A multidisciplinary approach to the study of protein dynamics and signal transmission

Allostery is a phenomenon of fundamental importance in biology, allowing regulation of function and dynamic adaptability of enzymes and proteins. Despite the allosteric effect was first observed more than a century ago allostery remains a biophysical enigma, defined as the “second secret of life”. The challenge is mainly associated to the rather complex nature of the allosteric mechanisms, which manifests itself as the alteration of the biological function of a protein/enzyme (e.g. ligand/substrate binding at the active site) by binding of “other object” (“allos stereos” in Greek) at a site distant (> 1 nanometer) from the active site, namely the effector site. Thus, at the heart of allostery there is signal propagation from the effector to the active site through a dense protein matrix, with a fundamental challenge being represented by the elucidation of the physico-chemical interactions between amino acid residues allowing communicatio n between the two binding sites, i.e. the “allosteric pathways”. Here, we propose a multidisciplinary approach based on a combination of computational chemistry, involving molecular dynamics simulations of protein motions, (bio)physical analysis of allosteric systems, including multiple sequence alignments of known allosteric systems, and mathematical tools based on graph theory and machine learning that can greatly help understanding the complexity of dynamical interactions involved in the different allosteric systems. The project aims at developing robust and fast tools to identify unknown allosteric pathways. The characterization and predictions of such allosteric spots could elucidate and fully exploit the power of allosteric modulation in enzymes and DNA-protein complexes, with great potential applications in enzyme engineering and drug discovery.

High power density electrical machines with hairpin windings

Nowadays, electrical machines are seeing an ever-increasing development and extensive research is currently being dedicated to the improvement of their efficiency and torque/power density. Compared to conventional random windings, hairpin winding inherently features lower DC resistance, higher fill factor, better thermal performance, improved reliability, and an automated manufacturing process. However, several challenges need to be addressed, including electromagnetic, thermal, and manufacturing aspects. Of these, the high ohmic losses at high-frequency operations due to skin and proximity effects are the most severe, resulting in low efficiency or high-temperature values. In this work, the hairpin winding challenges were highlighted at high-frequency operations and at showing the limits of applicability of these standard approaches. Afterward, a multi-objective design optimization is proposed aiming to enhance the exploitation of the hairpin technology in electrical machines. Efficiency and volume power density are considered as main design objectives. Subsequently, a changing paradigm is made for the design of electric motors equipped with hairpin windings, where it is proven that a temperature-oriented approach would be beneficial when designing this type of pre-formed winding. Furthermore, the effect of the rotor topology on AC losses is also considered. After providing design recommendations and FE electromagnetic and thermal evaluations, experimental tests are also performed for validation purposes on a motorette wound with pre-formed conductors. The results show that operating the machine at higher temperatures could be beneficial to efficiency, particularly in high-frequency operations where AC losses are higher at low operating temperatures. The last part of the thesis focuses on comparing the main electromagnetic performance metrics for a conventional hairpin winding, wound onto a benchmark stator with a semi-closed slot opening design, and a continuous hairpin winding, in which the slot opening is open. Lastly, the adoption of semi-magnetic slot wedges is investigated to improve the overall performance of the motor.

Physical modeling and numerical simulations of degradation mechanisms in devices and insulators for power applications

In this thesis, a TCAD approach for the investigation of charge transport in amorphous silicon dioxide is presented for the first time. The proposed approach is used to investigate high-voltage silicon oxide thick TEOS capacitors embedded in the back-end inter-level dielectric layers for galvanic insulation applications. In the first part of this thesis, a detailed review of the main physical and chemical properties of silicon dioxide and the main physical models for the description of charge transport in insulators are presented. In the second part, the characterization of high-voltage MIM structures at different high-field stress conditions up to the breakdown is presented. The main physical mechanisms responsible of the observed results are then discussed in details. The third part is dedicated to the implementation of a TCAD approach capable of describing charge transport in silicon dioxide layers in order to gain insight into the microscopic physical mechanisms responsible of the leakage current in MIM structures. In particular, I investigated and modeled the role of charge injection at contacts and charge build-up due to trapping and de-trapping mechanisms in the oxide layer to the purpose of understanding its behavior under DC and AC stress conditions. In addition, oxide breakdown due to impact-ionization of carriers has been taken into account in order to have a complete representation of the oxide behavior at very high fields. Numerical simulations have been compared against experiments to quantitatively validate the proposed approach. In the last part of the thesis, the proposed approach has been applied to simulate the breakdown in realistic structures under different stress conditions. The TCAD tool has been used to carry out a detailed analysis of the most relevant physical quantities, in order to gain a detailed understanding on the main mechanisms responsible for breakdown and guide design optimization.