Abstract
In this thesis, we explore the application of various molecular simulations techniques to give insights into the self-assembly of supramolecular systems.
Chapter 1 explains the importance of molecular simulation to study the selfassembly process. In chapter 2 we study self-assembly of a derivative of 1,3,5-triamidocyclohexane (CTA) using common techniques: simulations of selfassembly from randomly distributed molecules and simulations of the final structure. The results show the importance of the choice of force-field and limitations of conventional molecular dynamics to give insights into processes
which occur on a long timescale. In Chapter 3 we tackle the timescale issue by
using an adaptive sampling method. The results provide a unique insight into the kinetic pathways of the self-assembly process. Moreover, we were able to provide insights into the next stages of the self-assembly. Although, the method provides insight at a level of detail hardly accessible by any other technique it is
limited to rather small systems. In Chapter 4 we study self-assembly of long functionalized alkanes on a graphite flake. We use coarse-grained molecular
dynamics to tackle both temporal and spatial scales instead of the high resolution of the all-atomistic model. These results give insights into the mechanism of self-assembly of monolayers on graphite. Chapter 5 is an extension to Chapter 4. Here, we study the last stage of the self-assembly process, Ostwald ripening, responsible for correction of the structure, which leads to high quality long-range ordered assemblies.
The results presented in this thesis have two major outcomes: (a) methodology to simulate of self-assembly, and (b) insights into self-assembly process.
Chapter 1 explains the importance of molecular simulation to study the selfassembly process. In chapter 2 we study self-assembly of a derivative of 1,3,5-triamidocyclohexane (CTA) using common techniques: simulations of selfassembly from randomly distributed molecules and simulations of the final structure. The results show the importance of the choice of force-field and limitations of conventional molecular dynamics to give insights into processes
which occur on a long timescale. In Chapter 3 we tackle the timescale issue by
using an adaptive sampling method. The results provide a unique insight into the kinetic pathways of the self-assembly process. Moreover, we were able to provide insights into the next stages of the self-assembly. Although, the method provides insight at a level of detail hardly accessible by any other technique it is
limited to rather small systems. In Chapter 4 we study self-assembly of long functionalized alkanes on a graphite flake. We use coarse-grained molecular
dynamics to tackle both temporal and spatial scales instead of the high resolution of the all-atomistic model. These results give insights into the mechanism of self-assembly of monolayers on graphite. Chapter 5 is an extension to Chapter 4. Here, we study the last stage of the self-assembly process, Ostwald ripening, responsible for correction of the structure, which leads to high quality long-range ordered assemblies.
The results presented in this thesis have two major outcomes: (a) methodology to simulate of self-assembly, and (b) insights into self-assembly process.
| Original language | English |
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| Award date | 5 Sept 2019 |
| Print ISBNs | 978-94-028-1665-5 |
| DOIs | |
| Publication status | Published - 2019 |