Google Summer of Code Students 2021
19 May 2021We are happy to announce that MDAnalysis is hosting two GSoC students this year – @ojeda-e, and @orioncohen. MDAnalysis has been accepted as its own organization with GSoC for a second year running and we are grateful to Google for granting us two student slots for two exciting projects. Both the students and mentors have a very exciting few months ahead!
Estefania Barreto-Ojeda: Curvature analysis of biological membranes
Interested in contributing to an open-source initiative, Estefania will expand the capabilities of MDAnalysis by integrating a new MDAnalysis module to calculate membrane curvature to derive and visualize membrane curvature profiles of protein-membrane/membrane-only systems obtained from Molecular Dynamics (MD) simulations. With the introduction of this analysis module, users will rapidly extract mean and gaussian curvature of biological membranes and their respective visualization in 2D-profile maps.
Estefania is a Ph.D. candidate in Biophysical Chemistry at The University of Calgary, Canada in the research group of Peter Tieleman. Her research work is focused on membrane curvature induced by ABC transporters, a superfamily of transmembrane proteins involved in cancer and antibiotic resistance. A typical day for Estefania includes running Coarse-Grained (CG) MD simulations using the Martini force field, reading literature on ABCs, and working on cool data visualization workflows. In her free time, she enjoys camping and road tripping in the Canadian Rockie Mountains and going for long bike rides.
Estefania can be found on github as @ojeda-e and on twitter as @ebojeda.
Her journey will be documented on the blog Le Mirroir.
Orion Cohen: A Solvation Module for MDAnalysis
The macroscopic behavior of a liquid is determined by its microscopic structure. For ionic systems, like batteries and many enzymes, the solvation environment surrounding ions is especially important. By studying the solvation of interesting materials, scientists can better understand, engineer, and design new technologies. The aim of this project is to implement a robust and cohesive set of methods for solvation analysis that would be widely useful in both biomolecular and battery electrolyte simulations. The core of the solvation module will be a set of functions for easily working with ionic solvation shells. Building from that core functionality, the module will implement several analysis methods for analyzing ion pairing, ion speciation, residence times, and shell association and dissociation.
Orion is a Ph.D. student at the University of California Berkeley, working with Dr. Kristin Persson at the Lawrence Berkeley National Laboratory. His work leverages high-throughput chemical simulations and machine learning to discover new materials for Lithium-ion batteries. Orion is passionate about making science more accessible, reproducible, and efficient with powerful open-source software. If he isn’t toiling at his computer, Orion is probably playing board games, camping, or relaxing in the temperate Berkeley sun.
Orion is on Github as @orioncohen and on twitter as @orion__archer.
He will be sharing his experience with GSoC on his website.
— @richardjgowers @IAlibay @fiona-naughton @orbeckst @lilyminium @hmacdope (mentors)