Molecular search with conformational change: One-dimensional discrete-state stochastic model

Area of Science:

• Chemical physics
• Biophysics
• Statistical mechanics

Background:

• Molecular search is crucial in chemical and biological systems.
• Particles often navigate complex, inhomogeneous environments with changing dynamics.
• Understanding alternating dynamics is key to molecular search mechanisms.

Purpose of the Study:

• Investigate molecular search dynamics with stochastic transitions between two conformations.
• Analyze search processes in a one-dimensional discrete-state stochastic model.
• Develop a general dynamic phase diagram for alternating dynamics.

Main Methods:

• Utilized the first-passage time probability method for detailed analysis.
• Employed a one-dimensional discrete-state stochastic model.
• Performed Monte Carlo computer simulations to validate theoretical predictions.

Main Results:

• Identified several distinct dynamic regimes in molecular search with conformational transitions.
• Found that these regimes are determined by the relative values of system length scales.
• Developed a general dynamic phase diagram illustrating these regimes.

Conclusions:

• The study provides a comprehensive dynamic description of molecular search with alternating dynamics.
• Theoretical predictions regarding dynamic regimes and length scales are robustly supported by simulations.
• The findings offer insights into optimizing molecular search strategies in complex environments.