Complex carbohydrates or glycans are one of the four main biomolecules essential for life. They play crucial roles in molecular recognition events that regulate immune responses, cellular communications and pathogen-host interactions. Despite their importance, characterising glycan structure and dynamics remains a significant challenge for structural biologists due to their inherent flexibility, combinatorial complexity and structural heterogeneity. Throughout my PhD, I used molecular dynamics (MD) simulations to characterise glycan structures and dynamics, revealing how their conformational behaviour dictates recognition and binding to protein receptors and enzymes, regulating processes from glycan biosynthesis to bacterial adhesion. Based on collaborative projects with experimental glycobiologists and microbiologists, the my research focused on identifying the distinctive structural and dynamic features, or signatures, of free glycan structures regulating their molecular recognition. More specifically, I analysed multiatennary N-glycans, ABH and Lewis blood group antigens, and α(2-8)-linked polysialic acids. The data I generated from the MD analysis of these glycan structures contributed to the GlycoShape Glycan 3D Structure Database (https://glycoshape.org), a web-based open access (OA) resource designed, developed and curated by our research group to advance structural glycobiology. Bisected N-glycan structures have been linked to specific disease states and progression. Using comparative analysis between free biantennary and triantennary N-glycan structures, I explored the structural consequences of N-glycan bisection, demonstrating how this modification alters glycan architecture and disrupts interactions with key enzymes in the N-glycosylation maturation pathway, namely B4GalT1 and FUT8, thereby preventing further functionalisation of the antennae. My results confirm and reconcile apparently discordant experimental results, ultimately suggesting an alternative biosynthetic pathway for the maturation of bisected Nglycan forms. Experimental validation of such pathway is in progress through a collaboration with Prof Daniel Kolarich and Dr Andrea Maggioni at the Institute of Biomedicine and Glycomics, Griffith University, QLD, Australia. To understand how glycan structure and dynamics modulates recognition, I investigated glycan-protein interactions in the context of bacterial adhesion, focusing on Type IV pili (T4P) of Neisseria meningitidis and Neisseria gonorrhoeae, causative agents of meningococcal disease and gonorrhoea, respectively. My MD simulations revealed that T4P subunits form multi-subunit carbohydrate-binding pockets, enabling high-avidity interactions with α(2-8)- linked polysialic acids, mediated by conserved polar residues and post-translational modifications (PTMs) such as phosphorylcholine (ChoP) and O-linked bacterial glycosylation. Binding assays by surface plasmon resonance (SPR), I ran with guidance and support by Dr Chris Day and Dr Freda Jen during my internship in Prof Michael Jennings laboratory at the Institute of Biomedicine and Glycomics, Griffith University, QLD, Australia, confirmed the Ng and NmT4P binding specificity for α(2-8)-polysialic acids motifs. Further to this, the SPR data indicate that T4P mutants lacking bacterial glycosylation showed an increased binding affinity, suggesting that T4P glycosylation may hinder binding possibly by restricting access to the glycan-binding site. Through the scope of MD simulations, my thesis provides further insight into how glycan sequence and branching regulate their structure and dynamics which in turn can affect biosynthetic pathways, and molecular recognition, such as in glycan-mediated bacterial adhesion. My findings highlight the intricate relationship between glycan architecture and function and represent a 3D template that can used to inform the design of glycan-based diagnostics and glycomimetic therapeutics.