Ju n 20 21 I NFORMATION PROCESSING IN BIOLOGICAL MOLECULAR MACHINES

Biological molecular machines are bi-functional enzymes that simultaneously catalyze two processes: one providing free energy and second accepting it. Recent studies show that most protein enzymes have a rich dynamics of stochastic transitions between the multitude of conformation substates making up their native state. It is often manifested in fluctuating rates of the catalyzed processes and the presence of short-term memory resulting from the preference of selected conformations. For arbitrary stochastic dynamics of the protein machine, we proved the generalized fluctuation theorem, which leads to the extension of the second law of thermodynamics to include information that turns out to be a function of process changing the value of free energy. The subject of our analysis was the time course of the catalyzed processes expressed by sequences of jumps at random moments of time. Since similar signals can be registered in the observation of real systems, all theses of the paper are open to experimental verification. From a broader physical point of view, the division of free energy into the operation and organization energies is worth emphasizing.