title: Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide.
abstract: The finite-temperature string method proposed by E, et al. [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002)] is a very effective way of identifying transition mechanisms and transition rates between metastable states in systems with complex energy landscapes. In this paper, we discuss the theoretical background and algorithmic details of the finite-temperature string method, as well as the application to the study of isomerization reaction of the alanine dipeptide, both in vacuum and in explicit solvent. We demonstrate that the method allows us to identify directly the isocommittor surfaces, which are approximated by hyperplanes, in the region of configuration space where the most probable transition trajectories are concentrated. These results are verified subsequently by computing directly the committor distribution on the hyperplanes that define the transition state region.
authors.affiliation: Department of Mathematics, Princeton University, Princeton, New Jersey 08544, USA. weiqing@math.princeton.edu
authors.forename: Weiqing
authors.initials: W
authors.lastname: Ren
authors.forename: Eric
authors.initials: E
authors.lastname: Vanden-Eijnden
authors.forename: Paul
authors.initials: P
authors.lastname: Maragakis
authors.forename: Weinan
authors.initials: W
authors.lastname: E
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000465:Algorithms; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D007536:Isomerism; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D013696:Temperature; D013816:Thermodynamics
chemical_list: D004151:Dipeptides; D000409:Alanine