Research Interests

 

My main research interests are in the field of formal and biological complex systems.

In particular, the work on formal complex system is mainly related to Cellular Automata. The leading motif in

this context is the the investigation of possible intersections between Computation Theory and Dynamical

System Theory. The research in this field consists of the following topics:

  1. formal proofs of the (un)decidability of properties related to the dynamics of Cellular Automata,

  2. investigation of the computational capabilities and Turing-universality of Cellular Automata,

  3. classification of the dynamical behavior of Cellular Automata in terms of their computational properties.


The work in the field of biological complex systems in mainly related to the Protein Folding problem. The

work in this context is mostly oriented to the development of heuristic and machine-learning algorithms:

  1. development of heuristic algorithms for NP-complete problems, such as the problem of reconstructing

   protein three-dimensional structures from the two-dimensional graph representation of their map of

   inter-residue contacts (contact maps) and the problem of aligning two-dimensional contact maps,

   as a measure of protein structure similarity,

  1. development of machine learning methods (neural networks, support vector machines, gradient

   descent-based algorithms) for the prediction of protein inter-residue contacts,

  1. development of algorithms for protein remote homology detection.