Thesis (M.Sc.)--Memorial University of Newfoundland, 2004. / Bibliography: leaves 79-90.

Thesis (Ph. D.)--Drexel University, 2007. / Includes abstract and vita. Includes bibliographical references (leaves 101-108).

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The main aim of work presented here is to design, develop and characterize a colorimetric model membrane (liposome) systems, which can bind with proteins, enzymes, bacteria, virus and other biomolecules. PDA molecules are utilized as a scaffold for the bilayer membrane, and a colorimetric assay is carried out. The holy grail of present work contributes towards the better understanding of protein interactions with the cell bilayer surface. Chapter 1 introduces a brief history on the advent of bilayer systems for cellular research exploration. We presented a literature survey about how liposome systems are used as a complementary technique to understand the fundamental principles of cellular membrane functions. Furthermore, we describe about membrane protein functions and recent findings on how proteins interact with the cell membrane. Finally, we explain conjugated systems and their exploration in bilayer membrane as a colorimetric scaffold. We also touch bases with major fluorescence techniques used in our experiments. Chapter 2 provides details on the preparation protocols of liposome and liposome-protein complexes. We confirmed protein-bilayer interactions by monitoring FRET between PDA and rhodamine molecules. Furthermore, we performed streptavidin-biotin binding studies on the PDA bilayer. Protein binding changed the spectral overlap (J) between PDA and rhodamine, which ultimately increased the fluorescence emission of rhodamine. The goal of performing these studies was to present a complete protocol for the preparation of liposome and protein-liposome complex. In chapter 3, we investigate how proteins bind on the cell membrane. Additionally, we propose a model of protein-bilayer complex. We reported that, by harnessing cell bilayer with specific bio-molecules, we monitored protein--bilayer, protein--protein and enzyme--substrate signal transduction. We have developed a colorimetric system for monitoring vital stimulations occur on the liposomal membrane surface. Bilayer was modified to covalently bind the amino group of lysine residues present on protein molecules. These bio-molecular interactions on bilayer surface provide differential stimulus, which turned out to be the major cause of differential spectroscopic signals depending upon size and shape of the protein bounded to the bilayer. Polydiacetylene (PDA) liposomes are the core of our color based system. These liposomes are used to monitor subtle interactions on the bilayer surface. We have also developed a semi-quantitative method based on the colorimetric response of PDA liposomes; we were able to detect protein molecules at sub-nanomolar concentrations in the solution. It's capability of distinguishing protein molecules based on their chemical and physical interactions to bilayer contributes towards the identity of our system. Interestingly, our mass spectroscopic data suggested non-specific enzymatic cleavage of membrane-bound proteins. These fragments were not present in bulk protein cleavage. We also proposed a model that depicts the covalent binding of protein at the bilayer of liposomes. These studies are intended to investigate protein-bilayer and enzyme-protein interaction occurring on the cell surface. In chapter 4, we focus on the kinetics of protein interaction on bilayer surface and we also attempt to visualize these interactions by exploring fluorescence microscopy. A self-assembled cell membrane is consisted of various lipids, which cluster themselves in their preferred phase separated regions. Lipid clusters are very important for lipid specific protein interactions. We investigated protein binding on such phase separated regions under a fluorescence microscope. Furthermore, we enzymatically catalyzed proteins, which were covalently bonded on the bilayer surface. This catalytic reaction was monitored both spectroscopically and under a fluorescence microscope. These studies were performed to help us in the better understanding of biological interactions at cell surface. Chapter 5, describes the encapsulation and controlled delivery of antimicrobial compounds from liposomes. Use of antimicrobial coatings on food packaging is one of the important technologies of active packaging for improving food safety. There is growing demand for natural antimicrobials because of fear of adverse health effects of synthetic preservatives. The main objective of this study is to compare antimicrobial activity of free versus encapsulated curcumin. Glass surfaces coated with nano-encapsulated curcumin may be used as an active packaging material in preserving liquid foods; however, further study is required to improve antimicrobial activities of polylactic acid PLA surfaces. In chapter 6, we investigate interactions between receptors and ligands at bilayer surface of polydiacetylene (PDA) liposomal nanoparticles using changes in electronic absorption spectroscopy and fluorescence resonance energy transfer (FRET). We study the effect of mode of linkage (covalent versus noncovalent) between the receptor and liposome bilayer. We also examine the effect of size-dependent interactions between liposome and analyte through electronic absorption and FRET responses. Glucose (receptor) molecules were either covalently or noncovalently attached at the bilayer of nanoparticles, and they provided selectivity for molecular interactions between glucose and glycoprotein ligands of E. coli. These interactions induced stress on conjugated PDA chain which resulted in changes (blue to red) in the absorption spectrum of PDA. The changes in electronic absorbance also led to changes in FRET efficiency between conjugated PDA chains (acceptor) and fluorophores (Sulphorhodamine-101) (donor) attached to the bilayer surface. Interestingly, we did not find significant differences in UV−Vis and FRET responses for covalently and noncovalently bound glucose to liposomes following their interactions with E. coli. We attributed these results to close proximity of glucose receptor molecules to the liposome bilayer surface such that induced stress were similar in both the cases. We also found that PDA emission from direct excitation mechanism was ∼2−10 times larger than that of the FRET-based response. These differences in emission signals were attributed to three major reasons: nonspecific interactions between E. coli and liposomes, size differences between analyte and liposomes, and a much higher PDA concentration with respect to sulforhodamine (SR-101). We have proposed a model to explain our experimental observations. Our fundamental studies reported here will help in enhancing our knowledge regarding interactions involved between soft particles at molecular levels. In chapter 7, we conclude the summary of all work carried out in previous chapters.

