title: Stationary distribution of self-organized states and biological information generation.
abstract: Self-organization, where spontaneous orderings occur under driven conditions, is one of the hallmarks of biological systems. We consider a statistical mechanical treatment of the biased distribution of such organized states, which become favored as a result of their catalytic activity under chemical driving forces. A generalization of the equilibrium canonical distribution describes the stationary state, which can be used to model shifts in conformational ensembles sampled by an enzyme in working conditions. The basic idea is applied to the process of biological information generation from random sequences of heteropolymers, where unfavorable Shannon entropy is overcome by the catalytic activities of selected genes. The ordering process is demonstrated with the genetic distance to a genotype with high catalytic activity as an order parameter. The resulting free energy can have multiple minima, corresponding to disordered and organized phases with first-order transitions between them.
authors.affiliation: Henry M. Jackson Foundation for the Advancement of Military Medicine, 2405 Whittier Drive, Frederick, Maryland, 21702, USA.
authors.forename: Hyung Jun
authors.initials: HJ
authors.lastname: Woo
mesh_terms: D002384:Catalysis; D004247:DNA / Q000378:metabolism*; D019277:Entropy; D004798:Enzymes / Q000378:metabolism* / Q000493:pharmacokinetics*; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000378:metabolism*; D012313:RNA / Q000378:metabolism*
chemical_list: D004798:Enzymes; D011506:Proteins; D012313:RNA; D004247:DNA