Edis Jakupovic
Edis Jakupovic is a first year Physics Ph.D. at Arizona State University. In 2021, he graduated with a bachelors degree in Physics and Biochemistry from ASU.
Edis joined the Beckstein Lab in the summer of 2020 as an REU (research experience for undergraduates) student as part of the NSF DIBSS SPIDAL REU program. During that summer, he implemented an HDF5-based file reader and writer into the MDAnalysis library. HDF5-based files are of great importance to MD simulations due to the parallel read and write capabilities of HDF5 file systems when configured with parallel MPI compilers, which would increase the speed at which MD simulations could be analyzed. Following his REU experience, Edis continued working in the lab as an undergraduate researcher, testing the parallel I/O capabilities of the H5MD file format reader in MDAnalysis and ultimately published the results in the 2021 SciPy Proceedings.
For his first research rotation project as a graduate student, he continued working in the lab. In this project, he employed the Weighted Ensembled enhanced sampling method to sample the rare breaking of the K305-D156 salt bridge in the NapA protein to uncover the empirical details of the kinetics and energy landscape of the process.
Currently, Edis is exploring other exciting opportunities in the Center for Biological Physics and is working with Dr. Banu Ozkan’s group on a project aimed at modeling/quantifying the transmission of information modulated by the allosteric processes within a kinetic model of proteins.
Outside of studying and work, he enjoys playing soccer, working out, listening to podcasts, spending time with friends, and eating pints Ben n Jerry’s ice cream in the middle of the night. He can be found on GitHub (edisj).
Publications
Jakupovic, Edis (2020). “SPIDAL Summer REU 2020: Implementing an HDF5-based File Format Coordinate Reader into MDAnalysis.” Technical report, Arizona State University. doi: 10.6084/m9.figshare.12861215
Jakupovic, Edis and Beckstein, Oliver, “MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package,” in Proceedings of the 20th Python in Science Conference (Meghann Agarwal, Chris Calloway, Dillon Niederhut, and David Shupe, eds.), (Austin, TX), pp. 40–48, 2021. doi:10.25080/majora-1b6fd038-005
