Rolling resistance ranks among the top ten automobile megatrends, because it is directly linked to fuel efficiency and emissions reduction. The mechanisms controlling this phenomenon are hidden deeply inside the complexity of tire tread materials and do elude direct experimental observation. Here we use atomistic molecular modelling to identify a novel nano-mechanical mechanism for dissipative loss in silica filled elastomers when the latter are subjected to dynamic strain. The force-vs-particle separation curve of a single silica particle-to-silica particle contact, embedded inside a polyisoprene rubber matrix, is obtained, while the contact is opened and closed by a cyclic force. We confirm the occurrence of spontaneous relative displacements ('jolts') of the filler particles. These jolts give rise to energy dissipation in addition to the usual viscous loss in the polymer matrix. As the temperature is increased the new loss mechanism becomes dominant. This has important technical implications for the control and reduction of tire rolling resistance as well as for many other elastomer composite applications involving dynamic loading.