Single molecule studies of branched polymer dynamics

Polymer architecture plays a major role on the emergent physical and chemical properties of materials such as elasticity and wettability. Branched polymers exhibit strikingly different rheological behavior (e.g. enhanced stress dissipation and strain hardening) compared to linear polymers. In recent years, the dynamic properties of branched polymers have been studied using bulk rheological techniques (Chapter 1), but we still lack a full understanding of how molecular-scale interactions give rise to macroscopic properties for topologically complex polymers. Single molecule studies enable the direct observation of polymer chain dynamics at the molecular level; however, the vast majority of single polymer studies have only focused on linear DNA molecules (Chapter 2). In this dissertation, we extend single molecule techniques to study the dynamics of branched polymers, which effectively bridges the gap between bulk-scale rheological properties and molecular scale behavior. In particular, we explore the synthesis, characterization, single molecule dynamics, and Brownian dynamics simulations of DNA-based branched polymers. This approach enables us to interrogate the impact of distributions in molecular size and architecture, thereby holding the potential to fundamentally change our understanding of the rheological response of topologically complex polymers. We first developed a two-step synthesis method to generate branched polymers for single molecule visualization (Chapter 3). Here, we use a graft-onto synthesis method by linking side branches onto DNA backbones, thereby producing star, H-shaped, and comb-shaped polymers. In these experiments, DNA-based branched polymers are designed to contain short branches (1-10 kilobase pairs) and long backbones (10-40 kilobase pairs), where the branches and backbones are monodisperse and the branch distribution can be controlled in an average sense. Following synthesis and purification, we utilize single molecule fluorescence microscopy to observe the dynamics of these molecules, in particular by tracking the side branches and backbones independently (Chapter 4). In this way, this imaging method allows for characterization of these materials at the single molecule level, including quantification of polymer contour length and branch distributions for varying synthetic conditions. Moving beyond characterization, we study the dynamics of single branched polymers in flow using a molecular rheology approach. In one experiment, we study the dynamics of asymmetric star, H-shaped, and comb-shaped DNA polymers tethered to the surface in a microfluidic flow cell (Chapter 4). In this way, we study the impact of branch frequency and position on backbone chain relaxation from high stretch. In a second experiment, we utilize a microfluidic cross-slot device to hydrodynamically ‘trap’ branched DNA molecules in planar extensional flow, thereby studying the impact of branching on relaxation in solution, as well as transient and steady-state dynamics in flow (Chapter 5). We present results for branched polymer dynamics as functions of branch frequency and flow strength. We also conduct Brownian dynamics simulations based on a coarse-grained model for comb polymers (Chapter 6). Results from simulations and experiments agree qualitatively, and branched polymers exhibit a weaker dependence of relaxation on total polymer molecular weight in comparison to linear polymers. Overall, this work presents molecular-scale investigations of branched polymer dynamics. From a broad perspective, this research provides a molecular-based understanding of topologically complex polymers in flow, thereby holding the potential to advance the large-scale production of polymers. Importantly, this platform can be further extended to study branched polymers in alternate flow fields such as simple shear flow or linear mixed flows, semi-dilute solutions, and concentrated solutions. These experiments will provide a molecular basis for phenomena observed in branched polymers, from viscosity modification of blended branched polymer solutions to hierarchical relaxation mechanisms of entangled branched polymers to enhanced strain hardening of comb polymer melts