Computer modelling at the mesoscopic scale : matching structural and dynamical properties

My PhD project has been devoted to a broad exploration of coarse graining and multi-scale techniques, devised to model and simulate mesoscopic systems, spanning size scales from the nm to the μu, and time scales from ns to μs. In a first stage, I verified the validity of simple relations connecting linear dynamical coefficients to the static structure of homogeneous fluids. These relations have been used to predict the effects of coarse graining on the dynamics of the reduced model. In a second stage, I developed a new method to coarse grain Coulomb fluids, representing them as soft, overlapping distributions of positive and negative charge. I applied this approach to investigate fluctuating electric fields at the surface of room-temperature ionic liquids, which could be measured by AFM. A related model has been applied to the determination of structural and dynamical properties of fluid assemblies of macro-ions surrounded by an exponential distribution of counter-ions, aiming at the description of proteins in a water- electrolyte solution. A combined particle-continuum model has been implemented to simulate transmembrane proteins floating in a lipid bilayer, surrounded by an electrolyte solution. Particles represent proteins, the lipid bilayers is replaced by a geometric constraint confining particles on a plane, and the electrolyte solution is described by continuous density distributions of oppositely charged species, whose free energy is minimised at each simulation step. Although somewhat preliminary, the model represents a proof of principle that assemblies of membrane proteins could be simulated within the same framework. The study of entropy effects was pursued further in the form of a model for entropy driven aggregation in solute-solvent systems. An anisotropic solvent- solute interaction successfully produced the qualitative behaviour seen in real systems. Directions for further work along similar lines are discussed in the final chapter of the thesis.EThOS - Electronic Theses Online ServiceGBUnited Kingdo