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This lecture explores the current trends and challenges in Hierarchical Multi-scale Modeling of Molecular Systems, focusing on complex macromolecular systems and hybrid materials. It covers the characteristic length-time scales, atomistic simulations, and coarse-grained models, including their applications and open questions. The lecture delves into the time-length scales involved in complex molecular systems, the modeling of nanostructured polymer/graphene systems, and the spatial heterogeneities in confined polymer films. It also discusses the adsorption of monolayer polymer crystals on graphene, the modeling of complex systems through atomistic molecular simulations, and the development of effective coarse-grained interaction potentials. Various methods for systematic coarse-grained modeling and force matching techniques are presented, along with computational challenges and open questions in equilibrium and non-equilibrium systems.