Contacts:
Supervisor(s):
Prof. Benedetta Mennucci and Dr. Lorenzo Cupellini
Title of the PhD project:
Statistical Learning Strategies for the Modelling of Photoresponsive Proteins
Abstract of the PhD project:
The biological activation of photoresponsive proteins by means of the incident light lies at the basis of many relevant processes, of which photosynthesis may be the most striking example. These proteins embed one or more chromophores, small organic molecules responsible for the light absorption. Usually, conformational changes follow the initial light absorption, leading to an activation or deactivation of the protein. The biological (de)activation of these proteins is then a complex dynamic process, requiring the combined application of techniques from various fields such as physics, chemistry, biology, and statistics.
On one hand, describing the light absorption process and the interactions between excited pigments requires using accurate quantum chemistry protocols. On the other hand, the dynamic nature of these processes prevents drawing conclusions based on a static picture of the problem. As a result, molecular dynamics simulations have been extensively used to simulate the dynamics of these proteins. Conventional simulation and quantum chemistry techniques are nonetheless limited by their high computational cost. Promising routes for overcoming the computational cost of conventional simulations are enhanced sampling techniques, while statistical learning combined with quantum chemistry is proving to be an excellent strategy for retaining a high accuracy with a small computational cost.
The aim of my work is to combine enhanced sampling techniques with statistical learning to the study of photoresponsive proteins. At first, I am currently working on the modelling of excited state properties of pigments embedded in light-harvesting complexes.
Publications:
• Lapillo, M., Cignoni, E., Cupellini, L., & Mennucci, B. (2020). The energy transfer model of nonphotochemical quenching: Lessons from the minor CP29 antenna complex of plants. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 1861(11), 148282.
• Cignoni, E., Lapillo, M., Cupellini, L. Gutiérrez, S. A., Gervasio, F. L., Mennucci, B. A different perspective for nonphotochemical quenching in plant antenna complexes. Nat Commun 12, 7152 (2021).
Oral communications at conferences:
• Cignoni, E., Lapillo, M., Cupellini, L., Gutièrrez, S. A., Gervasio, F. L., Mennucci, B., A new perspective for nonphotochemical quenching in plant antenna complexes; Computational Methods in Photosynthesis – From atoms to the mesoscale, from theory to experiment (Virtual meeting, 8th-11th November 2021)
Poster communications at conferences:
• Cignoni, E., Lapillo, M., Cupellini, L., Gutiérrez, S. A., Gervasio, F. L., Mennucci, B., Another perspective for nonphotochemical quenching in plant antenna complexes; CFF 2021 – Chemistry for the Future International Conference; Università di Pisa; Dipartimento di Chimica e Chimica Industriale, Via Giuseppe Moruzzi, 13 – Pisa, June 30 – July 2, 2021
Other achievements:
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