Matt Thompson
Senior Research Software Engineer at Open Force Field Initiative
Iowa City, Iowa, United States
Summary
👤
Senior🎓
Top SchoolMatt Thompson is a Senior Research Software Engineer with 11 years of experience building and maintaining scientific software for molecular simulation and analysis. Based in Iowa City, he contributes to the Open Force Field Initiative and the OMSF, bringing deep back-end expertise demonstrated by meaningful contributions to widely used projects like ParmEd and MDTraj—improving topology handling, nonbond parameter support, and trajectory parsing. Trained as a chemical engineer and PhD in Chemical and Biomolecular Engineering from Vanderbilt, he straddles domain science and production-grade code, turning complex physical models into reliable software. Known for improving test coverage and compatibility across Python ecosystems, he combines rigorous research instincts with pragmatic engineering practices that keep collaborative open-source projects healthy and reproducible.
11 years of coding experience
5 years of employment as a software developer
Bachelor of Science (B.S.), Chemical Engineering, Bachelor of Science (B.S.), Chemical Engineering at Iowa State UniversityDoctor of Philosophy (PhD), Chemical and Biomolecular Engineering, Doctor of Philosophy (PhD), Chemical and Biomolecular Engineering at Vanderbilt University
Github Skills (14)
pandas10
molecular-dynamics-simulation10
file-parsing10
python10
molecular-simulation10
grok10
numpy10
dynamics10
gr10
data-analysis9
testing9
unit-testing8
githubaction-workflow5
github-ci5
Programming languages (13)
Github contributions (5)
mdtraj/mdtraj
Feb 2017 - Nov 2022
An open library for the analysis of molecular dynamics trajectories
Role in this project:
Back-end Developer / Data Scientist
Back-end Developer / Data ScientistContributions:10 releases, 79 reviews, 29 commits in 5 years 9 months
Contributions summary:Matt primarily contributed to the molecular dynamics analysis library by implementing and refactoring functionalities related to file parsing and data processing. They added new features for computing geometric properties and center of mass, as well as corrected parsing issues and enhanced code readability. The user also worked on updating dependencies and ensuring compatibility with different versions of Python and external libraries like Pandas, reflecting their proficiency in maintaining and improving the core functionalities of the library.
pythonmdtrajmolecular-dynamicspdbpdb-files
ParmEd/ParmEd
Nov 2017 - Jun 2020
Parameter/topology editor and molecular simulator
Role in this project:Back-end Developer
Back-end DeveloperContributions:24 commits, 8 PRs, 64 comments in 2 years 7 months
Contributions summary:Matt primarily focused on enhancing the functionality of the Gromacs topology file within the ParmEd library. They added support for writing nonbond parameters, including NBFIX types. They also improved the code by fixing typos, removing unused variables, and ensuring that nonbond parameters are written correctly. Furthermore, they added tests to ensure reading and writing of the `nonbond_params` directive.
physicslammpssimulationmolecularparameter
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