Data di Pubblicazione:
2022
Citazione:
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.
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.
Tipologia IRIS:
Tesi di dottorato
Keywords:
complex-systems; active matter; phase transitions; biological matter; MD simulations; computational models
Elenco autori:
L. Ravazzano
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