Multiscale modeling of synthetic and biological supramolecular systems.

In this thesis, we exploited the synergistic combination of multiscale molecular modeling, molecular dynamics (MD), and enhanced sampling to tackle two complex systems. In the first case study, we investigated the intrinsic dynamic behavior of a Benzene 1,3,5-TricarboxAmide (BTA) supramolecular polymer in water. In the second case study, we inquired about the effect of functionalized amphiphilic gold nanoparticles (Au NPs) on the phase behavior of a multi-component lipid membrane. Through our simulations, we gained a deeper understanding of the structure and dynamics of a class of supramolecular polymers. Additionally, we identified the factors that control the exchange of monomers between the different fibers, which can be used to inform the design of novel supramolecular materials in the future. Our simulations provided insights into the mechanisms underlying the interaction between functionalized nanoparticles and lipid membranes, extrapolating the factors that influence the stability of the membrane phase separation. The acquired knowledge can be applied in drug delivery systems or to create new hybrid materials containing ordered two-dimensional NP lattices. In particular, it is worth noting that in both studies, using coarse-grained models with the proper (sub-molecular) resolution was crucial to overcoming the limitations of classic all-atom force fields while maintaining the needed chemical specificity. Overall, the results of these studies have broad implications for materials science and biophysics and demonstrate the potential of computational modeling to inform the design of novel materials and systems.