Biomacromolecules are the main functional constituents in living systems. They exhibit a great diversity of tasks depending on the composition of their monomers. Most protein and chromatin functions emerge from the interactions with other biomacromolecules. This dissertation focuses on viral proteins and chromatin systems, describing the relationship between their structure, composition and function using computational and theoretical models. Chapter 1 presents the motivation and describes the two main studied systems: the SARS-CoV-2 Spike protein and the eukaryote interphase genome. Chapter 2 focuses on the implementation of Structure Based Models to simulate the conformational change of the S2 subunit of the SARS-CoV-2 Spike protein associated with the membrane fusion process. We determined the transition states of the Spike protein, and predicted relevant intermediate states readily available to serve as druggable or vaccine targets. The simulated transitions highlight the role of post-translational modification (branched glycans) during viral entry. This model was further expanded to explore how the neutralizing CV3-25 antibody blocks viral entry by inhibiting the full transition of the Spike protein. Chapter 3 describes a pipeline to infer the efficiency of SARS-CoV-2 epitopes in scaffold vaccine strategies. Using explicit solvent simulations, we observed the dynamics of the target epitopes on exposed environments, similar to their context in scaffold-driven vaccines. When compared with experiments, we noticed that the most experimentally efficient epitope (S1Ep4) correlates with high thermal stability around the Wuhan-1 Spike protein conformation. To assess whether the S1Ep4 epitope would trigger immune response for SARS-CoV-2 variants, we performed explicit solvent simulations of the variant local environment of the epitope. The target epitope showed high conformational stability for all the variants around the Wuhan-1 strain structure. We determined that there is high likelihood the S1Ep4 epitope to incite immunoreponse on all the SARS-CoV-2 variants. Lastly, using the aforementioned simulated transitions of Spike during the membrane fusion, we identify new epitopes in the S2 subunit and the conformational study pipeline was implemented. Two new epitopes on the S2 subunit were proposed in highly conserved regions of the Spike protein, stepping towards pan-coronavirus vaccine strategies. Chapter 4 delves into the correlation between the biochemical composition of the DNA and its structural behavior. We expanded upon previous models to predict the subcompartment annotations of the chromatin based on biomarker enrichment along the genomes; including Histone Modification frequencies, transcriptor factor binding profiles and transcription activities. The prediction method, called PyMEGABASE (PYMB), is based on a graph model with a trainable Potts model. Within the model one node corresponds to the locus subcompartment and the remaining nodes are associated with the biomarker enrichment profiles. Using PYMB, we inferred the subcompartment annotations for hundreds of cell lines in multiple eukaryotes, which allow us to determine the cell identity from the subcompartment profile. In Chapter 5 we aim to increase the accuracy at predicting subcompartments by training a transformer architecture, called TECSAS. The new model is able to outperform PYMB's accuracy by more than 20%. From the new predictions, we determined that the transition region in sequence between subcompartments is approximately 150kbp. Finally, we expanded the model to predict the likelihood of genome loci to bind to nuclear bodies (Lamina, Nucleoli, and Speckles). We demonstrated based on the projection of the predicted likelihoods upon 3D chromatin data on the cell IMR-90 that both Lamina and Speckles create a stronger structural bias than the nucleoli. In summary, we explored the relationship between structure and function in the Spike protein's refolding pathway and demonstrated the significance of the conformational stability of epitopes around the target protein structure for vaccine efficiency. Further, the biochemical composition to structural behavior was examined for chromatin systems by the prediction of subcompartments from biochemical data, as well as the impact of the nuclear bodies, such as the lamina, in the overall ensemble behavior of chromatin systems. Overall, we determined that the mechanisms driving function of biomacromolecules are tightly correlated with their composition and structure.