Sequence logos, machine/channel capacity, Maxwell's demon, and molecular computers: a review of the theory of molecular machines

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Abstract
Living cells contain many molecules which can make simple decisions, such as whether to bind to a particular nucleotide sequence or not. A theory describing the practical limits of these molecular machines is reviewed. Level 0 theory uses Shannon's information theory to study genetic control systems. Level 1 theory uses Shannon's channel capacity theorem to explain how these biological molecules are able to make their decisions precisely in the face of the thermal maelstrom surrounding them. Level 2 theory shows how the Second Law of Thermodynamics defines the exact extent of the choices available to a molecular machine when it dissipates a given amount of energy. Even the famous Maxwell demon must obey this result. The theory also has implications for designing molecular computers.