Dissertations / Theses on the topic 'Nanoscience'

Molecular Dynamics is a very powerful technique for the investigation of matter at nanoscopic level. However, it’s application in many fields, such as the investigation of many relevant processes of cell biology, is restricted by issues of computational cost. Therefore, in recent years, a growing interest has been generated by the introduction of Coarse-Grained (CG) models, that allow the investigation of bigger systems for longer timescales. In this thesis, Molecular Dynamics was used in order to gain a quantitative understanding of mechanical and di.usive processes of DNA molecules in solution, and in order to parametrise a Coarse Grained model of DNA capable of a qualitative description of the mechanical behaviour of the all-atom model at equilibrium. A software package for the computation of Coarse-Grained interaction force-fields, making use of the recently developed Multiscale Coarse-Grained Method (MSCG) by Izvekov and Voth [1] was implemented. We tested and validated the method by performing a one-point-per-molecule coarse graining of TIP3P water. The resulting model was able to reproduce the fluid structure (its radial distribution function) in a satisfactory and nearly quantitative way. Finally, we applied the MSCG method to a more demanding problem, namely the parametrisation of a 3-point-per-residue coarse-grained model of double-stranded DNA. As a consequence, the agreement of the obtained CG model with the atomistic structure was still not quantitative. In particular, the helical geometry was qualitatively preserved and the Root-Mean-Square Displacement (RMSD) of the coarse-grained model was stable over the trajectory, but higher than its all-atom counterpart. We suggest several possible routes for future improvements. In particular, the explicit modeling of torsional degrees of freedom of the DNA backbone, and the use of recently introduced methods for the refinement of the MSCG estimation of force-field parameters, and a more accurate treatment of Coulombic interactions.

Recent studies have demonstrated that nanoscale crystalline iron oxide minerals are common in natural systems. The discipline of nanoscience suggests that these particles in the size range of approximately 1-50 nm will have properties that deviate from the bulk properties of the same material and that these properties will change as a function of particle size. This study begins to fill the void of corresponding experimental investigations that apply the principles of nanoscience to the geochemical reactivity of nanominerals. The rate of Mn²⁺(aq) oxidation on hematite with average diameters of 7.3 nm and 37 nm was measured in the presence of O₂(aq). In the pH range of 7-8, the surface area normalized rate was one to two orders of magnitude greater on the 7.3 nm average diameter particles. Based on the application of electron transfer theory, it is hypothesized that the particles with diameters less than approximately 10 nm have surface crystal chemical environments which distort the symmetry of the MnMn²⁺ surface complex, reducing the energy required to reorganize the coordinated ligands after oxidation to Mn³⁺. Cu²⁺, an analog for Mn³⁺, was used to probe for the presence and nature of the proposed changes in surface structure. Cu²⁺ and Mn³⁺ show similar electronic structure changes in response to the surrounding crystal field due to their d-electron configurations and Jahn-Teller coordinative distortions. Batch sorption experiments on hematite nanoparticles revealed a shift in the pH-dependent adsorption of Cu²⁺(aq). Specifically, an affinity sequence of 7 nm > 25 nm = 88 nm was determined based on the shift of the 7 nm sorption edge to approximately 0.8 pH units lower than that for the 25 nm and 88 nm samples. These data support the hypothesis that unique binding sites exist on the 7 nm nanoparticles that are not significantly present on the larger particles. The National Nanotechnology Initiative stresses the need to address the broader societal impacts of nanoscale research. This dissertation embraces this viewpoint through the development and inclusion of "Nano2Earth: Introducing Nanotechnology Through Investigations of Groundwater," a curriculum which combines nanoscience with the Earth sciences for high school students.
Ph. D.

