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Les membranes biologiques jouent un rôle essentiel dans la vie cellulaire. Afin d’étudier leur comportement et leurs interactions avec des molécules, des modèles de monocouches lipidiques ont été développés. Leur compression sur balance de Langmuir permet d’obtenir une isotherme pression de surface-aire moléculaire permettant de caractériser notamment les transitions de phase et le comportement interfacial des monocouches. Seules les études de simulations de dynamique moléculaire permettent d’obtenir les propriétés structurales des lipides organisés en monocouche à l’échelle atomique. Nous avons modélisé une monocouche de 1-palmitoyl-2-oléoyl-sn-glycéro-3-phosphocholine (POPC), phospholipides majoritaires des membranes, puis réalisé une série de dynamiques moléculaires à différentes tensions de surface en utilisant GROMACS et le champ de force tout atome GAFF. Une isotherme de compression de POPC a été obtenue pour la première fois par simulation de dynamique moléculaire. L’analyse structurale des POPC a mis en évidence des variations conformationelles avec l’augmentation de la pression ainsi qu'une distribution bimodale de l’orientation des têtes polaires. L’analyse des angles dièdres a permis d’identifier les torsions responsables de cette flexibilité. Un comportement indépendant des chaînes hydrophobes a été observé et corrélé à un assemblage préférentiel des chaînes oléoyle d’une part et palmitoyle d’autre part. La connaissance des propriétés structurales et organisationnelles des monocouches de POPC est essentielle à la caractérisation des interactions mises en jeu dans la cohésion des films lipidiques et fournit une base à l’étude de leur perturbation par des molécules. / Biomembranes play an essential role in many relevant processes in cellular biology. In order to gain insight into their behaviour and interactions with molecules, models such as lipid monolayers have been developed. Monolayer compression on Langmuir trough provides surface pressure – molecular area isotherms, and allows characterisation of phase and interfacial properties of the monolayer. Such a characterisation can be completed by atomistic study of the monolayer phospholipids and molecular interactions from molecular dynamic simulations. Our work is focused on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a lipid comprising a saturated and an unsaturated acyl chain, major lipids in eukaryotic cell membranes. We performed MD simulations at 293 K and 300 K at different surface pressures using the all-atom general amber force field (GAFF). Simulated surface pressure-area isotherms were obtained for the first time, and a good agreement was found with experimental isotherms. Based on the structural analyses, two orientations of the head groups clearly appear. We propose that the conformational variations around the bonds connecting the phosphorus atom to the adjacent oxygen are involved in these specific orientations. Both acyl chains have distinct structural properties upon compression and suggest an independent behavior of the saturated and unsaturated chains that could be correlated with the formation of chain-type clusters observed along the simulated trajectories. Molecular insight in structural properties of POPC monolayer provides essential clues for the study of membrane-molecule interaction.

Topological Insulator (TI) is new classes of materials with gapless surface states and insulating bulk. The topological connection can be traced back to the discovery of Integer Quantum Hall Effect in 1980. In the last decade, new categories of topological insulators were predicted and later discovered, that have gained a lot of attraction for room-temperature applications. Since the experimental observation of single Dirac cone on the surface states of Bismuth selenide (Bi2Se3) in 2009, it has emerged as the prototype. Bismuth Selenide has one of the highest bulk band gaps of 0.3 eV among all TI materials. While its single crystal properties are well documented, thin films are producing equally exciting discoveries. In this work, Bi2Se3 thin films were synthesized using magnetron sputtering method and a diverse set of physical properties, such as structural, optical, and electronic, are investigated. In particular, properties of few-layer (ultra-thin) Bi2Se3 thin films are studied. Optical properties of Bi2Se3 was particularly revealing. We observed a sharp increase (blue shift) in the bulk band gap of Bi2Se3 by almost 0.5 eV as it approached the two-dimensional limit. Strong thickness-dependent structural and transport properties were also observed.

