title: Thermodynamics of biochemical networks and duality theorems.
abstract: One interesting yet difficult computational issue has recently been posed in biophysics in regard to the implementation of thermodynamic constraints to complex networks. Biochemical networks of enzymes inside cells are among the most efficient, robust, differentiated, and flexible free-energy transducers in nature. How is the second law of thermodynamics encoded for these complex networks? In this article it is demonstrated that for chemical reaction networks in the steady state the exclusion (presence) of closed reaction cycles makes possible (impossible) the definition of a chemical potential vector. Interestingly, this statement is encoded in one of the key results in combinatorial optimization, i.e., the Gordan theorem of the alternatives. From a computational viewpoint, the theorem reveals that calculating a reaction's free energy and identifying infeasible loops in flux states are dual problems whose solutions are mutually exclusive, and this opens the way for efficient and scalable methods to perform the energy balance analysis of large-scale biochemical networks.
authors.affiliation: Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome.
authors.forename: Daniele
authors.initials: D
authors.lastname: De Martino
mesh_terms: D000818:Animals; D001704:Biopolymers / Q000737:chemistry / Q000378:metabolism*; D003198:Computer Simulation; D004735:Energy Transfer / Q000502:physiology*; D006801:Humans; D008954:Models, Biological; D008956:Models, Chemical; D009097:Multienzyme Complexes / Q000737:chemistry / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D013816:Thermodynamics
chemical_list: D001704:Biopolymers; D009097:Multienzyme Complexes