Stochastic modeling of macromolecules in solution. I. Relaxation processes

Area of Science:

• Computational chemistry
• Molecular dynamics
• Biophysics

Background:

• Describing relaxation processes in flexible macromolecules is crucial for understanding their dynamics.
• Existing models often lack a unified approach to include dissipative effects from an atomistic viewpoint.

Purpose of the Study:

• To introduce a novel framework for the stochastic description of relaxation processes in flexible macromolecules.
• To incorporate dissipative effects and enable interpretation of magnetic resonance relaxation experiments.

Main Methods:

• Utilizing projection-operator techniques to derive multidimensional Fokker-Planck operators.
• Developing a hierarchy of approaches with varying complexity.
• Employing atomistic descriptions and classic force fields for energetics and friction tensors.

Main Results:

• The framework provides parameters fully recoverable from classic force fields and continuum models.
• A unified context is established for describing relaxation dynamics.
• A test case using a harmonic internal Hamiltonian is presented.

Conclusions:

• The proposed framework offers a versatile tool for studying macromolecule dynamics.
• It facilitates the interpretation of magnetic resonance relaxation experiments.
• The atomistic approach provides a deeper understanding of relaxation mechanisms.