Submitted by Luiz Antonio Saska Júnior (mat09083@feg.unesp.br) on 2017-04-06T13:55:56Z No. of bitstreams: 1 Defesa Mestrado Luiz Antonio Saska Junior.pdf: 2401538 bytes, checksum: 4a12ff9f083a1dc7ffb358112e9d48a6 (MD5) / Approved for entry into archive by Luiz Galeffi (luizgaleffi@gmail.com) on 2017-04-12T19:12:08Z (GMT) No. of bitstreams: 1 saskajunior_la_me_bauru.pdf: 2401538 bytes, checksum: 4a12ff9f083a1dc7ffb358112e9d48a6 (MD5) / Made available in DSpace on 2017-04-12T19:12:08Z (GMT). No. of bitstreams: 1 saskajunior_la_me_bauru.pdf: 2401538 bytes, checksum: 4a12ff9f083a1dc7ffb358112e9d48a6 (MD5) Previous issue date: 2017-02-06 / Cerâmicas à base de CaCu3Ti4O12 (CCTO) com estrutura perovskita ABO3 geraram grande interesse científico devido à descoberta da constante dielétrica (κ) gigante, propriedade não ôhmica elevada e propriedade fotoluminescente. Neste trabalho foram preparadas cerâmicas policristalinas na forma de pó com a seguinte composição: Ca1-xSrxCu3Ti4O12 (0,0 ≤ x ≤ 1,0) na qual o Ca2+ (sitio A) foi gradativamente substituído pelo cátion Sr2+. Foram analisados os efeitos desta substituição gradativa nas propriedades estruturais e microestruturais dos pós policristalinos. Mediante técnicas de análise termogravimétrica dos pós, produzidos por reação do estado sólido, determinou a temperatura de calcinação a 950ºC. Analisando as fases presentes no material por meio da técnica de difratometria raios X observa-se que a estrutura cristalina formada é do tipo perovskita. Ao realizar os estudos semi-quantitativos, mediante microscopia eletrônica de varredura com detector de energia dispersiva, se obteve a morfologia e composição química dos pós cerâmicos. Por meio das técnicas de espectroscopia (de infravermelho, de absorção ultravioleta-visível e de fotoluminescência) foram obtidos os valores 548 cm-1, 500 cm-1 e 415 cm-1, para os módulos vibracionais das ligações O-Ti-O, o band gap de 2,85 eV para as amostras estudadas e determinou-se as propriedades ópticas da cerâmica policristalina na forma de pó. / Ceramics made of CaCu3Ti4O12 (CCTO) create great scientific interest after the discovery of its giant dielectric constant (κ), the high non-ohmic property and photolumenescence. In this study were prepared polycrystalline ceramics in the form of powder with the following composition: Ca1-xSrxCu3Ti4O12 (0.0 ≤ x ≤ 1.0), in which Ca2+ (site A) was gradually replaced by a cation Sr2+. The effects of this graduated replacement were analyzed in the structural and microstructure properties of polycrystalline powders. By the thermogravimetric analysis of the powders, produced by solid state reaction, determined the calcination temperature at 1223K. Analyzing the phases present in the material by the diffraction technique of X-rays its observed that the crystal structure formed is perovskite. When conducting semi-quantitative studies, by the scanning electron microscope with energy dispersive spectroscopy, it was obtained the morphology and chemical composition of the ceramics powders. By the techniques of spectroscopy (infrared, ultraviolet-visible absorption and photoluminescence) were obtained the values 548 cm-1, 500 cm-1 and 415 cm-1, for the vibrational modules of the bonding O-Ti-O, the band gap of 2,85 eV for the studied samples and the optical properties of the powder polycrystalline ceramics were determined.

Yes / In this paper we investigate the optical and structural properties of a zwitterionic poly[3-(N-(4-sulfonato-1-butyl)-N,N-diethylammonium)hexyl-2,5-thiophene] (P3SBDEAHT) conjugated polyelectrolyte (CPE) and its interaction in water with surfactants, using absorption, photoluminescence (PL), electrical conductivity, molecular dynamics simulations (MDS) and small-angle X-ray scattering (SAXS). Different surfactants were studied to evaluate the effect of the head group and chain length on the self-assembly. PL data emphasize the importance of polymer–surfactant electrostatic interactions in the formation of complexes. Nevertheless, conductivity and MDS data have shown that nonspecific interactions also play an important role. These seem to be responsible for the spatial position of the surfactant tail in the complex and, eventually, for breaking-up P3SBDEAHT aggregates. SAXS measurements on P3SBDEAHT-zwitterionic cocamidopropyl betaine (CAPB) surfactant complexes showed a specific structural organization of the system. The CAPB surfactant promotes a structural transition from pure P3SBDEAHT 3-dimensional aggregates (radius of gyration ∼85 Å) to thick cylindrical aggregates (∼20 Å) where all CAPB molecules are associated with the polymer. For molar ratios (in terms of the polymer repeat unit) >1 the SAXS interference maximum of the complexes resembles that of pure CAPB thus suggesting ongoing phase segregation in the formation of a “pure” CAPB phase. / The Coimbra Chemistry Centre is supported by the Fundação para a Ciência e a Tecnologia (FCT), Portuguese Agency for Scientific Research, through the project PEst-OE/QUI/UI0313/2014. TC and BS thank FCT, which has supported this work through Postdoctoral Grants (SFRH/BPD/47181/2008 and SFRH/BPD/82396/2011, respectively). DA acknowledges CNPq, Conselho Nacional de Desenvolvimento Científico e Tecnológico – Brasil, for financial support through the Grant “Bolsista do CNPq – Brasil”. The research leading to the SAXS data has received funding from the European Community's Seventh Framework Programme (FP7/2007–2013) CALIPSO under grant agreement no. 312284.

