This conference paper presents visualization strategies for lattice-based protein folding simulations, turning complex folding trajectories and energy-landscape transitions into interpretable interactive representations.
This paper develops an efficient flooding-style algorithm for exploring the low-energy part of discrete polymer landscapes, making barrier-tree analysis feasible without exhaustive enumeration.
This paper shows how barrier trees and numerical integration can approximate RNA folding dynamics efficiently enough to analyze bistable molecules and RNA switches on biologically relevant timescales.
This paper develops the barrier-tree formalism for degenerate landscapes and helped establish a general language for analyzing basins, saddle points, and transition barriers in complex discrete systems.