Using the velocity auto-correlation function to characterize functional ”noise” in bio-molecules

Characterization of current noise in simulated electrical systems relies on the Fourier transform of the auto-correlation of electrons velocity. A similar characterization can also be done in the simulation of biological systems, which relies on a statistical mechanics description through the calculation of the trajectories of the atoms over time. In such a system, the quantity calculated in the same way as electrical noise can be defining, whether it has functional significance or can be compared to experiments in the Mega to TeraHertz range. To exemplify this, we carried out the simulation of a model protein, the Bovine Serum Albumin, and outline the necessary precautions needed to obtain biologically relevant information.