Simulation of the kinetics of a sphere attached to a fluctuating polymer: Implications for target search by DNA-binding proteins

We simulate the dynamics of a sphere, bound with a certain probability onto the beads of a harmonic bead-spring polymer in a confined geometry. The sphere hops from ith to the spatially closest i+/-kth bead. There is a crossover between kinetics dominated by different mechanisms with increasing binding probability. We relate these observations to the context of a biologically important problem of target location by DNA-binding proteins within a genome.