QSAR Prediction of Monomer Pair Reactivity Ratios
Summer 2020 - Present
Working with Dr. Erik Sapper we began a project with the goal of using quantum chemical descriptors to predict monomer pair reactivity ratios for radical copolymerization. Descriptors were calculated using Dragon 7 and fed into a keras machine learning model built in Jupyter Notebook. To avoid overfitting with a small data set of fifty molecules, an iterated K-fold method was implemented. Currently we are working to optimize the models to the greatest extent possible, and publish a manuscript based on project.
Trajectory Analysis of Activated MEK01
Fall 2020 - Present
Working in the Computational Chemistry Group I began a project building on the work of a previous student using molecular dynamics to study the structure of MEK01 a duel action human kinase involved in the cell cycle. The analysis uses the MDAnalysis library of python.
As an REU student working in the Beckstein lab at Arizona State University I carried out a substantial update to the python package MDPOW. My work included adding python 2-3 cross compatibility to version 0.7.0 as well as analysis features being added in version 0.8.0.
The analysis features are centered around an EnsembleAnalysis framework simplifying the process of data collection for the collections of system generated by alchemical free energy simulations. As part of completing the requirement for the National Science Foundation grant requirements I also completed a technical report of my work.
Fall 2021 - Winter 2022
As part of my work on the MEK01 analysis in theComputational Chemistry Group we decided to look at the symmetry adapted perturbation theory (SAPT) energies between specific residues in the active site. Doing this using MDAnalysis to generate Psi4 input files, then manually running each on a cluster required a large amount of setup. This was due to the issue of residues when removed from a polypeptide backbone lacking a ballance spin multiplicity.
To simplify this process I decided to develop an MDAKit to handle setting up the coordinates and running the calculations using just a simple input file. The purpose of this kit is to create a simple way for us and other users to gain incite into the intermolecular interactions of MD simulations.