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A supplier of products and services aims to minimize the capacity investment cost and the operational cost incurred by unwanted byproducts, e.g. carbon dioxide emission. In this paper, we consider a sustainable supply chain network design problem, where the capacity and the product flow along each link are design variables. We formulate it as a multi-criteria optimization problem. A bio-inspired algorithm is developed to tackle this problem. We illustrate how to design a sustainable supply chain network in three steps. First, we develop a generalized model inspired by the foraging behaviour of slime mould Physarum polycephalum to handle the network optimization with multiple sinks. Second, we propose a strategy to update the link cost iteratively, thus making the Physarum model to converge to a user equilibrium. Third, we perform an equivalent operation to transform a system optimum problem into a corresponding user equilibrium problem so that it is solvable in the Physarum model. The efficiency of the proposed algorithm is illustrated with numerical examples. [ABSTRACT FROM AUTHOR]