Towards the Autonomous Optimization of Urban Logistics: Training Generative AI with Scientific Tools via Agentic Digital Twins and Model Context Protocol

Optimizing urban freight logistics is critical for developing sustainable, low-carbon cities. Traditional methods often rely on manual coordination of simulation tools, optimization solvers, and expert-driven workflows, limiting their efficiency and scalability. This paper presents an agentic system architecture that leverages the model context protocol (MCP) to orchestrate multi-agent collaboration among scientific tools for autonomous, simulation-informed optimization in urban logistics. The system integrates generative AI agents with domain-specific engines - such as Gurobi for optimization and AnyLogic for agent-based simulation - forming a generative digital twin capable of reasoning, planning, and acting across multimodal freight networks. By incorporating integrated chatbots, retrieval-augmented generation, and structured memory, the framework enables agents to interpret user intent from natural language conversations, retrieve relevant datasets and models, coordinate solvers and simulators, and execute complex workflows. We demonstrate this approach through a freight decarbonization case study, showcasing how MCP enables modular, interoperable, and adaptive agent behavior across diverse toolchains. The results reveal that our system transforms digital twins from static visualizations into autonomous, decision-capable systems, advancing the frontiers of urban operations research. By enabling context-aware, generative agents to operate scientific tools automatically and collaboratively, this framework supports more intelligent, accessible, and dynamic decision-making in transportation planning and smart city management.