On the reaction coordinate optimality for reversible aggregation kinetics
type: CreativeWork
description: Fluctuation-driven reversible transitions are present in a vast class of finite-sized systems, including atomic cluster transitions, macromolecular aggregation, and protein folding. As a consequence, potential applications related to these transitions span a myriad of scientific areas, from the development of phase change materials in material science to the treatment and prevention of proteinopathies in the biological sciences. Here we are particularly interested in aggregation processes in intrinsically finite macromolecular systems, such as colloidal suspensions and protein solutions. These systems undergo transitions between diluted and aggregated states, and our main objective is to quantitatively describe the kinetics of such transitions. In order to study the kinetic properties of these many-body systems, it is usually necessary to project the highly-dimensional configuration space onto low-dimensional reaction coordinates. One of the main contributions of this thesis is to develop a methodology to accurately determine an optimal coordinate, known as the committor, for many- body systems. With the committor, several kinetic properties are calculated exactly, and we demonstrate the applicability of our approach by considering Monte Carlo simulations of an anisotropic lattice model as well as Brownian simulations of a Lennard-Jones system. In the other main contribution, we employ a suitable separation of timescales in a way that the more usual energy variable can also be used as a reliable reaction coordinate. In particular, we validate our previously introduced analytical expressions for the aggregation and dilution rates, which are based on the microcanonical entropy, via the simulations of the lattice system. As a final contribution, we introduce a method based on mean first-passage times that predicts the microphase separation in aggregating systems with competing interactions. Keywords: aggregation; optimal reaction coordinates; microcanonical analysis; M…
abstract: Fluctuation-driven reversible transitions are present in a vast class of finite-sized systems, including atomic cluster transitions, macromolecular aggregation, and protein folding. As a consequence, potential applications related to these transitions span a myriad of scientific areas, from the development of phase change materials in material science to the treatment and prevention of proteinopathies in the biological sciences. Here we are particularly interested in aggregation processes in intrinsically finite macromolecular systems, such as colloidal suspensions and protein solutions. These systems undergo transitions between diluted and aggregated states, and our main objective is to quantitatively describe the kinetics of such transitions. In order to study the kinetic properties of these many-body systems, it is usually necessary to project the highly-dimensional configuration space onto low-dimensional reaction coordinates. One of the main contributions of this thesis is to develop a methodology to accurately determine an optimal coordinate, known as the committor, for many- body systems. With the committor, several kinetic properties are calculated exactly, and we demonstrate the applicability of our approach by considering Monte Carlo simulations of an anisotropic lattice model as well as Brownian simulations of a Lennard-Jones system. In the other main contribution, we employ a suitable separation of timescales in a way that the more usual energy variable can also be used as a reliable reaction coordinate. In particular, we validate our previously introduced analytical expressions for the aggregation and dilution rates, which are based on the microcanonical entropy, via the simulations of the lattice system. As a final contribution, we introduce a method based on mean first-passage times that predicts the microphase separation in aggregating systems with competing interactions. Keywords: aggregation; optimal reaction coordinates; microcanonical analysis; M…
author: Trugilho, Lair Figueiredo
language: eng
keywords: Processos de movimento browniano, Físico-química, Agregação (Química), Colóides - Propriedades, Proteínas - Propriedades, Solução (Química) - Propriedades
date published: 2025-12-12
date modified: 2026-07-24T01:21:08Z
provider: Brazil UFV
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: Universidade Federal de Viçosa

PropertyValue
property ID: DOI
value: 10.47328/ufvbbt.2026.033