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1-junctions 2-port elements action potentials active centers active transport Al-elements ansatz assumed asymptotically stable autocatalytic bath system biological membranes biological systems bond-graph network capacitance matrix Chapter chemical potential chemical reactions closed loops component concentration condition const coupling criterion defined depends derive diffusion dL/dt entropy production enzyme equations of motion example excitation model expressed external feedback formulation function given globally and asymptotically Hodgkin-Huxley Hodgkin-Huxley model inserting instable intensive variables interaction internal energy ions irreversible Ising model law of thermodynamics limit cycle linear macro-states membrane voltage model in Section molecular molecules network language nonequilibrium obtain particles phase space phenomenon physical pore model ports processes product ansatz rate constants reaction flux real system respect reverse rates saturation second law Section 2.2 so-called solution species stability stable steady steady state flux substrate subsystems temperature thermodynamic equilibrium thermodynamic system variables variations whereas