyGBe code,” Computer Physics Communications, 202: 23–32, doi: 10.1016/j.cpc.2015.12.019, arXiv:1506.03745
• Cooper, C.D, Clementi, N.C. and Barba, L.A. (2015), “Probing protein orientation near charged nanosurfaces for simulation-assisted biosensor design,” Journal of Chemical Physics, 143: 124709 doi: 10.1063/1.4931113, arXiv:1503.08150v4.