Doctor of Philosophy / Department of Civil Engineering / Kyle A. Riding / Finely ground glass has the potential for pozzolanic reactivity and can serve as a supplementary cementitious material (SCM). Glass reaction kinetics depends on both temperature and glass composition. Uniform composition, amorphous nature, and high silica content of glass make ground glass an ideal material for studying the effects of glass type and particle size on reactivity at different temperature. This study focuses on how three narrow size ranges of clear and green glass cullet, 63–75 [mu]m, 25–38 [mu]m, and smaller than 25 [mu]m, as well as combination of glass types and particle sizes affects the microstructure and performance properties of cementitious systems containing glass cullet as a SCM. Isothermal calorimetry, chemical shrinkage, thermogravimetric analysis (TGA), quantitative analysis of X-ray diffraction (XRD), and analysis of scanning electron microscope (SEM) images in backscattered (BS) mode were used to quantify the cement reaction kinetics and microstructure. Additionally, compressive strength and water sorptivity experiments were performed on mortar samples to correlate reactivity of cementitious materials containing glass to the performance of cementitious mixtures. A recently-developed modeling platform called “[mu]ic the model” was used to simulated pozzolanic reactivity of single type and fraction size and combined types and particle sizes of finely ground glass. Results showed that ground glass exhibits pozzolanic properties, especially when particles of clear and green glass below 25 [mu]m and their combination were used at elevated temperatures, reflecting that glass cullet is a temperature-sensitive SCM. Moreover, glass composition was seen to have a large impact on reactivity. In this study, green glass showed higher reactivity than clear glass. Results also revealed that the simultaneous effect of sizes and types of glass cullet (surface area) on the degree of hydration of glass particles can be accounted for through a linear addition, reflecting that the surface area would significantly affect glass cullet reactivity and that the effects of SCM material interaction on reaction kinetics were minimal. However, mechanical properties of cementitious systems containing combined glass types and sizes behaved differently, as they followed the weaker portion of the two particles. This behavior was attributed to the pores sizes, distruibution, and connectiity. Simulations of combined glass types and sizes showed that more work on microstructural models is needed to properly model the reactivity of mixed glass particle systems.

Thesis (M.Sc. (Agriculture)) --University of Limpopo,2008 / Cellulose is regarded as the most abundant polymer in nature and the first on which X-ray investigations had been performed, a year after the discovery of diffraction of X-rays on crystalline materials in 1912. It is one of the most abundant and important polymers on the planet. It comprises of four allomorphs, cellulose Iβ, II, III and IV1 and IV2 of which Iβ and II are the most stable and industrially important. Cellulose I is the native form of cellulose. Molecular dynamics (MD) simulations have been carried out to study the structural and mechanical properties of cellulose, cellulose Iβ, II, III and IV1 and IV2 bulk systems. Simulations were carried out using Polymer Consistence Force Field (PCFF) and Compass force field in conjunction with the Discover simulation program at various temperatures. We used molecular dynamics simulation to obtain a better insight about temperature dependence of cellulose. Further investigations on mechanical properties of this material at various temperatures were carried out. Using pair correlation functions g(r) or radial distribution functions (rdf’s) we were able to investigate phase transitions wherein as the temperature was increased we observed peak broadening. These enabled us to study the similarities between the structures investigated. Also studied was water uptake in celluloses by way of introducing water at different concentrations. Analysis of lattice parameters compared reasonably well with the experimental. Lattice parameters were calculated using PCFF and they compared well with results found using Compass force field. Calculation of temperature and pressure dependence on bulk systems has been done and it was noted that as the pressure increases the lattice parameters decrease. / National Research Foundation and CSIR

