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