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 »
Submitted: Inexact Krylov iterations and relaxation strategies with fast-multipole boundary element method
Submitted: 19 June 2015 This paper presents a method to algorithmically accelerate boundary element methods. The fast multipole method (FMM) is already used in this context to obtain O(N) computational complexity while solving a dense linear system. Using relaxed-accuracy matrix-vector multiplications in a Krylov solver, we can achieve speed-ups in the order of 4x... 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 »
Barba awarded computer center grant
Prof. Barba led a multi-institution bid to success in the call for research seed grants of the Massachusetts Green High-Performance Computing Center, MGHPCC. The award amounts to $130,487 for the duration of one year. This project is a collaboration among investigators in BU, Harvard and UMass aimed at creating an open and high-performance software infrastructure... Continue »
New paper published: CiSE journal
A new paper authored by Rio Yokota and Lorena Barba has appeared (published online 3 Jan. 2012) in Computing in Science and Engineering, the joint publication of the IEEE Computer Society and he American Institute of Physics. This paper presents a new hybrid treecode/FMM formulation that has been implemented in the ExaFMM code, recently released... Continue »