Application definition
Validated JSON
PyMOLVMDWeb
Python · JSON Schema · Web
AutoCLIP
Generate PyMOL, VMD, and web applications from one reusable specification.
9 structural-biology tools · 3 platforms
Software
Research methods. Usable implementations.
Open-source tools spanning molecular structures, parallel simulation, and consistent scientific interfaces. Each project links to its code, documentation, and underlying work.
Spatial domain decomposition
C++ · MPI · Linux
NERDSS-MPI
Scale particle-based reaction-diffusion simulation while checking distributed numerical behavior.
≈90× on 96 CPUs · 20,000-particle benchmark
Structure-to-simulation workflow
PDB / mmCIFStructures
CG modelReactions
NERDSSSimulation
Python · Structural data · PyQt6
ioNERDSS
Turn PDB/mmCIF structures into coarse-grained models and connect simulation, analysis, and visualization.
44,000+ structures · 3–720-subunit assemblies
Engineering approach
Correctness first. Reuse by design.
I work across algorithm development, numerical validation, APIs, tests, packaging, documentation, and deployment. My aim is to make a research method useful outside the codebase and context in which it was developed.
Read the project case studiesResearch & collaboration
Let’s talk about the next question.
I’m interested in molecular-modeling methods, biomolecular simulation, and reusable scientific software.