energy landscapes
Posts tagged “energy landscapes”.
Visualization of lattice-based protein folding simulations
This conference paper presents visualization strategies for lattice-based protein folding simulations, turning complex folding trajectories and energy-landscape transitions into interpretable interactive representations.
Exploring the Lower Part of Discrete Polymer Model Energy Landscapes
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.
Efficient computation of RNA folding dynamics
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.
Barrier trees: mapping minima, saddles and basins of energy landscapes
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.