Projects

Scientific questions translated into algorithms and software.

These case studies show the complete path from problem definition and method design to implementation, validation, and reusable research infrastructure.

Diagram showing a Qt interface and CLI metadata transformed into JSON and then into VMD, PyMOL, and web applications.

Open source

Research software2025 – 2026

One specification, multiple scientific interfaces

A Python framework that converts a designed interface and CLI metadata into a validated, platform-independent JSON specification, then generates consistent scientific applications for desktop molecular viewers and web environments.

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Ongoing work

Molecular modeling2026 – Present

Inverse-kinematics protein backbone sampling

An extension of tripeptide loop-closure sampling that releases terminal constraints, introduces SE(3) motions and shifted sampling frames, and couples broad backbone geometric exploration to all-atom structural validation.

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Workflow from an atomic protein complex through a coarse-grained model and reaction network to a domain-decomposed parallel simulation.

Open source

Scientific infrastructure2022 – 2025

From atomic structures to scalable self-assembly simulation

A connected software stack that transforms PDB or mmCIF structures into simulation-ready coarse-grained models and runs explicit particle-based reaction-diffusion and self-assembly at larger spatial and computational scales.

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Abstract membrane with assembling clathrin-like lattice, a budding viral lattice, and dynamin molecules concentrating into clusters.

Published

Computational biophysics2020 – 2024

Mechanistic models of membrane-associated assembly

Structure-resolved stochastic and kinetic models of clathrin lattices, HIV-1 Gag assembly, and dynamin recruitment that integrate experimental constraints and produce testable system-level predictions.

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