Automatic Design of Synthetic Gene Circuits through Mixed Integer Non-linear Programming

Automatic Design of Synthetic Gene Circuits through Mixed Integer Non-linear Programming

Automatic design of synthetic gene circuits poses a significant challenge to synthetic biology, primarily due to the complexity of biological systems, and the lack of rigorous optimization methods that can cope with the combinatorial explosion as the number of biological parts increases. Current optimization methods for synthetic gene design rely on heuristic algorithms that are usually not det...

Automated Design of Synthetic Gene Circuits through Linear Approximation and Mixed Integer Optimization

Synthetic biology aspires to revolutionize the way we construct biological circuits, as it promises fast time-to-market synthetic systems through part standardization, model abstraction, design and process automation. However, the automated design of synthetic circuits remains an unsolved problem, despite the increasing number of practitioners in the field. One reason behind that, is the absenc...

Application-oriented mixed integer non-linear programming

A Mixed Integer Linear Programming Model for the Design of Remanufacturing Closed–loop Supply Chain Network

Closed-loop supply chain network design is a critical issue due to its impact on both economic and environmental performances of the supply chain. In this paper, we address the problem of designing a multi-echelon, multi-product and capacitated closed-loop supply chain network. First, a mixed-integer linear programming formulation is developed to maximize the total profit. The main contribution...

Automatic Design of Digital Synthetic Gene Circuits

De novo computational design of synthetic gene circuits that achieve well-defined target functions is a hard task. Existing, brute-force approaches run optimization algorithms on the structure and on the kinetic parameter values of the network. However, more direct rational methods for automatic circuit design are lacking. Focusing on digital synthetic gene circuits, we developed a methodology ...