Ph.D. in Mathematics and Informatics, thesis:
Optimization and Ontology for Computational and Systems Biology, 2010.

In the context of my PhD I studied, mostly, problems that find their location in the bioinformatics and bioengineering fields. More precisely, I tackled problems and issues in biological engineering and synthetic biology; my research spanned from the developed of new algorithms to the engineering of specific metabolic pathways, to the data integration for synthetic biology purposes.

In the context of the artificial photosynthesis, I studied the C3 carbon metabolism; among the others, efficient sequestrations of carbon dioxide and the optimization of the nitrogen cycle have been targeted. In this context, I have individuated which are the enzymes responsible for an efficient and robust trade-off between maximization of functional tasks (e.g., CO2 uptake) and minimization resource employment.

Geobacter sulfurreducens, a microorganism capable of employing biomass to produce electrons, has been studied as well; an ad-hoc tuning through bioengineering of its fluxes would bring a new strain particularly important for biotechnological issues.

Results obtained in the study of C3 carbon metabolism and Geobacter sulfurreducens, are currently under consideration for “in vitro” and “in vivo” implementations, respectively.

New algorithmic approaches have been developed as well. Introducing the concept of migration in a genetic algorithm framework, different niches of solutions are let evolve; promising solutions obtained by different algorithms are shared through the exchange of solution portions in an archipelago fashion.

With respect to synthetic biology and systems biology, a data integration problem has been also tackled. Where biological and medical resources are concerned, I have developed a library whose aim is the recognition of overlaps among runnable pathways. An integration based on ontologies has been implemented. The system has been tested against a well-know database; several redundancies and duplications have been identified there, and a new sorted dictionary of synthetic components has been derived. The resulting software is currently embedded in the project Cytosolve@MIT, where it is employed to ensure correct parallel simulation of multiple models.

On a parallel track, I also studied problems that are modeled in terms of Cellular Automata, that are a computing environment that shows a straight inspiration from natural phenomena.

See Research section for details on each topic.