Simulations of living filaments

TL;DR

This paper introduces a hybrid simulation model combining Molecular Dynamics, Multi-particle Collision Dynamics, and Monte Carlo methods to study equilibrium properties of self-assembled semiflexible filaments, such as actin.

Contribution

The paper presents a novel integrated simulation framework for equilibrium filament dynamics, including detailed balance in polymerization and depolymerization processes.

Findings

Distribution of filament lengths obtained

Dynamical fluctuations characterized

Model applicable to various biological filaments

Abstract

We propose a hybrid Molecular Dynamics/Multi-particle Collision Dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte-Carlo scheme to deal with single monomer addition (polymerization) or removal (depolymerization), satisfying the detailed balance condition within a proper statistical mechanical framework. This model of filaments, based on the wormlike chain, aims to represent equilibrium polymers with distinct reaction rates at both ends, such as self-assembled ADP-actin filaments in the absence of ATP hydrolysis and other proteins. We report the distribution of filament lengths and the corresponding dynamical fluctuations on an equilibrium trajectory. Potential generalizations of this method to include irreversible steps like ATP-actin hydrolysis are discussed.