Covering all the bases: coarse-grained model design and application for nucleic acids

Nucleic acids play a crucial role in the storage, transportation and expression of our genetic information. They have also become an interesting tool for many applications in nanotechnology. Studying biomolecular systems containing nucleic acids using experimental and imaging techniques has its challenges and the level of detail that can be obtained with such techniques is limited. To obtain a more complete understanding of nucleic acid behavior, computational modelling can be used to support and supplement experimental observations. Molecular dynamics simulations are a popular computational tool to reveal molecular level interactions and mechanisms of biomolecular systems by calculating the forces and movements of all particles that constitute the system. The goal of such simulations is to predict on a very detailed level how the systems behave. The downside of the high level of detail such simulations provide is their extremely high computational cost. One of the methods to make such simulations computationally less expensive is coarse-graining where some details from the simulation model are removed by describing small groups of atoms together as single larger particles. This thesis describes the development and characterization of a model for nucleic acids using the coarse-grained Martini force field as well as an application of the model in studying a DNA-membrane system on a scale that is accessible only using coarse-grained simulations