Multiscale Modelling of Self-assembly in Soft Matter

This thesis presents all-atom molecular dynamics simulations and the development of coarse-grained models for various classes of liquid crystals. The overall aim was to parametrise chemically specific models, propagating information between different resolutions through multiscale modelling approaches, to investigate hierarchical self-assembly in soft matter systems. Common coarse-graining methods were assessed in terms of their representability and transferability for applications involving thermotropic calamitic and discotic mesogens, and lyotropic chromonic liquid crystals. Extensive all-atom simulations were performed on: bent liquid crystal dimers, such as CB7CB; ionic cyanine dyes in aqueous solution (PIC, PCYN, TTBC and BIC); a chromonic perylene bisimide dye (PER); and its thermotropic discotic analogue (PEROEG). These serve as references to parametrise/validate lower resolution models and to provide insights into these systems at the molecular level. For CB7CB, the twist-bend nematic (NTB) phase is observed and characterised. The self-assembly of cyanine dyes and chromonic mesogens was studied by calculating $\Delta G_{\rm{assoc}}$, $\Delta H_{\rm{assoc}}$ and $\Delta S_{\rm{assoc}}$ for the association of $n$-mers (where $n$ = 2, 3 or 4). Structures of H-aggregate stacks, with shift and Y junction defects, and J-aggregates with a brickwork arrangement were detected. Coarse-graining approaches including iterative Boltzmann inversion (IBI), multiscale coarse-graining (MS-CG) in the form of hybrid force matching (FM) and the Martini 3 force field were utilised for the aforementioned systems. A FM model of CB7CB demonstrates high representability and transferability; the NTB phase is captured and the full phase diagram can be explored via heating or cooling. An optimised Martini model correctly exhibits the chromonic nematic and hexagonal phases for PER at the expected concentrations. For PEROEG, an IBI model was found to be superior in modelling the columnar-hexagonal phase. This thesis discusses, in detail, the successes and failures of the various coarse-graining strategies. While successful coarse-graining of liquid crystals remains a challenge, this thesis demonstrates that, with the right choice of method, high-quality coarse-grained models can be developed for both thermotropic and lyotropic systems