The work presented in this PhD Thesis aims to investigate, with the methods of soft matter physics, systems of biological interest. Inspired by the observation of algae, migrating cells and and protein complexes inside the single cell, simple mathematical models have been implemented to obtain computer simulations of complex systems of biological interest and to deepen our understanding on their physical properties. The first part of the work deals with active matter systems, in which each particle is able to self-propel. Active self-rotations are rarely studied in this context, although present in biological systems such as Chlamydomonas reinhardtii algae. We built a simple model for active particles in 2D based on ABPs (Active Brownian Particles) model, accounting for inter-particle interactions and adding an active torque to each particle to simulate the ability of self-rotating. Employing MD simulations, we studied this model system of active rotators in different conditions, to shed light on the role of self- rotation in active matter systems at the jammed-unjammed transition. We then applied our model based on ABPs to the study of interacting active matter invading narrow channels, to investigate the role of single particles properties in determining invasion behavior. The second part of the work deals with nuclear pores, protein complexes inserted in the nuclear envelope of eukaryotic cells, acting as communication gates between nucleus and cytoplasm. Nuclear pores spatial organization and geometric arrangement on the nuclear surface are still poorly understood. Hence we propose the use of tools commonly employed to study the atomic structural and topological features of soft matter, to study nuclear pores spatial organization. Furthermore, to interpret the experimental results, we hypothesize an effective interaction among nuclear pores and implemented it in extensive numerical simulations of octagonal clusters, mimicking typical pore shapes.

STRUCTURE, DYNAMICS AND PHASE TRANSITIONS OF BIOLOGICAL MATTER / L. Ravazzano ; supervisor of the thesis: S. Zapperi ; director of the school: M. Paris. - : . Università degli Studi di Milano, 2022 Apr 13. ((34. ciclo, Anno Accademico 2021.

STRUCTURE, DYNAMICS AND PHASE TRANSITIONS OF BIOLOGICAL MATTER

L. Ravazzano
2022-04-13

Abstract

The work presented in this PhD Thesis aims to investigate, with the methods of soft matter physics, systems of biological interest. Inspired by the observation of algae, migrating cells and and protein complexes inside the single cell, simple mathematical models have been implemented to obtain computer simulations of complex systems of biological interest and to deepen our understanding on their physical properties. The first part of the work deals with active matter systems, in which each particle is able to self-propel. Active self-rotations are rarely studied in this context, although present in biological systems such as Chlamydomonas reinhardtii algae. We built a simple model for active particles in 2D based on ABPs (Active Brownian Particles) model, accounting for inter-particle interactions and adding an active torque to each particle to simulate the ability of self-rotating. Employing MD simulations, we studied this model system of active rotators in different conditions, to shed light on the role of self- rotation in active matter systems at the jammed-unjammed transition. We then applied our model based on ABPs to the study of interacting active matter invading narrow channels, to investigate the role of single particles properties in determining invasion behavior. The second part of the work deals with nuclear pores, protein complexes inserted in the nuclear envelope of eukaryotic cells, acting as communication gates between nucleus and cytoplasm. Nuclear pores spatial organization and geometric arrangement on the nuclear surface are still poorly understood. Hence we propose the use of tools commonly employed to study the atomic structural and topological features of soft matter, to study nuclear pores spatial organization. Furthermore, to interpret the experimental results, we hypothesize an effective interaction among nuclear pores and implemented it in extensive numerical simulations of octagonal clusters, mimicking typical pore shapes.
ZAPPERI, STEFANO
PARIS, MATTEO
complex-systems; active matter; phase transitions; biological matter; MD simulations; computational models
Settore FIS/03 - Fisica della Materia
STRUCTURE, DYNAMICS AND PHASE TRANSITIONS OF BIOLOGICAL MATTER / L. Ravazzano ; supervisor of the thesis: S. Zapperi ; director of the school: M. Paris. - : . Università degli Studi di Milano, 2022 Apr 13. ((34. ciclo, Anno Accademico 2021.
Doctoral Thesis
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/926571
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