This position paper contributes to the debate on perspectives for simulating the social processes of science through the specific angle of participatory research. This new way of producing science is still in its infancy and needs some step back and analysis, to understand what is taking place on the boundaries between academic, policy and lay worlds. We argue that social simulation of this practice of cooperation can help in understanding further this new way of doing science, building on existing experience in simulation of knowledge flows as well as pragmatic approaches in social sciences