The mathematics class in Protégé has two sub-classes: Calculus (building, communicating and considering equations, formulas and functions to communicate chemical engineering definitions) and Geometry (showing the importance of the difference in carrying out transfer phenomena in members of biological systems with different shapes).
This direct class includes members of penetration, convective mass transfer, and displacement transfer. which are related or defined to other variables according to their expressions and equations as well as the geometry of the object, and the effects of other variables on them or vice versa are shown. In this section, the concepts of the transfer of soluble substances and the types of transfer methods from the membrane of a living cell, and especially the concept of chemical potential, will be more important.
Heat transfer class in Protégé: This class includes three subclasses: convective heat transfer, conductive heat transfer, and radiant heat transfer. A living system can gain or lose heat through heat exchange mechanisms. Cells, as the basic unit of life, undergo continuous heat transfer and loss during their metabolism. Heat transfer and loss in cells is not only related to the basic cellular functions of biochemical reactions, but also related to several important applications, including the control of biological processes caused by heat.
Thermodynamic class in Protégé: This class includes thermodynamic variables whose members are energy, enthalpy, equilibrium, free energy, heat and work, and each of these variables is related to or defined as sub-variables according to their geometry and how they are calculated. The effects of other variables on them or vice versa are shown. Finally, according to the chemical reactions of oxidation and reduction and considering the laws of systems and phases, they are related to biological systems. This section also deals with the biological concepts of enzymes and their kinetics