Computer simulation techniques for exploring the microscopic world are quickly gaining popularity as a tool to complement theoretical and experimental approaches. Molecular dynamics (MD) simulations allow the motion of an N-body soft matter system to be solved using a classical mechanics description. The scope of these simulations are however limited by the available computational power, requiring the development of multiscale methods to make better use of available resources.Dual scale models are a novel form of molecular model which simultaneously feature particles at two levels of resolution. This allows a combination of atomistic and coarse-grained (CG) force fields to be used to describe the interactions between particles. By using this approach, targeted details in a molecule can be described at high resolution while other areas are treated with fewer degrees of freedom. This approach aims to allow for simulating the key features of a system at a reduced computational cost. In this thesis, two generations of a methodology for constructing dual scale models are presented and applied to various materials including polyamide, polyethene, polystyrene and octanol. Alongside a variety of well known atomistic force fields, these models all use iterative Boltzmann inversion (IBI) force fields to describe the CG interactions. In addition the algorithms and data structures for implementing dual scale MD are detailed, and expanded to include a multiple time step (MTS) scheme for optimising its peformance.Overall the IBI and atomistic force fields were compatible with each other and able to correctly reproduce the expected structural results. The first generation methodology featured bonds directly between atoms and beads, however these did not produce the correct structures. The second generation used only atomistic resolution bonds and this improved the intramolecular structures greatly for a relatively minor cost. In both the polyamide and octanol systems studied, the models were also able to properly describe the hydrogen bonding. For the CG half of the force field, it was possible to either use preexisting force field parameters or develop new parameters in situ. The resulting dynamical behaviour of the models was unpredictable and remains an open question both for CG and dual scale models.The theoretical performance of these models is faster than the atomistic counterpart because of the reduced number of pairwise interactions that must be calculated and this scaling was seen with the proposed reference implementation. The MTS scheme was successful in improving the performance with no effects on the quality of results. In summary this work has shown that dual scale models are able to correctly reproduce the structural behaviour of atomistic models at a reduced computational cost. With further steps towards making these models more accessible, they will become an exciting new option for many types of simulation.
|Date of Award
|1 Aug 2016
- The University of Manchester
|Paola Carbone (Supervisor) & Flor Siperstein (Supervisor)
- molecular dynamics