Banca de DEFESA: ALYSON BRUNO FONSECA NEVES

Uma banca de DEFESA de DOUTORADO foi cadastrada pelo programa.
STUDENT : ALYSON BRUNO FONSECA NEVES
DATE: 03/03/2020
TIME: 09:00
LOCAL: Auditório do CCET
TITLE:

Effective field theory and geometry of long molecules

KEY WORDS:

Effective field theory. Solitons. Structure Protein.

PAGES: 106
BIG AREA: Ciências Exatas e da Terra
AREA: Física
SUMMARY:

The goal of this thesis is to construct an effective description of the dynamics of curves in three dimensions applicable in the context of protein physics. The model is intended to reproduce a variety of geometric characteristics observed in real proteins, assuming that proteins can be approximated by long continuous curves. The degrees of freedom in the effective description are parameterized by the curvature and torsion functions. The minimal necessary model is constructed in terms of an energy functional depending on four phenomenological parameters. We discuss static configurations of the effective model, which appear in two different classes: minima of the effective potential and soliton-like configurations interpolating between pairs of minima. In proteins such classes correspond to most common secondary structures (alpha-helices and beta-strands) and motifs connecting those structures (loops, turns, hairpins etc.) In order to obtain the values for the parameters, the solutions of the model are compared with real protein structures extracted from the Protein Data Bank. A very specific relation between the curvature and torsion predicted by the model allows us to universally fix three of the parameters of the model. We show that the fourth parameter is not universal. It controls the characteristic size of the motifs connecting alpha-helices and beta-strands and may be used to explain the absence of beta-strands in some proteins and their abundance in the others. In the most appealing scenario the model features ``stable'' alpha-helices and ``metastable'' beta-strands. We study the classical and quantum stability of the metastable configurations. We derive estimates for the temperatures of classical phase transitions and show that quantum transitions are suppressed. We also discuss how realistic discrete proteins “stabilize” beta strands and hairpin-like motifs.

BANKING MEMBERS:
Externo à Instituição - DIONISIO BAZEIA FILHO - UFPB
Presidente - 2335088 - DMITRY MELNIKOV
Interno - 1672854 - RAIMUNDO SILVA JUNIOR
Interno - 2337952 - RICCARDO STURANI
Externo à Instituição - VITOR BARBANTI PEREIRA LEITE - UNESP