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Collagen is one of the major protein constituents in mammals and is present in all tissues and organs with the exceptions of keratin tissues such as hair and nails. Collagen monomers self-aggregate into a number of structures. In order to understand the physical bases for the structural polymorphism observed in collagen, a good starting point is one of the simplest collagen aggregates, segmental long spacing (SLS) collagen. Although SLS collagen formation induced by the presence of adenosine 5’-triphosphate is widely known, effects of other triphosphates, on the other hand, are much less studied. By varying the pH, it is discovered that all the nucleoside 5’-triphophsates, as well as inorganic triphosphate, are able to induce SLS formation over certain pH ranges. Adenosine 5’-diphosphate and para-nitrophenylphosphate cannot induce SLS formation at any pH. Based on the pH ranges at which SLS collagen can be formed, it is concluded the triphosphate functionality, with one negative charge per phosphate group, is primarily responsible for the formation of SLS collagen. Since inorganic triphosphate is able to induce SLS collagen formation, the presence of the nucleoside is optional for the assembly process; however if present, the assembly process prefers the nucleosides carrying acidic protons. Using electron spectroscopic imaging (ESI) technique, it is found phosphorus, present only in nucleotides but not in polypeptides, is localized in certain regions of SLS collagen, forming a unique banding pattern transverse the long axis of the SLS collagen. Nitrogen mapping indicates the localization of phosphorus is not due to accumulation of materials. The phosphorus banding pattern demonstrates an excellent consistency across SLS collagen assembled from both bovine and recombinant human collagen monomers. Results from molecular simulation are consistent with the experimental results. All threephosphate groups seem to be involved in the assembly process to some degree. In the last chapter of the thesis, a reliable protocol to synthesis native type collagen fibers is introduced.

Collagen is one of the major protein constituents in mammals and is present in all tissues and organs with the exceptions of keratin tissues such as hair and nails. Collagen monomers self-aggregate into a number of structures. In order to understand the physical bases for the structural polymorphism observed in collagen, a good starting point is one of the simplest collagen aggregates, segmental long spacing (SLS) collagen. Although SLS collagen formation induced by the presence of adenosine 5’-triphosphate is widely known, effects of other triphosphates, on the other hand, are much less studied. By varying the pH, it is discovered that all the nucleoside 5’-triphophsates, as well as inorganic triphosphate, are able to induce SLS formation over certain pH ranges. Adenosine 5’-diphosphate and para-nitrophenylphosphate cannot induce SLS formation at any pH. Based on the pH ranges at which SLS collagen can be formed, it is concluded the triphosphate functionality, with one negative charge per phosphate group, is primarily responsible for the formation of SLS collagen. Since inorganic triphosphate is able to induce SLS collagen formation, the presence of the nucleoside is optional for the assembly process; however if present, the assembly process prefers the nucleosides carrying acidic protons. Using electron spectroscopic imaging (ESI) technique, it is found phosphorus, present only in nucleotides but not in polypeptides, is localized in certain regions of SLS collagen, forming a unique banding pattern transverse the long axis of the SLS collagen. Nitrogen mapping indicates the localization of phosphorus is not due to accumulation of materials. The phosphorus banding pattern demonstrates an excellent consistency across SLS collagen assembled from both bovine and recombinant human collagen monomers. Results from molecular simulation are consistent with the experimental results. All threephosphate groups seem to be involved in the assembly process to some degree. In the last chapter of the thesis, a reliable protocol to synthesis native type collagen fibers is introduced.

Near-membrane and trans-membrane proteins and their interactions with the extracellular matrix (ECM) can yield valuable information about cell dynamics. However, advances in the field of nanoscale cellular processes have been hindered, in part, due to limits imposed by current technology. In this work, a novel evanescent field (EF) imaging technique is designed, modeled, created and tested for near-field imaging in the apical surface of cells. This technique and Förster resonance energy transfer (FRET) were used to investigate interactions between integrins on the cell surface and the ECM protein, fibronectin. The goal was to monitor changes in the integrin density at the cell surface as a function of clustering after binding to fibronectin on the microsphere surface. For the EF technique, quantum dot (QD)-embedded polystyrene microspheres were used to couple light into whispering gallery modes (WGMs) inside the microspheres; the resulting EF at the surface of the microsphere was used as a near-field excitation source with ~50 nm axial resolution for exciting fluorescently-labeled integrins. For FRET measurements (~10 nm axial resolution), QDs (donors) were coated on the surface of microspheres and energy transfer to red fluorescent protein (RFP)-integrin constructs (acceptors) studied. In both techniques, the QD-modified microspheres were mounted on atomic force microscope (AFM) cantilevers, functionalized with fibronectin, and brought into contact with fluorescently-labeled HeLa or vascular smooth muscle (VSM) cells. The results obtained from both methods show the clustering and activity of the integrins and are in good agreement with each other. Amsterdam discrete dipole approximation (ADDA) was used to study the effects of inhomogeneous surrounding refractive index on the quality factor and position of the WGMs due to the attachment of a microsphere to an AFM cantilever. WGMs of various QD-embedded microspheres mounted on AFM cantilevers were experimentally measured and shown to be consistent with the model.

