Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer. - Ahmed Shalaby 005; Chris Thachuk; Damien Woods (DNA, 2023)

Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds. - Erik D. Demaine; Timothy Gomez; Elise Grizzell; Markus Hecher; Jayson Lynch; Robert T. Schweller; Ahmed Shalaby 005; Damien Woods (DNA, 2024)

Algorithmic Hardness of the Partition Function for Nucleic Acid Strands. - Gwendal Ducloz; Ahmed Shalaby 005; Damien Woods (DNA, 2025)

An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands. - Ahmed Shalaby 005; Damien Woods (ICALP, 2025)