Physics education in secondary schools can include biophysics topics as electives. An open simulation based on a simulation like Minecraft for learning the workings of the action potential in human cells was designed and tested for students in upper secondary physics education. In small design and test cycles both the simulation engine and the classroom materials were developed. The simulation shows realistic results that go beyond the accompanying textbook. The finished prototype of the engine and the materials were used to study student reasoning during their simulation of the action potential. Results show that students reason together about what they see in the simulation to come to theories on the action potential process, showing profound learning. The students did not master the more open inquiry final assignment.