Coarse-grained molecular dynamics and continuum models for the transport of protein molecules

Coarse-grained molecular dynamics and continuum models for the transport of protein molecules

The present work makes use of coarse-grained molecular dynamics simulations and continuum models to investigate the behavior of biomolecules in experiments such as mechanical pulling and driven transport across nanopores. The approach reproduces the wide phenomenology of experiments and allows one t...

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Detalles Bibliográficos
Otros Autores: Bacci, Marco, 1954- author (author)
Formato: Libro electrónico
Idioma:Inglés
Publicado: Firenze, Italy : Firenze University Press [2014]
Colección:Premio Tesi di dottorato.
Materias:
Chemistry, Organic.
Ver en Biblioteca Universitat Ramon Llull:https://discovery.url.edu/permalink/34CSUC_URL/1im36ta/alma991009746906206719
Tabla de Contenidos:
  • Abstract
  • Acknowledgements
  • Chapter 1. Introduction
  • 1. Preamble
  • 2. Translocation in biology
  • 2.1. Protein molecules
  • 2. Voltage-driven experiments and nanopore technology
  • 4. Outline of the thesis
  • Chapter 2. State of the Art
  • 1. Preamble
  • 2. Experimental work: a selected example from the literature
  • 3. Additional past work outline
  • 4. Analytical models and simulations of protein translocation
  • 4.1. Overview
  • 4.2. Coarse-grained molecular dynamics reference studies
  • Chapter 3. Molecular Dynamics Translocation Simulations
  • 1. Preamble
  • 2. Three-dimensional models for MBP simulations
  • 2.1. MBP numerical model: The Go-like approach ¯
  • 2.2. Pore and pulling models
  • 2.3. Langevin dynamics for the material points of the MBP
  • 3. Methods for translocation and stretching simulations
  • 3.1. Translocation simulations
  • 3.2. Stretching simulations
  • 4. Translocation and stretching numerical results
  • 4.1. Denaturation characterization
  • 4.2. Translocation dynamics
  • 4.3. Residence time statistics
  • 4.4. Stretching vs. translocation
  • 5. Discussion
  • 6. Remarks
  • Chapter 4. 1-Dimensional Continuum Models
  • 1. Preamble
  • 2. Overview
  • 2.1. The general framework
  • 3. Models and methods
  • 4. Results
  • 5. Remarks
  • Chapter 5. 1-Dimensional Continuum Models
  • 1. Preamble
  • 2. Introduction
  • 3. Models and methods
  • 3.1. Discrete scheme
  • 3.2. Continuum model
  • 3.3. Stretching simulations: methods
  • 3.4. Translocation simulations: methods
  • 4. Results
  • 4.1. Toy simulations and related remarks
  • 4.2. Three-dimensional atomic clusters
  • 4.3. Additional remarks
  • 4.4. Protein descriptor in MBP stretching simulations
  • 4.5. MBP morphological descriptor translocation results
  • 5. Additional continuum formulations
  • 5.1. Varying the meaning of v
  • 5.2. zs model 3 and 3*
  • 5.3. Remarks
  • References.

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