Computer simulations can be used in parallel with experimental techniques to gain\ud valuable insights into physical systems, test theoretical models or predict new be-\ud haviour of molecular materials. Long time and large length scales, in combination\ud with problems of phase space sampling, present a grand challenge for simulations\ud of self-organising molecular materials. In the work presented in this thesis, the aim\ud has been to develop and apply new or recent simulation models and methods to\ud address these issues, with the aim of producing improved simulations of molecular\ud materials.\ud A new anisotropic model for simulating mesogenic systems has been developed,\ud based on a soft core spherocylinder potential. This model is tested for single site\ud systems and a multipedal liquid crystalline molecule, using conventional molecular\ud dynamics simulations. It is used also to map out an approximate phase diagram\ud for a main chain liquid crystalline polymer as a function of the volume fraction of\ud the mesogenic unit; and to study the eﬀects of a chiral medium on ﬂexible achiral\ud dopant molecules. Results here, show a preferential selection of conformations of\ud similar chirality to the solvent. Later in the thesis, this new soft core spherocylinder\ud model, is combined with a recently developed simulation methdology, Statistical\ud Temperature Molecular Dynamics, to study the isotropic-nematic phase transition of a single site mesogen and the isotropic-lamellar phase transition of a model rod-\ud coil diblock copolymer, using a single simulation to span the temperature window\ud corresponding to the phase transition.\ud Additional simulations combine a mesoscopic simulation method, Stochastic Ro-\ud tational Dynamics, with a coarse grained surfactant model. This allows a computa-\ud tionally eﬃcient solvent description while maintaining correct hydrodynamics. Re-\ud sults presented here include the formation of a bilayer, via spontaneous self-assembly\ud of surfactant molecules, and information on the pathways of micelle formation.\ud In the ﬁnal result chapter of this thesis, Hamiltonian replica exchange simulations\ud are performed employing soft-core replicas for a Gay-Berne system. The simulation\ud results show an order of magnitude increase in equilibration speed of the ordered\ud phase when compared to conventional simulations of a Gay-Berne ﬂuid.\ud \u
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