Thesis Proposals

MACHINE-LEARNING FRAMEWORK FOR THE CHARACTERIZATION OF CHEMICAL BONDING

Supervisor: Sergio Rampino

Chemistry is discussed and rationalized in terms of concepts rooted in quantum mechanics that have their physical counterpart in large, intricate and often opaque data produced by solving the Schrödinger equation. This thesis project aims at developing a machine-learning framework for the characterization of chemical bonding based on volumetric data of molecular electron densities obtained by state-of-the-art quantum-chemistry calculations, with a focus on latent relationships between hidden data features and well-established concepts (e.g., donation, backdonation, hydrogen bonding). Applications will include comparison with available bond-analysis methods [1, 2] and the characterization of molecular systems exhibiting controversial features.


REFERENCES
[1] Bader RFW, A Quantum Theory of Molecular Structure and its Applications, Chemical Reviews 91, 893–928 (1991)
[2] Nottoli G, Ballotta B, Rampino S, Local Charge-Displacement Analysis: Targeting Local Charge-Flows in Complex Intermolecular Interactions, The Journal of Chemical Physics 157, 084107, 13pp (2022)

GENERATIVE ARTIFICIAL-INTELLIGENCE MODELS FOR MOLECULAR DISCOVERY

Supervisors: Sergio Rampino, Antonino Polimeno

Generative artificial-intelligence (AI) models have recently emerged as a new paradigm for molecular discovery [1, 2]. Within these models, a discrete molecular space is typically mapped into a continuous latent space which can then be explored for molecule extrapolation or interpolation driven by some optimization criteria. This thesis project will focus on the development and application of generative AI models for the discovery of new molecules featuring specific desired properties, with applications including drug discovery (e.g., targeting high efficiency for specific therapeutic purposes), advanced materials for energy harvesting, storage and conversion, and the design of sustainable deep-eutectic solvents for raw-material recycle.


REFERENCES
[1] Anstine DM, Isayev O, Generative Models as an Emerging Paradigm in the Chemical Sciences, Journal of the American Chemical Society 145, 8736–8750 (2023)
[2] Bilodeau C, Jin W, Jaakkola T, Barzilay R,  Jensen F, Generative Models for Molecular Discovery: Recent Advances and Challenges, WIREs Comput Mol Sci 12, e1608 (2022)

MACHINE-LEARNING MODELS FOR COMPLEX SPECTROSCOPIC DATA

Supervisors: Sergio Rampino, Antonino Polimeno

Modern spectroscopic techniques may produce a large amount of data which can be difficult to analyse and interpret with conventional techniques. In fluorescence lifetime imaging microscopy (FLIM) [1, 2] of biological cells, for instance, for each pixel of a targeted area a time-resolved signal is produced, resulting in a rich data structure intimately connected with the cell activity. This thesis project will focus on the definition and training of machine-learning models for the analysis and interpretation of spectroscopic experimental results obtained by FLIM measurements.


REFERENCES
[1] Zang Z, Xiao D, Wang Q, Li Z, Xie W, Chen Y, Li DDU, Fast Analysis of Time-Domain Fluorescence Lifetime Imaging via Extreme Learning Machine, Sensors 22, 3758 (2022)
[2] Speghini R, Buscato C, Marcato S, Fortunati I, Baldan B, Ferrante C, Response of Coccomyxa cimbrica sp.nov. to Increasing Doses of Cu(II) as a Function of Time: Comparison between Exposure in a Microfluidic Device or with Standard Protocols, Biosensors 13, 417 (2023)

EXACT-FACTORIZATION TECHNIQUES FOR QUANTUM REACTIVE SCATTERING

Supervisor: Sergio Rampino

Solving the time-dependent molecular Schrödinger equation typically involves the expansion of the molecular wavefunction in a set of time-independent electronic functions weighed by time-dependent nuclear functions. A promising emerging alternative approach is based on the idea of an exact factorization of the molecular wavefunction in a product of a single time-dependent nuclear function and a single time-dependent electronic function [1]. This thesis project will focus on the exploration of exact-factorization techniques for treating reactive quantum scattering [2] problems with applications to the modeling of nonadiabatic elementary chemical reactions.


REFERENCES
[1] Villaseco Arribas E, Agostini F, Maitra NT, Exact factorization adventures: a promising approach for non-bound states, Molecules 27, 4002 (2022) 
[2] Balakrishnan N, Kalyanaraman C, Sathyamurthy N, Time-Dependent Quantum Mechanical Approach to Reactive Scattering and Related Processes, Physics Report 280,  79144 (1997)

COMPUTATIONAL MODELING OF ORGANIC MOLECULES ADSORBED AT METAL SURFACES

Supervisors: Sergio Rampino, Antonino Polimeno

The physics and chemistry of organic molecules adsorbed at metal surfaces plays an important role in many applications of scientific and technological interest including catalysis, light-emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics [1]. This thesis project will focus on the computational modeling of the structure and dynamics of such hybrid organic/inorganic systems via Density Functional Theory (DFT), with emphasis on the interpretation of experimental results including Scanning Tunneling Microscopy (STM) [2], capable of rendering images of the adsorbed molecules with atomic-level resolution.


REFERENCES
[1] Liu W, Tkatchenko A, Scheffler M, Modeling Adsorption and Reactions of Organic Molecules at Metal Surfaces, Accounts Chemical Research 47, 3369–3377 (2014)
[2] Zandvliet HJ, van Houselt A, Scanning Tunneling Spectroscopy, Annual Review of Analytical Chemistry 2, 3755 (2009)