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

• Superior document: Premio Tesi di dottorato
• VerfasserIn: Bacci, Marco, 1954-
• Place / Publishing House: Firenze, Italy : : Firenze University Press,, [2014]; ©2014
• Year of Publication: 2014
• Language: English
• Series: Premio Tesi di dottorato.
• Physical Description: 1 online resource (134 pages).

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.

Table of 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 -- 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.