Vinícius Cruzeiro
Scientist II at Architect Therapeutics
San Diego, California, United States
Summary
👤
Senior🎓
Top SchoolVinícius Cruzeiro is a computational chemist and Scientist II at Architect Therapeutics with nearly a decade of focused experience applying CADD and rational design to small-molecule drug discovery. He brings deep expertise in protein dynamics, quantum chemistry, polarizable force fields, and ML-informed methods, and has a track record of accelerating QM/MM and GPU-accelerated workflows at Stanford and UC San Diego. A prolific researcher with 20+ peer-reviewed papers and multiple ACS awards, he also contributes to widely used open-source tools like ParmEd—adding pH- and redox-aware functionality and new AmberTools utilities that broaden molecular simulation capabilities. Known for pragmatic engineering, he builds interfaces (e.g., a protobuf-based TeraChem connector) that double performance while making advanced methods more accessible to researchers. Based in San Diego, he blends rigorous academic training (PhD, UF) with hands-on software development to translate cutting-edge theory into practical drug-discovery solutions.
9 years of coding experience
11 years of employment as a software developer
Bachelor's degree Physics, Bachelor's degree Physics at Universidade Federal de GoiásMaster's degree Physics, Master's degree Physics at USP - Universidade de São PauloDoctor of Philosophy - PhD Computational Chemistry, Doctor of Philosophy - PhD Computational Chemistry at University of Florida
English, Portuguese, Spanish
Github Skills (8)
file-handling10
file-processing10
parameterization10
file-access10
molecular-simulation10
fileio10
python10
testing9
Programming languages (6)
Github contributions (5)
ParmEd/ParmEd
Nov 2017 - Nov 2018
Parameter/topology editor and molecular simulator
Role in this project:
Back-end Developer
Back-end DeveloperContributions:1 review, 24 commits, 9 PRs in 1 year
Contributions summary:Vinícius primarily focused on enhancing and adapting the `parmed/parmed` repository for molecular simulation and parameterization. Their work involved modifying the `titratable_residues.py` file to support pH-active and redox-active residues, enabling the generation of CPIN and CEIN files. They also introduced new AmberTools and commands, such as `ceinutil.py` and `changeRedoxState`, extending the capabilities of the parameter/topology editor and molecular simulator. Furthermore, they updated the test suite to accommodate the new features and improvements.
physicslammpssimulationmolecularparameter
mtzgroup/tcpb-cpp
Sep 2021 - Oct 2022
Contributions:259 commits, 34 PRs, 107 pushes in 1 year
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