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Master thesis projects

In this section you can find a list of master thesis projects offered by members of the SBP group.

Sequence-property relation of lattice polymers studied through the zeroes of the partition function

Supervisor: Raffaello Potestio

Background. In spite of their simplicity, lattice models of polymers are capable of providing a substantial qualitative and even quantitative insight in the physics of real polymeric macromolecules. A still open problem is the design of polymers featuring desired characteristics, that is, to define a sequence of monomers with known chemical properties such that the whole macromolecule displays a specific (structural or thermodynamical) behaviour.

Objective. This project aims at addressing this problem in general terms, establishing a link between the sequence of the polymer and the resulting thermodynamics. This analysis will be carried out making use of the well-known relationship existing between the location of zeroes of a system’s partition function and its thermodynamic properties.

Perks. This project is framed in the context of the VARIAMOLS ERC project; the student will have access to the computational resources of the research group.

CO2 dissociation through anharmonic vibrational energy transfer

Supervisors: Raffaello Potestio, Paolo Tosi

Background. CO2 dissociation is a topic of growing interest, also because of its possible applications to solve energetic and environmental problems. The CO2 –> CO + O reaction can be initiated by the electronic impact excitation of CO2 into a dissociative state, producing CO or O in an electronically excited state (the formation of the ground state CO(X1Σ+)+O(3P) is spin-forbidden). This process requires an energy larger than 7 eV. On the other hand, if dissociation were achieved through vibrational up-pumping mechanism, only 5.5 eV would be sufficient. This second mechanism relies on the vibrational energy transfer that takes place in collisions between CO2 molecules. The anharmonicity of the potential, in fact, favors the further energy transfer towards already highly excited molecules at the expenses of lesser excited ones. Several clues have been collected that vibrational up-pumping might indeed function. However, the quantification of the efficiency of this process has remained elusive. Recent works have tackled this issue employing semiclassical dynamics, see e.g.

• A. Lombardi et al. J. Chem. Phys. 143, 034307 (2015)
• A. Lombardi et al. Chemical Physics Letters 779 (2021) 138850

Objectives. In this thesis project we aim at studying the vibrational quanta exchange in CO2 molecule collisions, focusing in particular on dissiociation and vibrational up-pumping, employing molecular dynamics techniques. Specifically, the objective is to implement the potential energy surfaces developed in the aforementioned works in the molecular dynamics software package LAMMPS, and perform simulations to study the dissociation mechanism acquiring sufficient statistics.

Perks. This project is carried out in collaboration with Paolo Tosi from the Atomic and Molecular Physics group.

Characterisation of the entropic landscape of a polymer with adhesive beads

Supervisors: Luca Tubiana, Raffaello Potestio

Background. Polymers are long molecules constituted by small units connected one after the other in a linear chain. Many relevant molecules are polymers, such as DNA, RNA, proteins, as well as several artificial ones, plastic and rubber being among the most prominent examples. Single polymer chains can very likely be found in a self-entangled conformation, that is, the configurations that a polymer can attain at equilibrium will most likely contain one or more knots, just as in shoelaces or other cords. The knot spectrum of simple polymers has been thoroughly studied and is currently well understood, however the properties of knotted polymers become much more complex as soon as a few nontrivial interactions are allowed among the molecule’s constituents.

Objective. The goal of this master thesis work is to characterise the knotting properties of polymer chains featuring various patterns of simple attractive interactions. The investigation, relying on molecular dynamics simulations, will aim at describing the knotting process in terms of the conformational entropy of the system. This work bears great importance for the understanding of the knotting process in biological heteropolymers (e.g. proteins) and for the design of artificial molecules with tailored topological properties.