In this thesis, we use rst principles density functional theory (DFT) to study the energetics, structural and electronic properties of hydrogenated and lithiated bilayer graphene material systems. The newly developed four variants of the non-local van der Waals (vdW) exchange-correlation functionals (vdW-DF, vdW-DF2, vdW-DF C09x and vdW-DF2 C09x) are employed to explore all the possible con gurations of hydrogen adsorption at 50% and 100% coverage on a 1 1 unit cell. The results obtained are also compared with the GGA PBE functional. For 50% hydrogen coverage, 16 unique con gurations are identi ed in the unrelaxed state. Formation energy analysis reveals six possible energetically favourable con gurations with three low-energy competing con gurations. It is found that the properties of hydrogenated bilayer graphene greatly depend on the hydrogen con guration. For instance, the formation of a hydrogen dimer within the layers decouples the structure, whereas the dimer formation outside surfaces does not have a signi cant in uence on the van der Waals forces; thus the bilayers remain coupled. In this coupled con guration, the vdW-DF C09x functional predicts the lowest formation energy and shortest interlayer separation, whereas the GGA PBE functional gives the highest formation energy and largest interlayer distance. The reasons behind the variation of these functionals are discussed. Two of the three low-energy competing con gurations exhibit semimetallic behaviour, whereas the remaining con guration is a wide band gap material. The wide band gap structure is found to undergo a hydrogen-induced spontaneous phase transformation from hexagonal to tetrahedral (diamond-like) geometry. We conclude that this wide band gap con guration represents a viable template for synthesizing nanodiamonds from graphene by hydrogenation. At 100% coverage, ten unique hydrogen con gurations are identi ed from a 1 1 unit cell. All exchange-correlation functionals predict nine of the structures to have negative formation energies. From these nine structures, three low-energy competing structures are noted and found to be wide band gap semiconductors, whereas the other con gurations exhibit either a semimetallic or metallic character. Although a 1 1 unit-cell is able to present a clear picture for the interaction between hydrogen and graphene, our results reveal that it limits the occurrence of other interesting physics. The cell size was increased to 2 1, to identify other low-energy con gurations that are not possible in a 1 1 cell. The identi ed con gurations have shown physically interesting hydrogen arrangements such as chair-like, zigzag-like and boat-like con gurations. Furthermore, our results reveal that hydrogenation reduces the elastic properties of the pristine structures. We further perform a systematic investigation of the e ects of lithium (Li) on AA and AB stacking sequences of bilayer graphene. Two Li atoms are considered to examine the e ects of the Li-Li interaction on bilayer graphene, and a total of 12 unique con gurations for AB and 9 for AA stackings are identi ed. The vdW-DF consistently predicts the highest formation energies, whereas vdW-DF2 C09x gives the lowest. Unlike in the case of the pristine structures, it is noted that for lithiated bilayer graphene, GGA PBE gives comparable results to the other functionals. One of the Li intercalated con gurations undergoes a spontaneous translation from the AB to AA stacking, and is found to be the most energetically stable con guration. We therefore conclude that Li favours the AA stacking, and that con guration represents a feasible template for experimentally synthesizing and characterizing a Li-based anode material. We noticed that all identi ed Li con gurations exhibit metallic behaviour. Lastly, we found that the intercalated Li dimer weakly interacts with the graphene layers, whereas the intercalated isolated Li atom exhibits strong interaction. / Thesis (PhD)--University of Pretoria, 2014. / gm2014 / Physics / unrestricted

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Membranes are essential components of all living organisms forming the borders of cells and their organelles. Planar lipid membranes deposited on solid substrates (solid supported membranes) provide models to study the functions of membrane proteins and are used as biosensing platforms. However, despite remarkable progress, solid supported membranes are not stable to harsh conditions such as dehydration, high temperature and pressure, and mechanical stress. In addition, the direct deposition of membranes onto a solid substrate often causes restricted mobility and denaturation of reconstituted membrane proteins. Membrane stability can be addressed by altering the structure of the component lipids. Bolalipids are an interesting class of bipolar lipids that have been proposed for biosensing applications. Membranes formed from mixtures of a bolalipid, C20BAS, and dioleoylphosphaphatidylcholine, POPC, were characterized by atomic force spectroscopy (AFM). The lipid mixtures produced a phase separated membrane consisting of thinner bolalipid-rich and thicker monopolar-rich POPC regions, with a height