Lorena A. Barba group


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High-productivity, high-performance workflow for virus-scale electrostatic simulations with Bempp-Exafmm

Preprint: arXiv:2103.01048, 1 Mar 2021. Submitted: 22 Mar. 2021. Abstract Biomolecular electrostatics is key in protein function and the chemical processes affecting it.Implicit-solvent models expressed by the Poisson-Boltzmann (PB) equation can provide insights with less computational power than full atomistic models, making large-system studies—at the scale of viruses, for example —accessible to more researchers. This paper... Continue »

Reproducible validation and replication studies in nanoscale physics

Preprint: arXiv 2008.05414, 12 Aug 2020. Submitted: July 27, 2020. Accepted: September 23, 2020. Published online: 29/03/2021 Published in print: 17/05/2021 Philosophical Transactions of the Royal Society A, 379(2197):20200068 (March 2021). https://doi.org/10.1098/rsta.2020.0068 Theme issue: ‘Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico’ – compiled and edited by P. V. Coveney, D.... Continue »

Nature TechBlog: My digital toolbox

Jeffrey Perkel, Technology Editor for Nature, interviewed Prof. Lorena A. Barba about her research group's reproducibility practices and the digital tools that enable them. She talked about the group's computational research interests, their avant-garde use of digital tools and repositories to create "repro-packs," and how these allow her to share research figures freely even when part... Continue »

Submitted: "Lift and wakes of flying snakes"

Submitted: September 16, 2013. Accepted in Physics of Fluids: February 10, 2014. This paper presents a computational study of the aerodynamics of an anatomically correct cross-section of Chrysopelia paradisi, the flying snake. These animals inhabit the canopy of rainforests in East Asia, and have a very peculiar method of locomotion: they jump from tree branches, change... Continue »

How will the fast-multipole method fare in the exascale era?

SIAM News (Vol. 46, issue 6) has published on the front page our piece about the future of algorithms in the exascale era. This piece was written by invitation on the aftermath of a very successful SIAM Conference on Computational Science and Engineering, held in Boston last February. At this conference several minisymposia focused on... Continue »

New exaFMM paper accepted

FMM-based vortex method for simulation of isotropic turbulence on GPUs, compared with a spectral method, Rio Yokota, L. A. Barba, Computers & Fluids, in press (available online 13 August 2012), doi:10.1016/j.compfluid.2012.08.002 This paper presents the results of comparing a Lagrangian vortex method with a trusted spectral method for the simulation of isotropic fluid turbulence. The numerical engine of the vorticity-based fluid... Continue »