Transition Pathways: The String Method
This video introduces the string method, as a way of finding optimal pathways between different stats for a system. Useful references include:
1. Maragliano, L., A. Fischer, E. Vanden-Eijnden, and G. Ciccotti, 2006. String method in collective variables: Minimum free energy paths and isocommittor surfaces. The Journal of Chemical Physics 125:024106
2. E, W., W. Ren, and E. Vanden-Eijnden, 2007. Simplified and improved string method for computing the minimum energy paths in barrier-crossing events. The Journal of Chemical Physics 126:164103
3. Cheng, X., L. Lin, W. E, P. Zhang, and A.-C. Shi, 2010. Nucleation of Ordered Phases in Block Copolymers. Physical Review Letters 104:148301 (String method example that I showed)
4. Spencer, R. K. W., I. Santos-Pérez, I. Rodríguez-Renovales, J. M. M. Galvez, A. V. Shnyrova, and M. Müller, 2024. Membrane fission via transmembrane contact. Nature Communications 15:2793 (Other string method example)
Chapters:
0:00 Intro
0:32 Nucleation
3:17 Parameterization
4:58 FE Landscape
6:36 Relaxing
8:08 Spring
9:36 Interpolation
10:36 Perp. Update
12:35 Example 1
13:01 Example 2
13:22 Spring 2
14:34 Warning