difference of approximately 1-2 nm. This confirmed an earlier prediction that some bolalipid/PC membranes would phase separate due to the hydrophobic mismatch between the two lipids. Interestingly, the surface coverage of the two phases was inconsistent with what one would expect from the initial starting lipid ratios. The complex membrane morphologies observed were accredited to the interplay of several factors, including a compositionally heterogeneous vesicle population, exchange of lipid between the vesicle solution and solid substrate during formation of the supported membrane, and slow equilibration of domains due to pinning of the lipids to the solid support. Decoupling the membrane from its underlying surface is one strategy to maintain the structure and mobility of membrane proteins. This decoupling can be achieved by depositing the membrane on a soft cushion composed of a water swelling hydrophilic polymer. A polyelectrolyte multilayer (PEM) and a tethered poly(ethylene) glycol (PEG) polymer are the two types of polymer cushions used in this study. The PEMs consist of the charged polysaccharides, chitosan (CHI) and hyaluronic acid (HA) which offer the advantage of biocompatibility over synthetic PEMs. DOPC lipid bilayers were formed at pH 4 and 6.5 on (CHI/HA)5 films. At higher pH adsorbed lipids had low mobility and large immobile lipid fractions; fluorescence and AFM showed that this was accredited to the formation of poor quality membranes with defects and pinned lipids rather than to a layer of surface-adsorbed vesicles. However, more uniform bilayers with mobile lipids were produced at pH 4. Measured diffusion coefficients were similar to those for bilayers on PEG cushions and considerably higher than those measured on other polyelectrolyte films. The results suggest that the polymer surface charge is more important than the surface roughness in controlling formation of mobile supported bilayers. The suitability of polymer supported membranes for the incorporation of integral membrane proteins was also assessed. The integral membrane protein Ste14p, a 26 kDa methyltransferase enzyme, was reconstituted into POPC membranes on PEM and PEG supports. A combination of fluorescence microscopy, FRAP, AFM and an in situ methyltransferase activity assay were utilized to characterize the protein incorporated polymer supported membranes. Fluorescence measurements showed that more protein was incorporated in model membranes formed on the PEG support, compared to either glass or PEM cushions. However, the protein activity on a PEG support was comparable to that of the protein in a membrane on glass. FRAP measurements showed that the lipid mobilities of the POPC:Ste14p bilayers on the various supports were also comparable. Lastly, as a new platform for manipulating and handling membrane proteins, nanodiscs containing reconstituted Ste14p were studied. Nanodiscs are small, soluble and stable bilayer discs that permit the study of membrane proteins in a uniform phospholipid bilayer environment. Empty and protein containing nanodiscs were deposited on a mica surface and imaged by AFM. AFM showed that protein containing samples possessed two subpopulations of nanodiscs with a height difference of ~1 nm. The taller discs, ~20% of the population, contained protein. Other experiments showed that the packing of the nanodisc samples was influenced by their initial stock concentration and that both imaging force and the addition of Mg2+ caused formation of larger bilayer patches.

Thesis (M. Sc. (Physics)) -- University of Limpopo, 2016. / Bilayer graphene and single-walled carbon nanotubes were studied through classical molecular dynamics using Tersoff potential. The Tersoff potential has been the most successful model to replicate much of the semiconducting properties in carbon structures. The simulations were performed within a canonical (NVT) ensemble for structural properties and isothermal–isobaric ensemble (NPT) for thermodynamic properties of both materials. The bilayer graphene consists of two models of 64 and 256 atoms. Single-walled carbon nanotubes consist of three chiral structures of 264 atoms which is cnt(12,10), 260 atoms which is cnt(10,12) and armchair structure of 312 atoms which is cnt(12,12). The structural and thermodynamics properties were investigated in a range of temperature from 300 - 5000 K. It has been found that some of the properties of the graphene and carbon nanotube are similar. Graphene256 was found to be more stable than graphene64 and the armchair cnt(12,12) appears to be more mechanically stable than chiral cnt(12,10). Graphene and single-walled carbon nanotubes were also studied using X-ray diffraction and atomic force microscopy (AFM). The lattice constant for both materials were calculated and they agree well with the computational results. For carbon nanotubes, different solvents were used for characterization using the AFM. Chloroform was the best solvent since we managed to find some bundles of carbon nanotube. For ethanol and toluene solvents we did not managed to get any bundles. The diameter of single-walled carbon nanotube was determined only on a solution that chloroform solvent was used.

