Computational analysis of nucleic acids structures using graph neural networks

Unified Nanotechnology Format

A tool for quickly generating DNA origami nanostructures from 3D polyhedral meshes, based on the vHelix Autodesk Maya plugin: http://www.vhelix.net/

A Python library for nucleic acid thermodynamics, kinetics, and DNA/RNA circuit design with end-to-end simulation pipelines.

Main Repository for #-CAD, a cross-platform design platform for crisscross megastructures.

Open-source desktop nanofactory + honest synthesizer thesis: an AI compiler turns a shape into an orderable DNA-origami recipe (scaffold + optimized staples + wet-lab protocol + 3D oxDNA), behind one request router over water/drink/print/molecular makers. Citation-gated, buildable from <$1500 of parts; reproducible physics research.

This code accompanies the following publication: '“Turbo-Charged” DNA Motors with Optimized Sequence Enable Single-Molecule Nucleic Acid Sensing' by Zhang & Piranej et al., Angewandte Chemie International Edition 2024

This code accompanies the research article titled "Programmable mechanophoresis of molecular cargoes mediated by autonomous DNA motor carriers" by Zhang & Salaita et al.

Welcome to my personal website! 😊

Desktop tool for fluorescence plate reader analysis — DNA strand displacement, FRET, kinetic modelling | Python/PyQt5

Ranking seven real programmable-matter technologies (DNA nanotech, modular robots, acoustic assembly, and more) against the 'utility fog' dream — and the L² scaling law that explains why none has closed the gap. Article, figures, scripts, and scored research.