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Trust the force, but pull wisely: Structural insights into non-equilibrium response forces from pulling MD

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Area of Science:

  • * Computational chemistry and biophysics.
  • * Statistical mechanics of non-equilibrium systems.

Background:

  • * Molecular dynamics simulations are essential for understanding molecular processes.
  • * Analyzing systems under external driving requires advanced theoretical frameworks.

Purpose of the Study:

  • * To generalize Mori's Langevin equation for driven molecular systems.
  • * To investigate the spatial structure of forces in driven systems.
  • * To compare non-equilibrium response forces with mean forces in simulations.

Main Methods:

  • * Coarse-grained equations of motion analysis.
  • * Targeted and steered molecular dynamics simulations.
  • * Derivation of a generalized Langevin equation.

Main Results:

  • * Developed a generalized Langevin equation with memory kernel, driving force, and non-equilibrium response force.
  • * Demonstrated spatial structure in both stationary fluctuating forces and non-equilibrium response forces.
  • * Found discrepancies between non-equilibrium response and mean forces for specific pulling protocols.

Conclusions:

  • * The non-equilibrium response force is sensitive to driving protocols.
  • * Solvent effects in pulling simulations must be carefully considered.
  • * The generalized Langevin equation provides a robust framework for driven systems.