Many fundamental biological processes, such as all enzymatic reactions and some ligand-protein interactions, involve mechanisms in which chemical bonds are formed and/or broken, as well as large electronic reorganization. For instance, when oxygen binds to the active center of hemoglobin, the heme prosthetic group  changes from a quintuplet spin state to a singlet state whose electron distribution has long been debated.  At the same time, a covalent bond between the oxygen molecule and the heme iron atom develops. Our research is focused on computational simulation of biological processes that involve large electronic changes from an atomistic point of view. Our main tools are ab initio molecular dynamics (Car-Parrinello MD), enhanced sampling methods (metadynamics and umbrella sampling), classical MD and hybrid quantum mechanics/molecular mechanics (QM/MM) methods.  Most projects are being performed in collaboration with experimental groups of biochemistry, synthetic biology and structural chemical biology.       

Currently our research focuses on:  
  •  Enzymatic synthesis and degradation of carbohydrates.
  • Catalase and peroxidase catalytic mechanisms.
  • Gold clusters and nanoparticles and their interaction with proteins.
  We participate in the H2020 project:logo
Recent representative publications


The conformational free energy landscape of the mannoimidazole inhibitor (center panel) displays a strong preference for the transition state conformations found in beta-mannanases (Angew. Chem. Int. Ed. 53, 1087, 2014)