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Maxwell's Demons, Protein Molecular Machines, and Information Processing in Biophysics
Published: 03 November 2014 by MDPI in 1st International Electronic Conference on Entropy and Its Applications session Chemistry and Biology
Abstract: In the intention of its creator, Maxwell's demon was thought to be an intelligent being able to perform work at the expense of the entropy reduction of a closed operating system. The perplexing notion of the demon's intelligence was formalized in terms of the information processing by Szilard, who pointed out that, in order for the system to be consistent with the second law of thermodynamics, the entropy reduction should be compensated for by, at least, the same entropy increase related to the demon's information on the operating system state. A mechanical (non-informational) formulation of the problem was proposed by Smoluchowski and popularized by Feynman as the ratchet and pawl machine, which can operate only in agreement with the second law. A. F. Huxley and followers adopted this way of thinking to propose numerous thermal ratchet mechanisms of the biological molecular machines action. Here we show that, because of the necessary energy dissipation, both for the thermal ratchet and the concurrent power stroke models, no entropy reduction takes place. It is possible only for protein machine models with a number of conformational states organized in a network of transitions that allow the performance of work in a variety of ways. For such models, no information processing is necessary for the generalized fluctuation theorem to be satisfied. A computer realization is investigated of the conformational network, displaying, like networks of the systems biology, a transition from the fractal organization on a small length-scale to the small-world organization on the large length-scale. This model is able to explain a surprising observation to Yanagida and co-workers that the myosin II head can take several steps along the actin filament per ATP molecule hydrolysed. From a broader perspective, of especial importance could be the supposition that the mechanism of the action of small G-proteins, having a common ancestor with the myosin II, is, after a malignant transformation, similar. Presumably, also transcription factors look actively and not passively for their target on the genome.
Keywords: Maxwell’s demons; protein machine models