Inverse Boltzmann Iterative Multi-Scale Molecular Dynamics Study between Carbon Nanotubes and Amino Acids

Area of Science:

• Computational chemistry
• Materials science
• Biophysics

Background:

• Coarse-grained (CG) models simplify complex molecular systems for large-scale simulations.
• Accurate CG models require precise interaction potentials, often derived from All-Atom Molecular Dynamics (AAMD) simulations.
• Traditional methods for deriving CG potentials can be computationally intensive and may lack accuracy.

Purpose of the Study:

• To apply Iterative Boltzmann Inversion (IBI) for accurate coarse-grained modeling of amino acid-carbon nanotube interactions.
• To validate the IBI method by comparing coarse-grained molecular dynamics simulation (CGMD) results with AAMD data.
• To establish a robust methodology for developing force fields for large biomolecules and nanoparticles.

Main Methods:

• Utilized Iterative Boltzmann Inversion (IBI), a multi-scale simulation technique.
• Performed AAMD simulations to obtain target distribution functions and Potential of Mean Force (PMF).
• Iteratively refined CG potentials using IBI for over 100 cycles, comparing CGMD and AAMD distributions.

Main Results:

• Achieved effective overlap between CGMD and AAMD distribution results after extensive IBI iterations.
• Demonstrated IBI's capability to accurately modify CG models derived from PMF.
• Successfully simulated the coarse-grained interaction between 20 amino acids and a representative carbon nanotube (CNT55L3).

Conclusions:

• IBI is a powerful tool for developing accurate coarse-grained force fields.
• The developed methodology provides a foundation for simulating large-scale biological systems and nanomaterials.
• This work enhances the predictive power of CG simulations in nanoscience and structural biology.