The quantum simulation of large molecular systems is a formidable task. We explore the use of effective potentials based on the Feynman path centroid variable in order to simulate large quantum clusters at a reduced computational cost. This centroid can be viewed as the “most” classical variable of a quantum system. Earlier work has shown that one can use a pairwise centroid pseudo-potential to simulate the quantum dynamics of hydrogen in the bulk phase at 25 K and 14 K [Chem. Phys. Lett. 249, 231, (1996)]. Bulk hydrogen, however, freezes below 14 K, so we focus on hydrogen clusters and nanodroplets in the very low temperature regime in order to study their structural behaviours. The calculation of the effective centroid potential is addressed along with its use in the context of molecular dynamics simulations. The effective pseudo-potential of a cluster is temperature dependent and shares similar behaviour as that in the bulk phase. Centroid structural properties in three dimensional space are presented and compared to the results of reference path-integral Monte Carlo simulations. The centroid pseudo-potential approach yields a great reduction in computation cost. With large cluster sizes, the approximate pseudo-potential results are in agreement with the exact reference calculations. An approach to deconvolute centroid structural properties in order to obtain real space results for hydrogen clusters of a wide range of sizes is also presented. The extension of the approach to the treatment of confined hydrogen is discussed, and concluding remarks are presented.

This study aimed synthesizing hydroxylapatite (HA) and Zn2+, F- and Cl- doped HA by solution precipitation method. The synthesized compounds were sintered at 1100&deg / C for 1h. For structural characterization, density of the samples were measured by Archimedes&rsquo / method. It was observed that Zn2+ addition increased the density significantly whereas F- caused a decrease and Cl- increased the density with a little amount. XRD was applied to the samples and it was found that co-doping of Zn2+ and F- ions decreased the unit cell volume of HA with F- addition. Other compositions gave fluctuated results in terms of unit cell volumes. HA phase and a little amount of CaO phase were detected in some samples. FTIR spectroscopy was used to detect whether Zn2+, F- and Cl- ions were incorporated to the HA structure or not by observing the bands corresponding to the bonds in the molecules. The amount of addition was also detected by FTIR. Results showed that ion incorporation to the HA structure was done successfully. SEM images were v analyzed and grain sizes of samples were calculated by Rietvelt analysis. Grain sizes of the samples increased by Cl- addition and decreased by Zn2+ and/or F- addition. For mechanical characterization, Vickers microhardness test was applied. Fracture toughness was calculated from Vickers microhardness results. According to the results, the highest microhardness values were found for F- and Zn2+ co-doped samples. It was also shown that fracture toughness decreased by Zn2+ addition. However, Zn2+ and F- co-doped samples gave higher fracture toughness results when compared with pure HA. Cl- addition also decreased the fracture toughness. The best compositions in terms of structural and mechanical properties was chosen as Zn2+ and F- co-doped samples and biological characterization was applied to these samples. Saos-2 cell line was used in biological examinations. For biological characterizations, Alamar Blue&trade / assay to detect viability and alkaline phosphatase activity (ALP) assay to detect differentiation were done. It was observed that 2 mol.% Zn2+ addition increased the cell viability and alkaline phosphatase activity. 1 mol.% F- addition also improved cell viability and alkaline phosphatase activiy. SEM images were analyzed to observe the morphology of the cells on HA and selected doped HA discs. In accordance with Alamar Blue&trade / assay and alkaline phosphatase activity assay, cells showed dendritic shapes on 2 Zn and 2 Zn 1 F sample which was the indicator of good material-cell interaction. Dissolution test was also applied by immersing the samples in simulated body fluid (SBF). pH change and SEM images for Ca2+ deposition were investigated. Increase in pH change with time was observed. F- included samples gave the lowest pH change results, especially 2 Zn 1 F. Dissolution pits and some apatitic formations were observed in SEM images.

The quantum simulation of large molecular systems is a formidable task. We explore the use of effective potentials based on the Feynman path centroid variable in order to simulate large quantum clusters at a reduced computational cost. This centroid can be viewed as the “most” classical variable of a quantum system. Earlier work has shown that one can use a pairwise centroid pseudo-potential to simulate the quantum dynamics of hydrogen in the bulk phase at 25 K and 14 K [Chem. Phys. Lett. 249, 231, (1996)]. Bulk hydrogen, however, freezes below 14 K, so we focus on hydrogen clusters and nanodroplets in the very low temperature regime in order to study their structural behaviours. The calculation of the effective centroid potential is addressed along with its use in the context of molecular dynamics simulations. The effective pseudo-potential of a cluster is temperature dependent and shares similar behaviour as that in the bulk phase. Centroid structural properties in three dimensional space are presented and compared to the results of reference path-integral Monte Carlo simulations. The centroid pseudo-potential approach yields a great reduction in computation cost. With large cluster sizes, the approximate pseudo-potential results are in agreement with the exact reference calculations. An approach to deconvolute centroid structural properties in order to obtain real space results for hydrogen clusters of a wide range of sizes is also presented. The extension of the approach to the treatment of confined hydrogen is discussed, and concluding remarks are presented.