Non-Equilibrium Thermodynamics Modeling of Coupled Biochemical Cycles in Living Cells
Y. Demirel

Department of Chemical and Biomolecular Engineering, University of Nebraska Lincoln United States

Abstract: Every developed and adapted biological system extracts useful energy from outside, converts to the adenosine triphosphate (ATP), and uses for the coupled biochemical cycles and transport processes, protein synthesis, and other energy utilizing processes. The coupling refers that a flow occurs without or against its primary thermodynamic driving force, which may be a gradient of temperature, or chemical potential, or reaction affinity. The principles of thermodynamics allow the progress of a process without or against its primary driving force only if it is coupled with another spontaneous process. This is consistent with the statement of second law, which states that a finite amount of organization may be obtained at the expense of a greater amount of disorganization in a series of coupled spontaneous processes. A living cell has to maintain nonvanishing thermodynamic forces, such as electrochemical potential gradient, and hence is an open, nonequilibrium system. This study presents the modeling equations for thermodynamically and mathematically coupled system of an elementary reaction with heat and mass flows and external resistances. The modeling is based on the linear nonequilibrium thermodynamics (LNET) formulations by assuming that the system is in the vicinity of global equilibrium (GE). Experimental investigations revealed that LNET is capable of describing thermodynamically coupled processes of oxidative phosphorylation, mitochondrial H+ pumps, and (Na+ and K+)]-ATPase, because mainly due to enzymatic feedback. Moreover, the LNET formulation does not require the detailed mechanism of the coupling. Kinetic descriptions and considerations may lead to a loss of the generality characteristics of thermodynamic formulations, since the kinetics is based on specific models. The modeling equations have produced some unique cross coefficients between scalar process of chemical reaction and vectorial processes of heat and mass flows. These coefficients relate the cross interactions to measurable kinetic parameters, transport coefficients, and degrees of thermodynamic couplings. Some representative solutions of thermodynamically coupled reaction]transport systems are presented and discussed.