The study of asphalt chemo-mechanics requires a basic understanding of the physical properties and chemical composition of asphalt and how these properties are linked to changes in performance induced by chemical modifications. This work uniquely implements the framework of chemo-mechanics by investigating two types of chemical modification processes, natural (oxidative aging) and synthetic (chemical doping) as they relate not only to macro-scale properties of asphalt binder but also to the asphalt microstructure and nanorheology. Furthermore, this study demonstrates the application of atomic force microscopy (AFM) imaging and the extraction of nano-scale engineering properties, i.e. elastic modulus, relaxation modulus, and surface energy, as a method to predict performance related to the fatigue characteristics of asphalt binders by modeling intrinsic material flaws present amongst phase interfaces. It was revealed that oxidative aging induces substantial microstructural changes in asphalt, including variations in phase structure, phase properties, and phase distribution. It has also been shown that certain asphalt chemical parameters have a consistent and measureable effect on the asphalt microstructure that is observed with AFM. In fact, particular phases that emerged via chemical doping revealed a surprising correlation between oxidative aging and the saturates chemical parameter of asphalt in terms of how they explicitly impact durability and performance of asphalt. By implementing a crack initiation model – which requires measureable microstructural characteristics as an input parameter – it was found that microstructural flaws (depending on the extremity) can have a more profound impact on asphalt performance than the properties of the material located between the flaws. It was also discovered by comparing the findings to performance data in the Strategic Highway Research Program’s (SHRP’s) Materials Reference Library (MRL), that the crack initiation model predicts very similar performance as the SHRP’s distress resistance indicators. Overall, this body of work yields improved input values for asphalt prediction models and serves as the basis for ongoing studies in the areas of asphalt chemical mapping, modeling of nano-damage, and nano-modification using AFM.

This work presents the novel applications of heated AFM tip in nanolithography. Different strategies were investigated for patterning materials using heated AFM tip. New materials were developed for these new nanolithography methods. Simulation and modeling work was done to further understand the heat transfer and chemical reactions involved in the thermal writing process. The selective thermal decomposition of polymer was the first thermal patterning method we¡¯ve investigated. A couple of different sacrificial polymers were used as the writing materials. Among these materials, the cross-linked amorphous polycarbonate (CPC-IV) was the best material for this application. The effect of cross-linking density on the performance of the material was investigated. A novel 3D thermal writing technology was developed by using cross-linked polymer as the writing material. A combined method utilizing the heated cantilever probe to pattern a polymer masking layer that can serve as a template for area selective atomic layer deposition techniques was developed. Another thermal probe nanolithography method, thermal probe top surface imaging, was also developed. In this method, the heated AFM tip was used to generate functional groups on the polymer surface, and ALD was used to selectively deposit TiO2 on the surface where contains those functional groups. A new poly (hydroxyl styrene) based copolymer was developed for this method. We also investigated self assembly monolayers (SAMs) as the thermal writing material. Two different SAMs were investigated. One the APTES and the other one is THP-MPTES. We demonstrated that the APTES can be patterned using thermal AFM probe, and other materials can be selectively deposited on the patterned APTES SAMs. Thermal AFM probe was used to selectively generate thiol groups from THP-MPTES SAMs, and then use these thiol groups to guide the deposition AuNPs. Some simulation and modeling works were also done to further understand these processes. FemLab was used to analyze the heat transfer in the thermal cantilever and between the heated tip and substrate. Based on kinetics of polymer thermal decomposition, we built a simple model for the selective thermal decomposition nanolithography. The experimental results can be very well fitted by this model.

The research described covers fundamental studies of environmentally-responsive microgel-based thin films as a function of film architecture, microgel chemistry, film thickness, and environmental stimulus. Studies of multi-layer microgel thin films were conducted primarily using atomic force microscopy (AFM), quartz crystal microgravimetry (QCM), and surface plasmon resonance (SPR), each of which probed different aspects the film architecture as a function of pH of the environment around the film. Binary thin films were constructed by changing the ratios and composition of the microgels in solution to create multi-functional thin films for surface modification applications and were studied using AFM. The basic understanding of how these components create films at surfaces gives us insight into how the films perform and will allow for greater diversity without the guesswork. The morphology of films created from microgels with a degradable cross-linker was examined by AFM as a function of degradation of the particles structure. This thesis focuses mainly on very thin microgel films (<5 layers) studied using QCM, SPR, and AFM. Additional studies involving the characterization of semi-soft colloidal paint-on photonics are discussed in Appendix A.

Thesis (PhD)--University of South Australia, 2001.

Diss. Stockholm : Karol. inst., 2004.