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 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 the binding mechanism
that is performed using the coordinate demonstrates that the lipid
bilayer undergoes a series of concerted changes in structure as the
nanoparticle binds.