Interfaces between graphene and dissimilar materials are needed for making devices, but those interfaces also modify the graphene properties due to charge transfer and/or symmetry breaking. In this dissertation we investigate the technology of preparing graphene on different substrates and how the substrate influences the electronic properties of graphene. Synthesizing large area graphene on late transition metals by chemical vapor deposition is a promising approach for many applications of graphene. Among the transition metals, nickel has advantages because the good lattice match and strong interaction between graphene/Ni(111) enables the synthesis of a single domain of graphene on Ni(111). However, the nickel substrate alters the electronic structure of graphene due to substrate induced symmetry breaking and chemical interaction of the metal d-band with graphene. Similar chemical interactions are observed for other transition metals with a d-band close to the Fermi-level. On the other hand, graphene mainly physisorbs on transition metals with a lower lying d-band center. In this thesis we investigate the growth of graphene on nickel by vacuum chemical vapor deposition (CVD). In particular, we present our studies of graphene synthesis on Ni(111) substrates. We demonstrate the self-limiting monolayer of single domain of graphene can be grown on single crystal Ni(111). Our studies also show that selective twisted bilayer graphene can be grown by carbon segregation on Ni(111)-films. To modify the interaction between graphene and the nickel substrate we investigated the intercalation of tin. In the case of graphene physisorbed on weakly interacting metals, some charge doping of graphene occurs due to work function differences between graphene and the metal. Using x-ray photoemission spectroscopy (XPS) we correlate the charge doping of graphene on different metals with the C-1s binding energy. This study demonstrate that XPS can be used to determine the Fermi-level in graphene. While metal intercalation can alter the interaction with the substrate it does not avoid overlap of electronics states at the Fermi-level. Therefore a band gap material should be inserted between the graphene and the metal growth substrate (in this case Pt(111)). This is accomplished by oxidation of intercalated iron at elevated oxygen pressure. We demonstrate that a 2D-FeO layer can be formed in between graphene and the Pt(111) surface. We discuss the role of the 2D-FeO moiré-structure on the nanoscale electronic properties of graphene. To date good quality graphene can only be grown by CVD on late transition metals. To obtain graphene on other substrates the graphene can be transferred mechanically from a growth substrate to various other materials. We demonstrate that this transfer can also be achieved to tungsten, an early transition metal that easily forms a carbide. In our studies to avoid oxidation of the tungsten substrate and reaction of the graphene with the tungsten substrate under thermal treatment, protection of the W(110) surface with sulfur has been explored. For the integration of graphene into device architectures, graphene has to be interfaced with high-κ dielectrics. However, because of the inert nature of graphene, most high-κ do not wet graphene and thus preventing formation of contiguous dielectric layers. Yttrium oxide (Y2O3) has been demonstrated to be an exception and we characterized the growth of Y2O3 on various metal supported graphene and graphene transferred to SiO2. We showed that such a Y2O3 layer can also act as seeding layer for the growth of alumina, which is the preferred dielectric material in many applications. Finally, we investigate the charge doping of graphene in a metal/graphene/dielectric stack and find that the charge doping of graphene is a function of both the work function of the metal as well as the covering dielectric. Thus the dielectric layer can modify the charge doping of graphene at a metal contact.

