Designed and executed all-atom simulations of Fe-Fe hydrogenase enzymes to help the further development of their usage for the production of molecular hydrogen sustainably. Through the modeling of variants coming from different organisms, I was able to elucidate the possible pathways of entrance of CO into the active site and inhibit the formation of hydrogen and designed and simulated several mutant models, which were later replicated experimentally by our collaborators in Marseille, France. Set up the models and scripts to carry out the computational simulations using either GPUs or the institution's supercomputing clusters, via parallelization with OpenMPI. Automated workflow and testing via Bash and Python scripts. Analyzed and manipulated simulation data to elucidate all possible stages and transitions during the CO-induced inhibition of the enzymes using machine and deep learning with libraries such as Pandas, Sklearn, Scipy and Tensorflow. Created visualizations and dashboards to communicate findings with coworkers. Worked remotely for several weeks via SSH.

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Designed mathematical models to describe the process of formation of amyloid fibrils and its association with type II diabetes. Produced and executed computational simulations on a variety of protein complexes to study the characteristics and formation of amylin aggregates and to quantitatively predict a broad array of experimental data. Studied mechanical properties of proteins by Atomic Force Microscopy and analyzed outcoming data. Developed proficiency in writing for academic purposes and submissions and presenting for technical and non-technical audiences. Designed Bash scripts to clean and transformed raw data from simulations for posterior advanced analysis. Transformed raw data and carried out dimensionality reduction for feature extraction. Analyzed simulation data to identify and monitor the conformational and aggregation states of proteins using unsupervised learning methods. Applied network analysis and graph theory to gain insight of the pathways of formation of amylin deposits.

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