The work described here has focused on two types of supramolecular assemblies, supported lipid bilayers (SLBs) and giant vesicles (GVs) from polymerizable lipids. SLBs are explored extensively as structural models in biophysical studies of cell membranes and biosensor coatings. With regard to implementation as biocompatible scaffoldings for receptor-based molecular devices, fluid SLBs lack chemical, thermal and mechanical stability as lipids are self-organized by weak, noncovalent forces. One possible solution is to use synthetic lipid monomers that can be polymerized to form robust bilayers. A key question is how polymerization affects transmembrane protein structure and activity. Specifically it is unclear if lipid cross-linking can be achieved without adversely affecting the activity of incorporated proteins. In this work the effect of lipid polymerization on transmembrane protein activity was studied with rhodopsin. The protein was reconstituted into SLBs composed of polymerizable lipids, bis-SorbPC, bis-SorbPC:mono-SorbPC, bis-DenPC and bis-SorbPC:mono-SorbPE. Rhodopsin photoactivity was monitored using plasmon waveguide spectroscopy. The results show that reconstitution of rhodopsin into SLBs composed of phosphatidylcholine with the polymerizable moiety in the acyl chain terminus, followed by photoinduced cross-linking of the lipids, does not significantly perturb protein function. A possible explanation is that a bilayer with relatively low Xn retains sufficient elasticity to accommodate the membrane deformation that accompanies the conformational change associated with rhodopsin photoactivation when polymerized in the acyl chain terminus. GVs have diameters ranging from several to few hundred micrometers and thus can be observed by optical microscopic methods. This allows manipulation of individual vesicles and observation of their transformations in real time. GVs have attracted attention as microcontainers for enzymes and drugs, and as biosensors. With the aim of increasing stability for these types of applications, GVs were prepared from synthetic dienoyl lipids that can be polymerized to form robust vesicles. The stability of these vesicles after polymerization was investigated by surfactant treatment, drying and rehydration, and temperature variations. The structure of poly(GVs) was largely retained under these conditions which destroy unpolymerized vesicles. Permeability studies on poly(GVs) suggests that they could be potentially used in a variety of technological applications, including sensors, macromolecular carriers, and microreactors.

Polymer coatings on periodic nanostructures have facilitated advanced applications in various fields. The performance of these structures is intimately linked to their nanoscale characteristics. Smart polymer coatings responsive to environmental stimuli such as temperature, pH level, and ionic strength have found important uses in these applications. Therefore, to optimize their performance and improve their design, precise characterization techniques are essential for understanding the nanoscale properties of polymer coating, especially in response to stimuli and interactions with the surrounding medium. Due to their layered compositions, applying non-destructive measurement methods by X-ray/neutron scattering is optimal. These approaches offer unique insights into the structure, dynamics, and kinetics of polymeric coatings and interfaces. The caveat is that scattering methods require non-trivial data modeling, particularly in the case of periodic structures, which result in strong correlations between scattered beams. The dynamical theory (DT) model offers an exact model for interpreting off-specular signals from periodically structured surfaces and has been validated on substrates measured by neutron scattering. In this dissertation, we improved the model using a computational optimization approach that simultaneously fits specular and off-specular scattering signals and efficiently retrieves the three-dimensional sample profile with high precision. In addition, we extended this to the case of X-ray scattering. We applied this approach to characterize polymer brushes for nanofluidic applications and protein binding to modulated lipid membranes. This approach opens new possibilities in developing soft matter nanostructured substrates with desired properties for various applications. / Doctor of Philosophy / Polymer coatings on nanopatterned surfaces have recently facilitated advanced applications in various fields, particularly biotechnology. For example, multichannel surfaces coated with polymer can serve as nanofluidic devices for precise control of fluid flow in drug screening and detection of specific biomolecules. Moreover, polymer-coated nanopatterned surfaces, which possess similar properties to the extracellular matrix, provide excellent substrates for biological studies. The performance of these systems is closely tied to their nanoscale features, such as the thickness and conformation of the polymer layers. Therefore, high-resolution non-invasive nanoscale characterization techniques are essential for investigating these coatings to optimize their performance and enhance their design. X-ray/neutron scattering offers a non-destructive measurement method with unique capabilities in the nanoscale characterization of polymer coatings. However, scattering methods require non-trivial data modeling, particularly in the case of layered coatings on patterned surfaces. To tackle this challenge, we improved a dynamical theory (DT) model that allows for precise modeling of neutron and X-ray scattering signals from such systems. Using a computational optimization approach, the model enables efficient retrieval of the three-dimensional sample profile with high accuracy. We applied this approach to characterize polymer brushes for nanofluidic applications and protein binding to modulated lipid membranes. This methodology opens up new avenues for developing customizable, nanostructured substrates made from soft materials that possess tailored properties for a wide range of uses.