Using Intrinsic Surfaces to Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes

A reaction coordinate that can be used when investigating binding to dynamical surfaces with molecular dynamics is introduced. This coordinate measures the distance between the adsorbate and an isocontour in a density field. Furthermore, the coordinate is continuous so simulation biases that are a function of this coordinate can be added to the Hamiltonian in order to increase the rate of adsorption/desorption. The efficacy of this new coordinates is demonstrated by performing metadynamics simulations to measure the strength with which a hydrophilic nanoparticle binds to a lipid bilayer. An investigation of this binding mechanism that is performed using the coordinate demonstrates that the structure of the lipid bilayer undergoes a series of concerted changes in structure as the nanoparticle binds.