Material design using Martini: Accelerating discovery through coarse-grained simulations

Advanced materials are a fundamental aspect of our modern everyday life. From batteries to solar cells and vaccines, the development of new functional materials is key in addressing societal challenges of the 21st century, yet the development process is often slow and expensive. Computational studies can accelerate this process but to fully realize their potential, they require infrastructure in the form of software, protocols, and benchmarks of these protocols. The thesis at hand starts with an in-depth review of the current usage of the Martini coarse-grained (CG) simulation technique in the field of material science. Subsequently, it lays the groundwork to realize the next stage of the rational design of complex heterogeneous materials utilizing Martini CG simulations. In particular, two newly developed software tools are introduced to facilitate high-throughput workflows. The open-source Vermouth python library and Polyply software suite efficiently automate the simulation setup of complex materials and sharing of simulation input parameters. Subsequently, two libraries of simulation parameters for carbohydrates and synthetic polymers are presented and benchmarked. Finally, a proof-of-concept method is presented to incorporate pH effects in Martini simulations. This protocol allows to study the response of materials to changes in pH, which is a common mechanism to functionalize materials. Taken together these developments enable the simulation of highly complex materials and offer a comprehensive collection of Martini (bio)-polymer parameters.