Figure 3

Two scenarios demonstrating the application of KMFA. (A) Scenario I: Making a non-functional design functional. If we have a non-functional original design, as indicated by the dynamics of the deterministic and stochastic simulation shown, we can transform its kinetic parameters into efficiency levels and look in the handbook of kinetic motifs (Additional file 1: Table S3) for a similar, but functional, design to replace some of the ribosome binding sites (RBS, denoted as R and represented by triangles) and/or protein degradation tags (PDT, denoted as T and represented by hexagons) with others with a suitable efficiency level to render the modified design functional. In this example, two different routes of minimal changes (Hamming distance (D) of replacement = 2) were found. (B) Scenario II: Improving a functional design. In this example, the original, already functional, design is that reported by Chen and Wu [31], the ranking of which in our performance table (Additional file 1: Table S3) can be improved by selecting components with an RBS and/or PTD that can work with other components to generate a better system performance (i.e. better performance ranking in Additional file 1: Table S3). All notations and symbols are the same as those in (A).