Optimization and Ontology for Computational Systems Biology

In the context of my PhD I studied mostly problems that nd their location in the bioinformatics and bioengineering elds. The arti cial photosynthesis has been object of my research and problems like the e cient sequestrations of CO2 and the optimization of the Nitrogen consumption have been taken as target. Geobacter sulfurreducens, a microorganism capable of employing biomasses to produce electrons, has been studied as well. New algorithmic approaches have been developed on both topics and new results obtained are currently un- der consideration for \in vitro" and \in vivo" implementations. The integration of the information coming from biological and medical re- sources is a problem that I tackled as well; in this case, the resulting software is currently embedded in the project Cytosolve@MIT. 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.