Isolated Closed and Open Systems
Every advanced theory has its origin in simple considerations, that are widened as the knowledge grows. It is therefore natural to split a complex process into parts, and analyse parts in isolation to then go further and to integrate this parts in a more complex theory. As our ability to understand processes is limited, we are forced to restrict our attention to a part of the universe, that we want to study in detail. Let us call this part the system. It shall be separated from the rest of the universe by the system boundary. To simplify our initial investigation, we assume, that at the system boundary, which we might choose randomly, there is no interaction with the rest of the universe. Or at least we can neglect the interaction. If we study this system we might find that energy in such a system is conserved. In the next step, we might extend our theory and study the interaction of such systems (or better subsystems) of a larger system, by allowing them to exchange energy. At this stage one possibly discovers the second law of thermodynamics. We are also able to investigate some thermodynamic processes. To go even further, we have to drop our assumption on negligible boundary conditions by one more criteria. We need to allow matter to flow through the boundary.
In thermodynamics one differs between three types of systems, they are characterised by the properties of their boundary. Isolated systems allow whether energy nor matter to be exchanged. Closed systems allows heat to pass the boundary but not matter. Open Systems allow both heat and energy to pass through the boundary.
Given enough time thermodynamic processes in an isolated systems reach equilibrium. Closed systems can exchange heat with the surrounding, this exchange of heat, can drive mechanical processes. This is the principle of an engine. Living organisms however maintain their energy needs by utilising the energy contained in matter. This means they depend on the continuous supply of nutrient sources from the environment. Whereas in isolated systems chemical reactions reach equilibrium, open systems are able to operate away from equilibrium in what is called a flow steady state (Fließgleichgewicht) or nonequilibrium steady state. In such a steady state there is continuous reaction flux through the system, converting nutrients into energy and biomass. This principle is the foundation of the so called Flux Balance Analysis (FBA) where these processes are modelled in detail.