A Stochastic Finite Element Model for the Dynamics of Globular Macromolecules

TL;DR

This paper introduces a new coarse-grained finite element simulation approach for modeling the thermal fluctuation-driven dynamics of globular macromolecules like proteins, validated against classical energy principles and applied to protein deformation over long timescales.

Contribution

The paper presents a novel finite element-based coarse-grained model that incorporates non-linear elasticity, viscosity, and thermal noise for simulating macromolecular dynamics.

Findings

Model accurately reproduces average kinetic and potential energies.

Fourier analysis confirms correct energy distribution in bending modes.

Simulated protein deformation aligns with atomistic molecular dynamics results.

Abstract

We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a non-linear treatment of elasticity and viscosity with thermal noise that is solved using finite element analysis. We have validated the method by demonstrating that the model provides average kinetic and potential energies that are in agreement with the classical equipartition theorem. In addition, we have performed Fourier analysis on the simulation trajectories obtained for a series of linear beams to confirm that the correct average energies are present in the first two Fourier bending modes. We have then used the new modelling method to simulate the thermal fluctuations of a representative protein over 500ns timescales. Using reasonable parameters for the material properties, we have demonstrated that the overall deformation of the biomolecule is consistent with the results obtained for proteins in general from atomistic molecular dynamics simulations.