Predicting non-equilibrium folding behavior of polymer chains using the steepest-entropy-ascent quantum thermodynamic...

Area of Science:

• Thermodynamics
• Polymer Physics
• Computational Chemistry

Background:

• Polymer chain folding is crucial for protein function.
• Understanding non-equilibrium dynamics is essential for predicting polymer behavior.
• Existing models often simplify the complex interplay of heating and cooling on polymer structures.

Purpose of the Study:

• To investigate the influence of heating and cooling on polymer chain folding kinetics using the SEAQT framework.
• To model the transition from non-equilibrium to equilibrium states along unique thermodynamic paths.
• To provide insights into structural properties under non-equilibrium conditions.

Main Methods:

• Utilized the steepest-entropy-ascent quantum thermodynamic (SEAQT) framework.
• Generated a discrete energy landscape using the Replica Exchange Wang-Landau method for a polymer chain model.
• Applied the SEAQT equation of motion to simulate chain conformation evolution.
• Fitted SEAQT-predicted kinetics to experimental protein folding data (cytochrome c) using Rouse dynamics.

Main Results:

• The SEAQT framework successfully predicts polymer chain movement from non-equilibrium to equilibrium states.
• Chain conformations exhibit continuous changes during heating and cooling, without sharp morphological transitions.
• Non-equilibrium paths show more drastic conformational changes compared to quasi-equilibrium paths.
• SEAQT-predicted kinetics align with experimental observations of cytochrome c folding.

Conclusions:

• The SEAQT framework offers a powerful tool for exploring non-equilibrium polymer dynamics.
• Continuous conformational changes are characteristic of polymer folding under thermal cycling.
• The model provides valuable insights into the structural behavior of polymers under dynamic conditions.