  Tethered particle motion (TPM) --- the motion of a micro- or nanoparticle
tethered to a substrate by a macromolecule --- is a system that has proven
extremely useful for its ability to reveal physical features of the tether,
because the thermal motion of the bound particle reports sensitively on
parameters like the length, the rigidity, or the folding state of its tether.
In this paper, we discuss a novel application of TPM, surveying its utility in
probing the kinetics of single secondary bonds: bonds that form and break
between the tethered particle and a substrate due, for instance, to
receptor/ligand pairs on particle and substrate. Much like the tether itself
affects the motion pattern, so do the presence and absence of such secondary
connections. Keeping the tether properties constant, we demonstrate how raw
positional TPM data may be parsed to generate detailed insights into the
association and dissociation kinetics of single secondary bonds. We do this
using coarse-grained molecular dynamics simulations, specifically developed to
treat the motion of particles close to interfaces.
