pygbe :: Lorena A. Barba Group

"ExaFMM - 10+ years, 7 re-writes. The tortuous progress of computational research"—my talk from July 2020 for the E… https://t.co/bsZZj18Fli View // Reply // Retweet // Like

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 »

"Student success has little to do with talent and a great deal to do with educational privilege"—Carl Wieman makes… https://t.co/ZKOmpOmSSV View // Reply // Retweet // Like

Reproducible validation and replication studies in nanoscale physics

Preprint: arXiv 2008.05414, 12 Aug 2020. Submitted: July 27, 2020. Accepted: September 23, 2020. Philosophical Transactions of the Royal Society A, 379(2197):20200068 (March 2021). Abstract Credibility building activities in computational research include verification and validation, reproducibility and replication, and uncertainty quantification. Though orthogonal to each other, they are related. This paper presents validation and replication... 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 »

Natalia Clementi presents PhD dissertation proposal

Natalia Clementi presented her PhD dissertation proposal on May 24, 2019.

PyGBe on Localized Surface Plasmon Resonance (LSPR)

This file set includes three Jupyter notebooks with a summary of the preliminary results of Localized surface plasmon resonance applications obtained using PyGBe.

It also contains the figures and css style to load the notebooks properly when they are download.

The... Continue »

#WomeninHPC at #GTC17—not many here! Less than 5%. I’m with @hpcprogrammer and @gridrebel; @anne_elster took the p… https://t.co/LkjC58LUeK View // Reply // Retweet // Like

RT @drphd2k7: @GWjaredwj @drphd2k7/@LorenaABarba makes critical point-about fundamental concept of instructional design & edtech: congruenc… View // Reply // Retweet // Like

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 »