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Molecular Machines

A molecular machine is a single macromolecule or macromolecular complex that performs a specific function for a living system [Schneider, 1991]. For example, single stranded DNA can hybridize to form duplex DNA [Britten & Kohne, 1968]. This operation is defined by two limiting states, before the operation when the strands are separated, and after the operation when complementary strands are paired. Consider the First Law of Thermodynamics for this operation:

$$\Delta U = q+ w$$ (1)

where $\Delta U$ is the change in internal energy, q is the heat flowing into the machine and w is the work done by the machine on the surroundings. (The defined directions of q and w reflect their original use to describe the input of heat and extraction of work from steam engines.) Since the DNA molecule does not do work on an external object when it hybridizes, w= 0. The internal energy of the machine decreases, $\Delta U < 0$, so heat is dissipated into the surroundings, q< 0. How can we characterize the action that the machine has taken if it does not do external work? Although the operation can be characterized by the energy dissipated, the important biological aspect of the operation is the number of choices that the machine makes. Thus, to form each base pair of DNA, only 4 out of 16 possibilities are acceptable. This 1 in 4 choice represents $\log_2 4 = 2$bits of information ``gained'' by the machine. Other examples and a detailed definition of molecular machines and their operations are given in [Schneider, 1991].