To accurately predict traffic flow and optimize the operations of freeway bottleneck areas in a mixed-vehicle driving environment, this paper proposes a traffic prediction model and a variable speed limit (VSL) cooperative control strategy. Firstly, a lane-level short-term traffic prediction model, physics informed Transformer and cell transmission model (PIT-CTM), is constructed by combining the Transformer neural network and lane-level cell transmission model (CTM) based on the physics-informed deep learning framework. On this basis, the accuracy and transferability of PIT-CTM are analysed. Secondly, a lane assignment decision model is presented, which enables the dynamic planning of the optimal traffic distribution across lanes. Furthermore, a lane-level VSL control model is constructed based on the model predictive control (MPC) framework. The model induces vehicles to change lanes earlier by setting the speed limit difference between lanes. By regulating the input flow in the bottleneck area of the freeway, it reduces conflicts between mainline vehicles and ramp vehicles. Finally, the feedback regulation between the lane assignment decision model and the lane-level VSL control model promotes the cooperative optimisation of the lateral and longitudinal flows and adapts the control strategy to the dynamic traffic characteristics. A three-lane freeway merging zone is selected, the numerical experiment is conducted and compared with differential lane-level VSL. The results show that the strategy can effectively optimise the mixed-vehicle traffic state and maintain better control performance under any connected and autonomous vehicle (CAV) penetration rates.
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