Coarse-grained molecular dynamics and continuum models for the transport of protein molecules / Marco Bacci.

Format:

Book

Author/Creator:

Bacci, Marco, 1954- author.

Series:

Premio Tesi di dottorato.

Premio Tesi di dottorato

Language:

English

Subjects (All):

Chemistry, Organic.

Physical Description:

1 online resource (134 pages).

Place of Publication:

Firenze, Italy : Firenze University Press, [2014]

Summary:

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 to maintain the main features of the transport by modeling the process as a 1D dynamics in a suited potential of the mean force. The standard 1D continuum view is enriched by proposing a model for the description of the shape of isolated molecules based on a tensorial representation and Cauchy-Born rule. Results indicate limitations for unconstrained dynamics and appropriateness for driven ones.

Contents:

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

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

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

2. Overview

2.1. The general framework

3. Models and methods

4. Results

5. Remarks

Chapter 5. 1-Dimensional Continuum Models

2. Introduction

3.1. Discrete scheme

3.2. Continuum model

3.3. Stretching simulations: methods

3.4. Translocation simulations: methods

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.

Notes:

Description based on publisher supplied metadata and other sources.

Includes bibliographical references.