Phonon properties of AB (Bernal) stacked bilayer graphene (BLG) with various types of defects have been investigated theoretically. Forced Vibrational (FV) method has been employed to compute the phonon modes of disordered BLG. A downward linear shift of E2g mode frequencies has been observed with an increasing amount of defect concentration. Moreover, two identical E2g peaks have been observed in PDOS of the bilayer system where the individual layer contains 12C and 13C atoms respectively. From computed typical mode patterns of in-plane K-point optical mode phonons, it has been noticed that phonons become strongly localized around a few nanometers area at the presence of defects and localized modes increase with the increasing amount of defect concentration. The edge effect on the localized phonon modes has also been discussed for bilayer armchair graphene nanoribbons (BiAGNRs). The impact of defects on the phonon conduction properties has also been studied for BiAGNRs. My investigated results can be convenient to study the thermal conductivity and electron-phonon interaction of bilayer graphene-based nanodevices and to interpret the Raman and infrared spectra of disordered system.

The presented thesis is a continuation of the bachelor work, in which the effects of monovalent ions on neutral model lipid membranes were characterized. Herein physical properties of physiologically relevant anionic membranes in the presence of monovalent cations and oxidized lipids were studied. Hydration and mobility of the lipid bilayer at glycerol level were investigated using fluorescent solvent relaxation technique. In the first part of this work the interactions of cations (Na+ , K+ , Cs+ ) with negatively charged POPC/POPS lipid mixture, which is a good model of inner leaflet of cellular membrane, were studied. The presence of cations resulted in dehydration and substantial hinderence of mobility of hydrated lipids at the glycerol level probed by Laurdan. Clear specificity of those effects, which correlated with Hofmeister series have been observed. In the second part of the work truncated oxidized phospholipids, oxPLs (PazePC, PoxnoPC, PGPC, POVPC), which are known to be important in pathophysiology of numerous diseases, were investigated. 10 mol% of each oxPL was incorporated into neutral and anionic lipid bilayers, the hydration and mobility of which were measured in water or in KCl solution. The results reveal complex interactions between oxPLs, negatively charged lipids, and K+ . In...

Mechanical injuries to the cell often lead to disruptions of the cell’s phospholipid bilayer membrane and potential detrimental effects including cell death. Understanding the mechanical states required to disrupt the phospholipid bilayer would result in better multiscale constitutive models and further knowledge of cell injury. The objectives of this research were to perform biaxial deformations of the phospholipid bilayer to quantify phospholipid bilayer disruption and to identify potential parameters that can be used in multiscale constitutive equations. We show that the von Mises stress, 26.6-61.1, increases linearly with the von Mises strain rate, 1.7e8-6.7e8, and that the strain at failure is dependent on the stress state with non- and equibiaxial being the most detrimental when failing at <.73 von Mises strain. Understanding the effects of nanoscale mechanical trauma to the cell provides a better understanding of cell injury and may provide insight regarding initiation and progression of cell damage.

