Rugged energy landscape

Straub, J.E. Rashkin, A. Thirumalai, D., Dynamics in rugged energy landscapes with applications to the S-peptide and Ribonuclease A, J. Am. Chem. Soc. 1994,116, 2049... 

Hyeon, C., and Thirumalai, D. (2008). Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins. JACS 130, 1538-1539. 

Stancik, A. L., and Brauns, E. B. (2008). Rearrangement of partially ordered stacked conformations contributes to the rugged energy landscape of a small ma hairpin. Biochemistry 47, 10834—10840. 

Smooth Energy Surface Rugged Energy Landscape... 

The elastic band method has been applied with remarkable success.63,64 However, it cannot be applied to problems that have rugged energy landscapes, like proteins. Recently, a similar method has been developed, that was designed to be applicable to rugged landscape systems. It is called the finite-temperature string method .65... 

One way to improve these methods is to couple them to new methods for accelerating the dynamics on rugged energy landscapes such as the J-walking method " or the S-walking method. ... 

Whenever this objective function defines a rugged energy landscape, with many local minima, straightforward minimization schemes (e.g., conjugate gradient) will fail. We will briefly touch on three optimization schemes that are useful in such situations and may be of relevance for protein design. 

---