Portfolio

Here, you’ll find projects focused on molecular dynamics and quantum chemical simulations, all aimed at advancing computational research and ensuring scientists have the tools they need to drive discovery.

PySCES

Semi-Classical Dynamics with On-the-fly Electronic Structure

A nonadiabatic, semiclassics simulation software that interfaces with TeraChem and GAMESS quantum chemistry programs. 

Article PDF | Publisher | GitHub Repo

This project also utilized the TeraChem Protobuffer Client to connect to GPU computing nodes.

Skills and Abilities: ​Distributed computing with Google Protobuffers and MPI, CUDA and GPU acceleration, and experience with large commercial codebases. 

PySCES-Plots

Plotting dashboard for visualizing PySCES Trajectories locally or remotely

GitHub Repository

With just a few clicks, you can load your HDF5 trajectory – which captures time-dependent energies, state populations, and nonadiabatic coupling (NAC) data – and explore key physical observables through an interactive dashboard.

Visualize your simulations either locally, or remotely from your working HPC environment!

Skills and Abilities: ​Data visualization, dashboard design, front-end development

AmberFD

Machine learned interaction potentials for RNA nuclear bases, trained on quantum chemical, energy decomposition calculations.

AmberFD is a​ library for extending OpenMM with a fluctuating density model.
Written as a Python API for ease-of-use, with a C++/OpenMP/Lapacke back-end for exceptional performance.


Pre-print on ChemRxiv.
Also check out it's documentation page!
The parameterization also used a nonlinear RESP charge and density fitting program that works with Q-Chem outputs. 

Skills and Abilities: ​C++ Multi-threading (OpenMP), gradient based, nonlinear optimization, custom loss-function development, physics-based modelling

CoSIMS

An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry

CoSIMS is a multithreaded trajectory-based CCS engine that accelerates ion mobility simulations by up to 100× while preserving accuracy. 

Designed for integration into experimental structural biology pipelines, it enables fast, reliable CCS calculations for large biomolecules. 

Checkout the publication in J. Phys. Chem!

Skills and Abilities: ​C++ multi-threading (OpenMP), molecular dynamics, numerical-method development,  experimental-computational collaboration

Other Favorite Coding Projects

Some of the various projects that I have built or contributed to may help you with your research goals: