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An Expanded Markov State Model-Transition Path Theory Framework for Ion Conduction Reactive Pathways through Membrane
Ramon Mendoza Uriarte1, Benoît Roux1,2
1Department of Chemistry, The University of Chicago, 5735 S Ellis Ave, Chicago, Illinois 60637, Chicago, Illinois 60637, United States.
The Journal of Physical Chemistry Letters
|April 3, 2026
Summary
Markov State Models (MSMs) combined with transition path theory (TPT) identify system dynamics. An expanded framework addresses challenges in analyzing unbound processes like ion channel conduction.
Area of Science:
- Computational Chemistry
- Biophysics
- Theoretical Biology
Background:
- Markov State Models (MSMs) approximate system dynamics via transitions between microstates.
- Transition Path Theory (TPT) rigorously identifies dominant reactive pathways in complex systems.
- Standard MSM/TPT is effective for bound systems but faces challenges with unbound processes.
Purpose of the Study:
- To adapt the MSM/TPT framework for analyzing unbound processes, specifically ion conduction through channels.
- To develop a generalized methodology applicable to open systems beyond ion channels.
Main Methods:
- An expanded formulation of the Markov State Model and Transition Path Theory framework was developed.
- This enhanced framework accommodates the characteristics of unbound processes.
Main Results:
- The study introduces a modified MSM/TPT approach capable of characterizing ion channel function.
- The generalized framework provides a novel method for analyzing open systems.
Conclusions:
- The expanded MSM/TPT framework successfully addresses limitations of standard methods for unbound processes.
- This generalized approach offers broad applicability to diverse molecular machines and open systems.
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