Single molecule studies of polymers and self-assembling materials: Effects of chain topology and entanglements

Understanding the dynamics of polymer solutions and functional materials in nonequilibrium flow conditions is of key importance for controlling materials properties during processing, which often involves highly nonequilibrium states that cannot be understood in terms of equilibrium principles or thermodynamics. From this view, it is essential to understand the rheological behavior of complex fluids in order to control materials properties during flow-based processing. This thesis focuses on investigating the dynamics of architecturally complex polymers (linear polymers vs. ring polymers) across multiple concentration regimes using a combination of single molecule fluorescence imaging and precise microfluidic flow manipulation under nonequilibrium flow conditions. This thesis also includes studies on the concentration-driven self-assembly and sol-gel transition of a new class of biohybrid functional materials comprised of synthetic pi-conjugated cores and sequence-defined oligopeptides using combined characterization tools. Over the past two decades, advances in fluorescence imaging and particle manipulation have enabled the direct observation of single polymer dynamics in model flows such as shear flow and planar extensional flow, which gives people access to molecular-level information on polymer dynamics. While the vast majority of single polymer studies has focused on chain dynamics using simple transient step forcing functions, there is a clear need to implement more complicated flow types and transient flow forcing functions in order to study single polymer dynamics in non-idealized 'model' flows. In the first project, we demonstrated the first molecular rheology experiment utilizing two-dimensional time-dependent control over the entire x-y flow plane by directly probing single polymer dynamics under large amplitude oscillatory extension (LAOE). We are able to generate both small and large amplitude sinusoidal oscillatory extensional flow in a cross-slot microfluidic device while imaging the conformational dynamics of single polymers trapped at the stagnation point. Using this experimental technique combined with Brownian dynamics (BD) simulations, we have uncovered hidden dynamics of single polymers under highly time-dependent and nonequilibrium flow conditions. In the second project, we continue to increase the polymer concentration into concentrated regime as concentrated polymer solutions exhibit complex dynamic behavior due to an interplay between topological entanglements and nonequilibrium effects. We directly observe the relaxation dynamics of single lambda-DNA molecules in semidilute entangled solutions (c_e < c < c**) and our results show that single polymer relaxation trajectories exhibit either a single-mode or double-mode exponential decay, which starkly contrasts relaxation behavior from ultra-dilute and semidilute unentangled solutions (c*< c < c_e). Through the concentration-dependent scaling of different relaxation timescales, we also provide physical interpretations of the relaxation behavior for these lightly entangled solutions. Moving forward, we extend single molecule studies to polymers with complex molecular topologies in nondilute solutions in order to reveal intermolecular interactions between polymers with different chain topologies. In the third project, we report the direct observation of ring polymer dynamics in semidilute unentangled solutions of linear chains (c*< c < c_e) in planer extensional flow. Remarkably, our results show that ring polymers drastically fluctuate in chain extension in extensional flow, which we hypothesize, is due to the transient 'threading' of linear polymers through open ring polymer chains in flow. To this end, we are also applying perspectives from polymer dynamics to inform the underlying physics during functional materials self-assembly, which could potentially inform the future 'bottom-up' design of functional polymeric materials based on different molecular building blocks. Taken together, combining single molecule fluorescent microscopy, microfluidic flow manipulation, BD simulations, confocal microscopy, electron microscopy, optical spectroscopy, and microrheology, we aim to provide fundamental molecular-level information of linear and ring polymer dynamics in nondilute solutions under time-dependent nonequilibrium flow fields. We also elucidated the self-assembly and sol-gel transition mechanisms of a new class of biohybrid functional materials. From a broader view, we are effectively understanding the link between micro-scale structural/dynamical properties and bulk-scale emergent properties of polymer solutions and functional materials. This would inform the future design and processing of these materials with 'programed' functionalities