This thesis considers coarse-grained models of DNA and RNA, developed in particular to study nanotechnological applications as well as some important biophysical processes. We first introduce sequence-dependent thermodynamics into a previously developed coarse-grained rigid base-pair model of DNA. This model is then used to study sequence-dependent effects in multiple DNA systems including: the heterogeneous stacking transition of single strands, the fraying of a duplex, the effects of stacking strength in the loop on the melting temperature of hairpins, the force-extension curve of single strands, and the structure of a kissing-loop complex. We further apply the DNA model to study in detail the properties of an autonomous unidirectionally propagating DNA nanotechnological device, called the ``burnt bridges motor''. We then apply the coarse-graining methods developed for the DNA model to construct a new sequence-dependent coarse-grained model of RNA, which aims to capture basic thermodynamic, structural and mechanical properties of RNA molecules. We test the model by studying its thermodynamics for a variety of secondary structure motifs and also consider the force-extension properties of an RNA duplex. This RNA model allows for efficient simulations of a variety of RNA systems up to hundreds or even thousands of base-pairs. Its versatility is further demonstrated by studying the thermodynamics of a pseudoknot folding, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin.

Plasticizers are a commonly used additive used in the polymer industry to make the plastic more pliable by reducing the glass transition temperature, Tg and Young's modulus, Y. As the plasticizer aids in polymer process-ability and making it suitable for applications from industrial cables to sensitive medical equipment, the mechanism of plasticization is not fully understood. There are three theories used to explain plasticization: lubricity theory, gel theory, and free volume theory. The latter is a fundamental concept of polymer science that is used to calculate many polymer properties, but they all do not give a clear picture on plasticization. With molecular dynamics (MD) simulation, a coarse-grained (CG) model - which consist of a simple bead-spring model that generalizes particles as a bead and connects them via a finite spring – is used to explore the impact of plasticizer size throughout the polymer system. The interaction characteristics of the plasticizer is explored by representing the plasticizer molecules as a single bead of varying size. This gives better control on the variability of the mixture and pinpoint the significant contributions to plasticization. A path to understanding the the mechanism of plasticization will give insight in glass formation, and can later be used to find an optimal plasticizer architecture to minimize the migration of the additive by tuning the compatibility. Current results show a decoupling between the Tg and Y of the polymer-additive system. The overall understanding of finite-size effects shows: as additive of increasing size is added, the polymer free volume increases which in-turn would decrease the Y, but Tg is shown to increase because the polymer and additive are not as mobile to reduce caging effect of monomeric units. / Thesis / Master of Applied Science (MASc)