Current Projects

Stay tuned for preprints!

aRLarm

aRLarm grid experiment

A small side project testing transformer policies + SAC for variable linkages (tested up to 6-DOF), bypassing explicit inverse kinematics. Trained multiple models at different step counts and linkage sizes on GPUs via a Slurm cluster.

Source code is available on GitHub: https://github.com/dfu99/aRLarm

Past Projects in DNA Nanotechnology

DNAxiS

DNAxiS

DNAxiS is a computational tool for generating design sequences for rotational DNA origami nanostructures.

You can find it kindly hosted by the Duke University Computer Science Department, here: caddna.cs.duke.edu

It can also be run on your local machine and the source is available on GitHub: https://github.com/dfu99/dnaxis

Our paper on this work was published in Science Advances: DOI: 10.1126/sciadv.ade4455.

Watch our reinforcement strategy in motion:

Single-layer Reinforced
Single-layer DNA origami trajectory Reinforced DNA origami trajectory

Trajectories produced by oxDNA.

Y-STAM

YSTAM

The Branching Signal-passing Tile Assembly Model (Y-STAM) is a model of branching self-assembly processes evaluated using DNA tile assembly as a substrate. It is currently presented as a simulator implemented in MATLAB.

The source code for the MATLAB simulation software is available on GitHub: https://github.com/dfu99/Y-STAM

Our paper on this work was published in the Journal of Royal Society Interface: DOI: 10.1098/rsif.2023.0755

Applications of Localized Hybridization Chain Reaction Circuits

Cancer Cell Membrane Targeting via HCR

We explored applications of localized hairpin-based HCR circuits [1]. We published work on using our architecture for cancer cell detection in JACS: DOI: 10.1021/jacs.9b05598.

Other