Indiana University-Purdue University Indianapolis (IUPUI) / Clinical evidence suggests that the use of liners in posterior composite restorations may increase the frequency of restoration fractures. Materials that have been used as liner materials for resin composite (RC) restoration include conventional glass ionomers, resin-modified glass ionomers (RMGI), and flowable composites. The aim of this study was to compare the flexural strength of a monolayer of resin composite with that of a bilayer of resin composite and liner. Four types of RC beams were tested: a monolayer control that is an un-lined RC (Tetric EvoCeram, Ivoclar Vivadent) and three “bilayer” specimens that consisted of this same RC lined with one of three liners. The three liners used included two RMGI cements (Vitrebond LC liner; 3M ESPE and, GC Fuji Lining LC; GC America) and a flowable resin composite (Tetric EvoFlow, Ivoclar Vivadent). Each group was tested after water storage for 24 h and 30 d. Altogether, eight, 12-specimen groups were fabricated and tested. Methods: A 25 x 2 x 2 mm mold was completely filled with the RC to form the control beams. To form the bilayer beams, this mold was filled with 0.5 mm of the liner and then with 1.5 mm of the RC. Specimens were stored in 37oC distilled for either 24 h or 30 d. Immediately prior to testing, the 30-day groups were also thermocycled 2500 times, between water baths at 7 oC and 48oC with a 30-s dwell time and a 10-s transit time. Flexural strength was determined using a three-point–bending device. A twoway analysis of variance (ANOVA) with interactions was used to investigate how liner group (or no liner) and storage time affected strength. Results: The interaction between liner type and storage time was significant (p = 0.0128). The un-lined RC (the monolayer beam) was significantly stronger after 24 h than after 30 d in water (p = 0.0098). Water storage between 24 h and 30 d did not change the flexural strength of any of the bilayer (lined) beams (p > 0.05). After storage for 24 h and also for storage for 30 d, both un-lined RC and RC lined with the flowable RC exhibited significantly higher flexural strength (p = 0.0001) than the bilayer beams lined with either RMGI liners.

Intermediate lipid structures such as inverted micelles and interlamellar attachment are thought to play a crucial role in different biological processes like viral infection. Lysophosphatidylcholine has been shown to inhibit membrane fusion at stabilizing concentrations (between 1 and 10% with respect to membrane lipids). Studies in this thesis looked at the effects of Lysophosphatidylcholine (LPC) properties on the inhibition of Sendai viral fusion. The effects of bilayer sidedness preference as well as flip-flop of Lysophosphatidylcholine (lyso PC) were examined. Octadecylrhodamine (R₁₈) lipid mixing assays were used to measure the fusion of Sendai virus with different biological, erythrocyte ghosts, and artificial systems consisting of different lipids and different viral receptor compositions. The data showed that external addition of LPC exhibits a dependency between the incubation time of the lysolipids and the inhibition of viral fusion. The results also demonstrate a relationship between the location of LPC in the bilayer and its ability to inhibit lipid mixing. LPC present only on the outer monolayer plays a role in the inhibition of viral fusion. Reorientation of LPC was also measured for the same incubation periods. A method using Bovine Serum Albumin (BSA) and radioactivity labelled LPC, was applied to measure the flip-flop. Significant transbilayer reorientation of Lyso PC in the bilayer was shown to take place. The rate of flip-flop was measured at 0.32 ± 0.08% LPC /min. Such reorientation can explain the time dependency observed earlier. The conclusions of this thesis lend support to stalk intermediate mechanism of viral membrane fusion. The ability of LPC to inhibit only when present on one side of the bilayer supports the idea of a negatively curved stalk intermediate. Moreover, it showed that the shape and curvature tendencies of the bilayer stabilizer determine its effects on viral fusion. / Thesis / Master of Science (MS)