Le sujet de cette thèse est l'observation de parois de domaines ferromagnétiques dans des nanofils cylindriques, ainsi que leur dynamique sous champs magnétiques appliqués. Ces nanostructures ont été électrodéposées par mes collègues dans des membranes d'alumine nanoporeuse servant de gabarits à géométrie adaptable. Les matériaux sont des alliages magnétiques doux de FeNi ou CoNi ; les diamètres vont de 150 nm à 250-300 nm, avec une longueur typique de 30 µm.Mon travail a d'abord englobé des développements instrumentaux de porte-échantillons et d'électronique haute fréquence visant au déplacement de parois sous champ. J'ai étudié cette dernière grâce au dichroïsme magnétique circulaire des rayons X couplé à la microscopie électronique de photoémission (XMCD-PEEM), en géométrie dite de transmission ou d'ombre. Cette technique synchrotron permet le suivi de la configuration interne de paroi avant et après déplacement ; en raison de la forte reproductibilité requise par le XMCD-PEEM résolu en temps, la dynamique en temps réel est pour le moment inaccessible.La réponse des parois de domaines ferromagnétiques à un champ magnétique est notoirement caractérisée par leur mobilité, c'est-à-dire le rapport de la vitesse atteinte sur le champ. Dans les nanofils cylindriques, un ingrédient nouveau apparaît dans le cas d'un type de paroi absent dans les bandes plates : la paroi à point de Bloch (Bloch point wall, BPW). Non seulement cette paroi comporte une singularité micromagnétique, c'est-à-dire un point où l'aimantation disparaît (le point de Bloch), mais elle possède également un degré de liberté discret représentant le sens d'enroulement d'aimantation autour de l'axe du fil. Il a été prédit que le déplacement de BPW sous champ suffisamment intense résulte en la sélection de l'un des deux seuls sens possibles. En d'autres termes, un des deux enroulements devient instable. Dans cette thèse, je rapporte l'observation expérimentale de cette sélection dans une majorité de déplacements de BPW.Il n'a pas été possible de mener des mesures de mobilité, néanmoins, mes expériences ont mis en évidence des transformations jusqu'ici non prévues en simulation entre types de parois. La BPW contenant un défaut topologique (le point de Bloch lui-même), ce comportement inattendu remet en question la protection topologique parfois attribuée aux textures topologiquement non-triviales. Bien que rappelant la conversion entre parois transverse et vortex dans les bandes, ces transformations dans les nanofils cylindriques impliquent des configurations micromagnétiques topologiquement non-équivalentes, par contraste avec les parois des bandes sus-mentionnées. De plus, la toute relative stabilité observée des types de parois suggère la prudence dans l'interprétation de future mesures de mobilité dans de tels systèmes dès lors que la configuration interne de paroi n'est pas résolue.En-dehors de tels échantillons électrodéposés, j'ai également étudié un nanofil cœur-coquille crû verticalement par des collègues. Cette nanostructure cylindrique créée par dépôt induit par faisceau d'électron focalisé (FEBID) possèdait un cœur nanocristallin de cobalt et une coquille de platine. Sa configuration magnétique a été également étudiée par XMCD-PEEM en transmission. Contrairement au fils précédemment mentionnés et posés sur leur substrat sur toute leur longueur, cet échantillon cœur-coquille était vertical et sans modulations de diamètre. En revanche, la géométrie coudée du fil a été conçue pour favoriser le piégeage de parois. Dans cette configuration innovante d'imagerie, le défi a été de remonter autant que possible à l'état magnétique du fil ; il m'a été possible de démontrer la présence d'au moins une paroi de domaine
The thesis is concerned with the observation of ferromagnetic domain walls in cylindrical nanowires, as well as their dynamics under applied magnetic fields. These nanostructures were electrodeposited by colleagues of mine into nanoporous alumina templates with a tailored pore geometry. The materials are soft FeNi or CoNi alloys; the diameters range from 150 nm to 250-300 nm, with a typical length of 30 µm.My work first comprised experimental developments of sample holders and high-frequency electronics towards field-induced domain wall motion. The latter I investigated with X-ray Magnetic Circular Dichroism coupled to transmission PhotoEmission Electron Microscopy (XMCD-PEEM). This synchrotron-based technique allows to monitor the internal domain wall configuration before and after displacement; due to the stringent requirements of time-resolved XMCD-PEEM experiments in terms of reproducibility, the real-time dynamics is out of reach as of yet.The response of ferromagnetic domain walls to applied magnetic fields is notably characterized by their mobility, i.e. the