Lorena A. Barba group


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 »

Computational nanoplasmonics in the quasistatic limit for biosensing applications

Preprint: arXiv 1812.10722 Dec. 31, 2018. Submitted: Dec. 31, 2018; Jan. 20, 2019; Mar. 20, 2019. Accepted: Nov. 1. Published: Dec. 16, 2019. DOI: 10.1103/PhysRevE.100.063305 Abstract This work uses the long-wavelength limit to compute LSPR response of biosensors, expanding the open-source PyGBe code to compute the extinction cross-section of metallic nanoparticles in the presence of any target... Continue »

Probing protein orientation near charged surfaces

First version submitted: 31 March 2015. Submission of split papers: June 7 & June 12. Accepted: 4 Sept. & 26 Dec. 2015.   UPDATE: The material in the original manuscript was split in two papers, submitted to different peer-reviewed journals. The editorial decision on the first submission was that the paper was out of scope... Continue »