All Publications

• "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

• "PyGBe: Python, GPUs and Boundary elements for biomolecular electrostatics", Christopher D. Cooper, Natalia C. Clementi, Gilbert Forsyth, Lorena A. Barba. The Journal of Open Source Software, 1(4) (August 2016). 10.21105/joss.00043 // Code repository
• "Accelerating PETSc-Based CFD Codes with Multi-GPU Computing", Pi-Yueh Chuang, Lorena A. Barba. The International Conference for High Performance Computing, Networking, Storage and Analysis organized by ACM, IEEE Computer Society (November 2016), Salt Lake City, UT. // SC16 poster abstract
• "The hard road to reproducibility", Barba, Lorena A.. Science, 354(6308):142 (October 2016), AAAS. 10.1126/science.354.6308.142 // PDF
• "Guest editorial: Flipped classrooms in STEM", Barba, Lorena A., Kaw, Autar, LeDoux, Joseph M.. Advances in Engineering Education, 5(3) (November 2016), American Society for Engineering Education. // PDF
• "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.

• "Grid convergence of PyGBe with a spherical molecule near spherical surface", Christopher D. Cooper, Lorena A. Barba. (March 2015). 10.6084/m9.figshare.1348841.v4 // Paper containing figure
  

  Reproducibility package including data, running script, plotting script, and figure of grid-convergence study using two spheres, one with prescribed potential. On figshare under CC-BY.

• "Grid convergence of PyGBe with protein G B1 D4'", Christopher D. Cooper, Lorena A. Barba. (March 2015). 10.6084/m9.figshare.1348803.v10 // Paper containing figure
  

  Reproducibility package including data, running script, plotting script and figure(s). On figshare under CC-BY.

• "Protein orientation near a charged surface using PyGBe and protein G B1 D4'", Christopher D. Cooper, Lorena A. Barba. (March 2015). https://dx.doi.org/10.6084/m9.figshare.1348804.v6 // Paper containing figure(s)
  

  Reproducibility package including data, running script, plotting script and figure. On figshare under CC-BY.

• "Grid convergence of PyGBe with immunoglobulin G near a charged surface", Christopher D. Cooper, Lorena A. Barba. (March 2015). 10.6084/m9.figshare.1348801.v8 // Paper containing figure
  

  Reproducibility package including data, running script, plotting script and figure. On figshare under CC-BY.

• "Protein orientation near charged surface using PyGBe with immunoglobulin G", Christopher D. Cooper, Lorena A. Barba. (March 2015). 10.6084/m9.figshare.1348802.v8 // Paper containing figure(s)
  

  Reproducibility package including data, running script, plotting script and figure. On figshare under CC-BY.

Refereed Journal Articles

• "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

• "PyGBe: Python, GPUs and Boundary elements for biomolecular electrostatics", Christopher D. Cooper, Natalia C. Clementi, Gilbert Forsyth, Lorena A. Barba. The Journal of Open Source Software, 1(4) (August 2016). 10.21105/joss.00043 // Code repository
• "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.

Open Research

• "Grid convergence of PyGBe with a spherical molecule near spherical surface", Christopher D. Cooper, Lorena A. Barba. (March 2015). 10.6084/m9.figshare.1348841.v4 // Paper containing figure
  

  Reproducibility package including data, running script, plotting script, and figure of grid-convergence study using two spheres, one with prescribed potential. On figshare under CC-BY.

• "Grid convergence of PyGBe with protein G B1 D4'", Christopher D. Cooper, Lorena A. Barba. (March 2015). 10.6084/m9.figshare.1348803.v10 // Paper containing figure
  

  Reproducibility package including data, running script, plotting script and figure(s). On figshare under CC-BY.

• "Protein orientation near a charged surface using PyGBe and protein G B1 D4'", Christopher D. Cooper, Lorena A. Barba. (March 2015). https://dx.doi.org/10.6084/m9.figshare.1348804.v6 // Paper containing figure(s)
  

  Reproducibility package including data, running script, plotting script and figure. On figshare under CC-BY.

• "Grid convergence of PyGBe with immunoglobulin G near a charged surface", Christopher D. Cooper, Lorena A. Barba. (March 2015). 10.6084/m9.figshare.1348801.v8 // Paper containing figure
  

  Reproducibility package including data, running script, plotting script and figure. On figshare under CC-BY.

• "Protein orientation near charged surface using PyGBe with immunoglobulin G", Christopher D. Cooper, Lorena A. Barba. (March 2015). 10.6084/m9.figshare.1348802.v8 // Paper containing figure(s)
  

  Reproducibility package including data, running script, plotting script and figure. On figshare under CC-BY.

Posters

• "Accelerating PETSc-Based CFD Codes with Multi-GPU Computing", Pi-Yueh Chuang, Lorena A. Barba. The International Conference for High Performance Computing, Networking, Storage and Analysis organized by ACM, IEEE Computer Society (November 2016), Salt Lake City, UT. // SC16 poster abstract

Periodicals

• "The hard road to reproducibility", Barba, Lorena A.. Science, 354(6308):142 (October 2016), AAAS. 10.1126/science.354.6308.142 // PDF
• "Guest editorial: Flipped classrooms in STEM", Barba, Lorena A., Kaw, Autar, LeDoux, Joseph M.. Advances in Engineering Education, 5(3) (November 2016), American Society for Engineering Education. // PDF