ratio of attained velocity to field strength. In cylindrical nanowires, a novel ingredient emerges in the case of one domain wall type that is absent in flat strips: the Bloch point domain wall. Not only does this domain wall host a micromagnetic singularity, that is to say a point where magnetization vanishes (the Bloch point), but it also possesses a discrete degree of freedom representing the sense of magnetization winding around the nanowire axis. It has been predicted that Bloch point wall motion under sufficiently high fields leads to this degree of freedom selecting one of its only two possible values. In other words, one winding becomes unstable. I report in this thesis experimental evidence of such a selection in a majority of Bloch point wall motion events.Although mobility measurements could not be carried out, my experiments have furthermore evidenced transformations between domain wall types that had not been predicted in simulations. Since the Bloch point wall contains a topological defect (the Bloch point itself), this unexpected behaviour questions the sometimes argued protection attributed to topologically non-trivial textures. While reminiscent of the well-known conversion between transverse and vortex walls in strips, these transformations in cylindrical nanowires involve topologically non-equivalent micromagnetic configurations, in contrast with the aforementioned transverse and vortex walls. Moreover, the observed only relative stability of domain wall types suggests caution in the interpretation of future mobility measurements in such systems, if the internal wall configuration cannot be resolved.Aside from such electrodeposited samples, I have also studied an upright core-shell nanowire grown by colleagues with Focused-Electron-Beam-Induced Deposition. This nanostructure featured a nanocrystalline cobalt core and a platinum shell. Its magnetic configuration was investigated with transmission XMCD-PEEM as well. Contrary to the aforementioned horizontally-lying wires, the core-shell sample was vertical with no diameter modulations. On the other hand, the geometry featured bends engineered to favour domain wall pinning. In this novel imaging configuration, the challenge was to recover as much of the nanowire's magnetic state as possible. I was able to demonstrate the presence of at least one domain wall

The reaction of HCl with clean, Cu(100) and (111), and Au/ Cu(100) surfaces was investigated using x-ray photoelectron spectroscopy (XPS) and scanning tunneling microscopy (STM) under ultra high vacuum (UHV) conditions. Exposure of the Cu(100) and (111) samples to HCl at room temperature leads to the formation of a saturated copper chloride monolayer. In the case of Cu(100), the saturated coverage was half monolayer corresponding to a c(2x2)-Cl reconstruction (half monolayer is 7.25x1014 cm-2) while for Cu(111) it was one third monolayer consistent with the reconstruction of (√3x√3)R30o (one third monolayer 5.9x1014 cm-2). The interaction of HCl with preoxidised Cu(100) and (111) showed different behaviour from those of clean copper surface depending on the way of interaction of oxygen with copper surface. Interaction of HCl with peroxidised Cu(111) at saturation oxygen coverage leads to the adsorption of chlorine on top of the copper surface with one third coverage. In contrast, presence of oxygen on Cu(100) surface at saturation coverage or less leads to adsorb chlorine but with an excess in chlorine concentration (more than the expected c(2x2) coverage). Oxidized Cu(100) and (111) surface at elevated temperature leads to the formation multi oxide layer. The two oxide surfaces („‟44‟‟ and „‟29‟‟) observed at the Cu(111) depend on the temperature of the substrate at the time of oxidation. The (√2x2√2)R45o structure was observed on the Cu(100) surface on heating which is the same structure formed at saturation coverage at room temperature. Interaction of HCl with Cu(100) and (111) surfaces covered by multilayers of oxide lead to adsorption of chlorine on top of the copper surface with a coverage more than more than the saturation coverage. Interaction of HCl with Au/Cu(100) showed two different behaviour depending on the gold coverage. Au/Cu(100) alloy formed at half monolayer of gold coverage, forming c(2x2) structure. Exposure of the Au/Cu(100) alloy at half monolayer of gold coverage to HCl leads to the formation of c(2x2)-Cl structure with saturation coverage of half monolayer in similar manner of interaction of HCl with the clean cu(100) surface. Interaction of HCl with Au/Cu(100) surface at gold coverage more than half monolayer leads to a dealloying of the gold from the copper surface and forming the Au(111) surface. Cu-Cl formed underneath the Au(111) surface with excess of chlorine concentration.

