Scientific software

Research code as a research contribution

Each project below is developed and maintained on GitHub. They aim to make specific sampling and representation-learning methods usable outside the group that developed them.

TRAILS-MD

Python

Lightweight, engine-agnostic framework for lineage-aware adaptive molecular-dynamics sampling.

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PathGennie

Python

Direction-guided adaptive-sampling framework for rapidly generating rare-event transition pathways.

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IceCoder

Python / PyTorch

Unsupervised representation-learning framework for classification and identification of ice polymorphs and liquid environments.

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SolOrder

Python / Numba

Pip-installable library of water structural order parameters (tetrahedrality, LSI, F4, Steinhardt, Voronoi, CHILL/CHILL+ and more) with parallel execution, validated on ice polymorphs and nucleation snapshots.

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MD Movie Maker

Python

Turns a molecular-dynamics trajectory into a multi-panel movie, with the molecule, synced analysis plots and free-energy-surface trails, exported to MP4 or GIF.

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SlideForge

JavaScript / Python

Free desktop presentation app for researchers: editable charts, curve fits, LaTeX equations and rotatable molecular structures on slides, with PowerPoint and PDF export.

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Repository details are maintained on GitHub; visit each project for documentation, examples, and release history.