CINQUEMANI , Eugenio

We address state estimation for gene regulatory networks at the level of single cells. We consider models that include both intrinsic noise, in terms of stochastic dynamics, and extrinsic noise, in terms of random parameter values. We take the Chemical Master Equation (CME) with random parameters as a reference modeling approach, and...

We address online estimation of microbial growth dynamics in bioreactors from measurements of a fluorescent reporter protein synthesized along with microbial growth. We consider an extended version of standard growth models that accounts for the dynamics of reporter synthesis. We develop state estimation from sampled, noisy measurements in the...

The bacterium E. coli is widely used to produce recombinant proteins such as growth hormone and insulin. One inconvenience with E. coli cultures is the secretion of acetate through overflow metabolism. Acetate inhibits cell growth and represents a carbon diversion, which results in several negative effects on protein production. One way to...

Synthetic microbial consortia have been increasingly utilized in biotechnology and experimental evidence shows that suitably engineered consortia can outperform individual species in the synthesis of valuable products. Despite significant achievements, though, a quantitative understanding of the conditions that make this possible, and of the...

We investigate optimization of an algal-bacterial consortium, where an exogenous control input modulates bacterial resource allocation between growth and synthesis of a resource that is limiting for algal growth. Maximization of algal biomass synthesis is pursued in a continuous bioreactor, with dilution rate as an additional control variable....

The growth of microorganisms is controlled by strategies for the dynamical allocation of available resources over different cellular functions. Synthetic biology approaches are considered nowadays to artificially modify these strategies and turn microbial populations into biotechnological factories for the production of metabolites of interest....

Recent works have demonstrated the experimental feasibility of real-time gene expression control based on deterministic controllers. By taking control of the level of intracellular proteins, one can probe single-cell dynamics with unprecedented flexibility. However, single-cell dynamics are stochastic in nature, and a control framework...

In this article, the problem of state estimation of a microbial consortium is discussed. This microbial consortium is composed of two strains, called producer and cleaner, in continuous culture. The producer strain grows by consuming glucose, while the cleaner grows by consuming the acetate excreted by the producer and toxifies the environment....

The growth of microorganisms involves the conversion of nutrients in the environment into biomass, mostly proteins and other macromolecules. This conversion is accomplished by networks of biochemical reactions cutting across cellular functions, such as metabolism, gene expression, transport and signalling. Mathematical modelling is a powerful...