Research portfolio

Methods, mechanisms, and reusable tools.

Selected projects in protein conformational sampling, biomolecular self-assembly, and scientific software.

Molecular modeling · Ongoing research

Protein conformational sampling

Problem: Fixed-end loop closure limits exploration of fragments and disordered regions, whose endpoints need to move.
Built: Extensions to a C++ sampler (released-endpoint moves, spatial-hash clash detection) plus an OpenMM all-atom validation workflow.
Result: Broader exploration than tested generative samplers on the evaluated systems (ongoing work).

Scientific computing · Open source

Problem: Building simulation models from molecular structures needed automation, and particle-based simulation needed to scale beyond a single process.
Built: C++/MPI spatial domain decomposition for NERDSS and automated structure-to-model Python workflows in ioNERDSS (co-developed).
Result: ≈90× speedup on 96 CPUs (20,000-particle benchmark) · 44,000+ structures benchmarked · validated across 7 benchmark models.

Research software · Open source

Problem: Each scientific tool needed a separate implementation for PyMOL, VMD, and the web.
Built: A specification-driven Python framework with JSON Schema validation, platform generators, and Linux/macOS CI.
Result: 9 structural-biology tools deployed across 3 platforms, one specification each.

Computational biophysics · Published research

Problem: Why do some molecular lattices stabilize while others fall apart or remodel?
Built: Stochastic reaction-diffusion models of clathrin and HIV Gag lattices.
Result: Reproduced experimental clathrin kinetics · identified an HIV binding-affinity range for stability and remodeling · first-author papers in PLOS Comp Biol and eLife, plus modeling for a Nature Communications study.

Research & collaboration

I’m interested in molecular-modeling methods, biomolecular simulation, and reusable scientific software.