Understanding the cellular membrane interaction with membrane active biomolecules and antimicrobial agents provides an insight in their working mechanism. Here, we studied the effect of antimicrobial agents; a recently developed peptidomimetics E107-3 and colistin as well as the N-terminal helix H0, of Endophilin A1 on the lipid bilayer. It is important to discern the interaction mechanism of antimicrobial peptides with lipid membranes in battling multidrug resistant bacterial pathogens. We study the modification of structural and mechanical properties with a recently reported peptidomimetic on lipid bilayer. The compound referred to as E107-3 is synthesized based on the acylated reduced amide scaffold and has been shown to exhibit good antimicrobial potency. This compound increases lipid bilayer permeability as indicated by our vesicle leakage essay. Micropipette aspiration experiment shows that exposure of GUV to the compound causes the protrusion length Lp to spontaneously increase and then decrease, followed by GUV rupture. Solution atomic force microscopy (AFM) is used to visualize lipid bilayer structural modulation within a nanoscopic regime. This compound induces nanoscopic heterogeneous structures rather than pore like structures as produced by melittin. Finally, we use AFM-based force spectroscopy to study the impact of the compound on lipid bilayer’s mechanical properties. With the incremental addition of this compound, we found the bilayer puncture force decreases moderately and a 39% decrease of the bilayer area compressibility modulus KA. To explain our experimental data, we propose a membrane interaction model encompassing disruption of lipid chain packing and extraction of lipid molecules. The later action mode is supported by our observation of a double-bilayer structure in the presence of fusogenic calcium ions. Polyanionic Lipopolysaccharides LPS are important in regulating the permeability of outer membrane (OM) of gram-negative bacteria. To initiate the bactericidal activity of polymyxins, it is essential to impair the LPS-enriched OM. Here, we study the mechanism of membrane permeability caused by colistin (Polymyxin E) of LPS/phospholipid bilayers. Our vesicle leakage experiment showed that colistin binding enhanced bilayer permeability; the maximum increase in the bilayer permeability was positively correlated with the LPS fraction. Addition of magnesium ions abolished the effect of LPS in enhancing bilayer permeabilization. Solution atomic force microscopy (AFM) measurements on planar lipid bilayers shows the formation of nano- and macro clusters which protruded from the bilayer by ~2nm. Moreover, increasing the fraction of LPS or colistin enhances the formation of clusters but inhibits by magnesium ions addition. To explain our experimental data, we proposed a lipid-clustering model where colistin binds to LPS to form large-scale complexes segregated from zwitterionic phospholipids. The discontinuity (and thickness mismatch) at the edge of LPS-colistin clusters will create a passage that allows solutes to permeate through. The proposed model is consistent with all data obtained from our leakage and AFM experiments. Our results of LPS-dependent membrane restructuring provided useful insights into the mechanism that could be used by polymyxins in impairing the permeability barrier of the OM of Gram-negative bacteria. Also, we studied the effect of helix H0 of a membrane modification inducing protein endophilin, on planar bilayer. We obtained transmembrane defects on the bilayer when scanned.with AFM.

The fractional–order capacitors add an additional degree of freedom over conventional capacitors in circuit design and facilitate circuit configurations that would be impractical or impossible to implement with conventional capacitors. We propose a generic strategy for fractional-order capacitor fabrication that integrates layers of conductive, semiconductor and ferroelectric polymer materials to create a composite with significantly improved constant phase angle, constant phase zone, and phase angle variation performance. Our approach involves a combination of dissolving the polymer powders, mixing distinct phases and making a film and capacitor of it. The resulting stack consisting of ferroelectric polymer-based composites shows constant phase angle over a broad range of frequencies. To prove the viability of this method, we have successfully fabricated fractional-order capacitors with the following: nanoparticles such as multiwall carbon nanotube (MWCNT), Molybdenum sulfide (MoS2) inserted ferroelectric polymers and PVDF based ferroelectric polymer blends. They show better performance in terms of fabrication cost and dynamic range of constant phase angle compared to fractional order capacitor from graphene percolated polymer composites. These results can be explained by a universal percolation model, where the combination of electron transport in fillers and the dielectric relaxation time distribution of the permanent dipoles of ferroelectric polymers increase the constant phase angle level and constant phase zone of fractional-order capacitors. This approach opens up a new avenue in fabricating fractional capacitors involving a variety of heterostructures combining the different fillers and different matrixes.

