Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide

Area of Science:

• Computational Chemistry
• Statistical Mechanics
• Physical Chemistry

Background:

• Complex energy landscapes pose challenges for studying molecular transitions.
• The finite-temperature string method offers a robust approach for identifying reaction mechanisms and rates.
• Understanding metastable states is crucial in various scientific domains.

Purpose of the Study:

• To detail the theoretical and algorithmic aspects of the finite-temperature string method.
• To apply the method to the isomerization of alanine dipeptide in different environments.
• To demonstrate the direct identification of isocommittor surfaces and transition states.

Main Methods:

• Utilizing the finite-temperature string method to analyze molecular dynamics.
• Applying the method to alanine dipeptide isomerization in vacuum and explicit solvent.
• Approximating isocommittor surfaces with hyperplanes in configuration space.

Main Results:

• The finite-temperature string method successfully identified transition mechanisms and rates.
• Direct identification of isocommittor surfaces was achieved in the relevant configuration space.
• Transition state regions were accurately defined by hyperplanes.

Conclusions:

• The finite-temperature string method is highly effective for studying complex systems.
• The method facilitates direct identification and characterization of transition states.
• Results were validated through direct computation of committor distributions.