In school education the concept of energy should be a unifying element between all natural science disciplines. Still, many characteristics of living systems appear to be in contradiction to the laws of physics. Physics often refer to energy conservation in a closed system, whereas biology is dominated by open ecological or physiological systems with a "dynamic equilibrium“. This makes the underlying, crosscutting scientific concept of energy hard to understand. Our study investigated, if the idea of an open energy system (with an in- and output of energy), located within an “idealized” closed system (in which the total amount of energy is conserved), offers the potential for a cross-disciplinary understanding. We developed a learning environment and applied interviews to identify students’ ability to think in open and closed systems. Four teaching experiments with focus groups of three students each (9th grade, secondary school, males = 10) were carried out. Within the learning environment a scaled model demonstrated processes in a biogas plant and illustrated the idea of an open system that is in direct exchange with the environment. Students easily described the conversion of energy within the scaled model, but faced severe difficulties when the energy was emitted into the environment. Consequently they showed scientifically wrong conceptions when energy could not be perceived through phenomena anymore. We propose the particle model to illustrate energy and to bridge the apparent macro- microscopic gap.