It has been found that the herbicide 2,4-D has the ability to increase the rate of transport of positive ions of several kinds and inhibit the transport of negatively charged tetraphenylborate ions in lipid bilayer membranes. Only the neutral molecules of 2,4-D are transport active. The ionized 2,4-D molecules do not modify the transport of ions, and do not by themselves permeate through lipid membranes. The results suggest that the enhancement of transport of positively charged ions is dominated by the increase of the ion translocation rate constant. It has been shown that membrane transport of negatively charged tetraphenylborate ions is suppressed by 2,4-D. The effect is dominated by the suppression of translocation of these ions across membrane interior, rather than by the decrease of their adsorption at the membrane surface. It has been shown that the enhancement of nonactin-mediated transport of potassium ions by 2,4-D can be accounted for by a simple carrier model. From the changes of kinetic parameters of nonactin-K('+) transport, membrane conductance due to positively charged tetraphenylarsonium ions and also from the changes of membrane conductance and relaxation time constant due to transport of negatively charged tetraphenylborate ions, the changes of the electric potential of the membrane interior have been estimated. The potential of the membrane interior becomes more negative in the presence of 2,4-D and its change is proportional to the aqueous concentration of 2,4-D. The effect of 2,4-D on ion transport was explained by the hypothesis that a layer of 2,4-D molecules is absorbed within the membrane/water interfacial region, and that the 2,4-D molecules are oriented in such a way that their dipole moment is directed toward the aqueous medium. The results suggest that this layer is located in the hydrocarbon side of the interface. The hypothesis has been confirmed by the measurements of changes of electric potential difference across air/water and air/lipid monolayer/water interfaces. It has been found that the electric potential of the nonpolar side of the interface decreases in the presence of neutral molecules of 2,4-D, which is in agreement with the conclusions drawn from the results of membrane experiments. The effect of the other auxin-type phenoxy herbicides, 2,4,5-T and 2,4-DB on lipid bilayer membranes has been found to be similar to that of 2,4-D. In contrast, the phenoxy acid 2,4,6-T, has very little or no herbicidal activity, and at the same time has small effect on ion transport in membranes. Biologically active 2,4-D derivatives, amino acid conjugates of 2,4-D (isoleucine, leucine and valine conjugates) have been found to be also transport active in a manner similar to 2,4-D. Similar conclusions have been drawn from experiments with natural auxin indole acetic acid. The results obtained in this work suggest the existence of correlation between the biological activity of herbicides acting as plant growth regulators and their ability to enhance transport of positively charged ions across lipid membranes. This work provides insight into the physical origin of such activity.

Indiana University-Purdue University Indianapolis (IUPUI) / The role of mechanical forces in the fate and function of adherent cells has been revealed to be a pivotal factor in understanding cell biology. Cells require certain physical cues to be present in their microenvironment or the cell will begin apoptosis. Mechanical signals from the environment are interpreted at the cellular level and biochemical responses are made due to the information from outside the cell, this process is known as mechanotransduction. Misinterpretation of physical cues has been indicated in many disease states, including heart disease and asthma. When a cell is bound to the ECM, proteins such as integrins are engaged at static and stable adhesion sites. These tight and static anchoring points found at the ECM exist in stark contrast to the dynamic conditions seen at intercellular junctions. Intercellular junctions, such as gap and adherens junctions, are formed between cells to act as a mechanism to relay information and exchange material. Due to the important role intercellular junctions play in processes of wound healing, epithelial-mesenchymal transition and cancer metastasis developing more sophisticated levels of understanding of these mechanisms would provide valuable insight. Complex biological processes, including immune cell signaling and cellular ECM adhesions, have been effectively replicated in model systems. These model systems have included the use of solid supported lipid bilayers and polymeric hydrogels that display cell adhesion molecules. Studies of cellular mechanotransduction at ECM adhesion sites has also been completed with covalently functionalized polymeric substrates of adjustable elasticity. However, developing model systems that allow the accurate reproduction of properties seen at intercellular junctions, while also allowing the investigation of cellular mechanosensitivity has proven to be a difficult task. Previous work has shown that polymer-tethered lipid bilayers (PTLBs) are a viable material to allow the replication of the dynamics and adhesion seen at intercellular junctions. Although efforts have been made to produce PTLBs with different mechanical properties, there is currently not a material with sufficient tunable elastic properties for the study of cellular mechanotransduction. To establish a system that allows the study of stiffness effects across a biologically relevant range (~0.50 – 40 kPa) while maintaining the dynamic properties seen at cell-to-cell junctions, polymer gel-tethered bilayers (PGTBs) were developed. A fabrication strategy was established to allow the incorporation of a hydrogel support with easily tunable stiffness and a tethered lipid bilayer coating, which produced a powerful platform to study the effects of stiffness at intercellular junctions. Careful attention was given to maintain the beneficial properties of membrane diffusion, and it was shown that on different linking architectures lipid bilayers could be established and diffusion was preserved. Microscopy-based FCS and FRAP methodology were utilized to measure lipid diffusion in these systems, while confocal microscopy was used to analyze cell spreading and adhesion. Three distinct architectures to link the lipid membrane to the underlying polyacrylamide hydrogel were pursued in this work, a non-covalent biotin-streptavidin system, a covalently linked design with fibronectin, and a direct covalent linkage utilizing crosslinker chemistry. In this work, it was shown that cells were able to spread and adhere on these substrates, with cell adhesion zones visualized under plated cells that demonstrate the capability of the cell to rearrange the presented linkers, while maintaining a stable material. Also confirmed is the tunability of the polymer hydrogel across a wide range of stiffness, this was shown by quantitative changes in cell spreading area in response to polymer properties.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第18596号 / 工博第3957号 / 新制||工||1608(附属図書館) / 31496 / 京都大学大学院工学研究科化学工学専攻 / (主査)教授 山本 量一, 教授 秋吉 一成, 准教授 谷口 貴志, 教授 大嶋 正裕 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM