Simulation of longitudinal string waves through a single polymer molecule

• Feasibility of single-molecule acoustics was investigated by simulation.
• DNA strand was subjected to longitudinal oscillation at one end.
• Resulting propagating oscillation was shown to be wave-like.
• Proof of concept experiment using optical tweezers setup proposed and simulated.

The capability of an individual polymer molecule to carry an acoustic wave along its length was investigated by a Brownian dynamics simulation using the algorithm of Ermak and McCammon and the discrete worm-like chain model. A 3 μm long DNA strand featuring 50 nm persistence length was subjected to longitudinal oscillations (2 kHz to 25 kHz) at one end, and the properties of the resulting propagating interaction were studied and shown to be wave-like. A proof of concept experiment is proposed, where an optical tweezers dumbbell experiment is conducted to induce and receive the wave, and the result is compared to that of a control experiment with the DNA strand absent. Simulations were conducted to show what one might expect to see in such an experiment.