3 papers
math.GT2026
Classification of (uncolored) bonded knots and links
Boštjan Gabrovšek, Matic Simonič, Wanda Niemyska
We present a systematic classification of uncolored bonded knots with singularity number at most seven. Bonded knots provide a topological model for closed protein chains with intr…
math.GT2025
Bonded braids and the Markov theorem
Paolo Cavicchioli, Boštjan Gabrovšek, Matic Simonič
Bonded knots arise naturally in topological protein modeling, where intramolecular interactions such as disulfide bridges stabilize folded configurations. These structures extend c…
math.GT2025
The bracket polynomial of bonded knots and applications to entangles proteins
Boštjan Gabrovšek, Matic Simonič
We model proteins with intramolecular bonds, such as disulfide bridges, using the concept of bonded knots -- closed loops in three-dimensional space equipped with additional bonds…