Multi-resolution dimer models in heat baths with short-range and long-range interactions

This work investigates multi-resolution methodologies for simulating dimer models. The solvent particles which make up the heat bath interact with the monomers of the dimer either through direct collisions (short-range) or through harmonic springs (long-range). Two types of multi-resolution methodologies are considered in detail: (a) describing parts of the solvent far away from the dimer by a coarser approach; (b) describing each monomer of the dimer by using a model with different level of resolution. These methodologies are then utilised to investigate the effect of a shared heat bath versus two uncoupled heat baths, one for each monomer. Furthermore the validity of the multi-resolution methods is discussed by comparison to dynamics of macroscopic Langevin equations.Comment: Submitted to Interface Focu

Multi-resolution modelling of biomolecules

This work investigates how multi-resolution modelling can be applied to study biomolecules as a means to improve the efficiency of simulations. In practice, we resolve aspects of a model that are of greatest biological or physical interest in high detail, while describing the remainder more coarsely. We begin by taking a multi-resolution approach to solvent in simulations, replacing the forces a simple dimer model experiences in short-range and long-range heat baths with macroscopic Langevin and generalised Langevin models. The parameters for these stochastic models are determined analytically, or inferred from molecular dynamic simulation data via force and velocity correlation statistics for comparison. Additionally, the solvent of each monomer in the dimer are also modelled with different level of resolution, with these methodologies used to investigate the effect of a shared heat bath versus two uncoupled heat baths, one for each monomer. Attention is then turned to models of a target molecule, with a multi-resolution methodology for modelling F-actin filaments presented. It provides detailed microscopic information at the level of individual monomers at a lower computational cost by replacing the monomer-based model in parts of the simulated filament by a rod-based Cosserat description. In the monomer-based description G-actin is represented by ellipsoids bound at the surface in a double helical configuration to form F-actin. The rod-based model is coarser, in which F-actin is described using a Cosserat model. The multi-resolution methodology is illustrated using case studies, designed to test the properties of F-actin under stretching, bending, shearing and twisting