  Biological molecular machines are enzymes that simultaneously catalyze two
processes, one donating free energy and second accepting it. Recent studies
show that most native protein enzymes have a rich stochastic dynamics that
often manifests in fluctuating rates of the catalyzed processes and the
presence of short-term memory resulting from transient non-ergodicity. For such
dynamics, we prove the generalized fluctuation theorem predicting a possible
reduction of energy dissipation at the expense of creating some information
stored in memory. The theoretical relationships are verified in computer
simulations of random walk on a model critical complex network. The transient
utilization of memory may turn out to be crucial for the movement of protein
motors and the reason for most protein machines to operate as dimers or higher
organized assemblies. From a broader physical point of view, the division of
free energy into the operation and organization energy is worth emphasizing.
Information can be assigned a physical meaning of a change in the value of both
these functions of state.