The study presented in this document is the result of three years of research into the complex world of Molecular Dynamics applied to biological cell membranes. The simulation of biological tissues involves not only an excellent knowledge of the numerical calculus and its related tools, but a profound comprehension of the biological and medical literature associated with the phenomenon. By the other hand, the use of high performance facilities is essential for the computation of the Molecular Dynamics models in order to obtain results in acceptable times, so the latest technological advances have played a decisive and important part in this eld of research. The presented obtained results about shock wave interaction with biological membranes, as well as the air ow through the alveolar surface, are part of a new line of research usually known as "virtual experimental". This name comes from the fact that any physical or chemical situation can be re-created into a computer system to calculate its propagation in time. The results of the interaction of shock waves with biological cell membranes have been particularly satisfactory and they have opened a new line of investigation into cancer research. A numerical proportional relation between the shock wave impulse and the value of lateral di usion (from 9.80 to 12.84 10 .7 cm2 s ), as well as the simulation of the transient provoked by the wave into a NPT ensemble are a successful achievement. Other computations of this type of interaction have been simulated into an NVE ensemble as well, however the obtained results for the lateral di usion, in the order of 10 .7 cm2 s , showed no trend regarding the shock wave and the transient e ect could not be simulated. On the other hand, the recreation of the air ow through the alveolar surface is an initial step into the solution of all the controversy surrounding this extremely complex system known as alveolar surface network. An alveolar membrane of around 7 nm has been successfully simulated in agreement with Scarpelli's experiments. This lipid-protein membrane model simulated can serve as a virtual experiment in order to solve the controversy about the alveolar surface. It points to the possibility of air ow through a stable two-layered DPPC phospholipid structure either from a numerical or physical and biological point of view and the existence of an alveolar membrane at the end of the bronchial tubes.

Chapter 1 includes a review on dendrimers, their synthesis and applications, with a particular focus on urea-linked dendritic species. The synthetic strategy utilised in this body of work was based on the preparation of a number of branched synthetic building blocks possessing differing terminal functionality. These branched dendrons, bearing three terminal residues and based on the cheap starting material tris(hydroxymethyl)aminomethane (TRIS) 23, involved the coupling of 3.3 equivalents of an appropriately para-substituted benzoic acid chloride with BOC protected TRIS 24 in DCM in the presence of triethylamine. The p-nitro, p-methoxy and p-methyl benzoyl chloride starting materials were obtained commercially, whilst N-(4-carboxyphenyl)maleimide was synthesised according to literature procedures. The BOC protected dendrons (25–27, 34) were synthesized in yields ranging from 50–92%. Deprotection of the BOC protected dendrons 25 and 26 in DCM with TFA, followed by the addition of 1M Na2CO3 afforded the TFA salts 35 and 36, respectively. The corresponding free base amines 37 and 38 were obtained on further treatment of the TFA salts with sodium carbonate. Deprotection of the BOC protected dendrons 27 and 34 afforded the free amines 39 and 48 directly after treatment with sodium carbonate. Synthesis of functionalised branched molecules containing 6- and 9-peripheral functionalities was achieved by refluxing 2 or 3 equivalents of the free amine dendrons with the bi- or tri- functional isocyanate cores, 15 and 45, in refluxing DCM, in most cases the products precipitated from the reaction mixture after 18 h and were isolated simply by filtration, otherwise the removal of the solvent from the reaction mixture afforded the spectroscopically pure product. Conversion of the peripheral nitro functionalised species 14 and 21 to the corresponding amines occurred smoothly via hydrogenation using 5% Pd/C under elevated temperature and pressure (DMF, 55 ºC, 600 psi) and afforded the polyamine 6-mer 51 in 92% yield and the 9-mer 50 in 90% yield, respectively. Similarly, conversion of the methoxy coated 9-mer 42, to the corresponding phenolic compound (AlBr3, dodecane thiol, DCM) afforded the 9-mer polyphenol 52 in an 87% yield. All compounds prepared were fully characterised and crystal structures were obtained for 26 and 35. Chapter 2 includes a review on self-assembled monolayers of organosulfur compounds on gold, applications, patterning techniques and techniques for the characterisation of these surfaces. A number of surface monomers were successfully synthesized, to be used for various surface functionalisations, including the formation of an amine reactive N-hydroxysuccinimide (NHS) disulfide 53, via the DCC coupling of 11,11’-dithiobisundecanoic acid 54 with N-hydroxysuccinimide with an isolated yield of 30%. A novel protein-resistant monomer 58 was also synthesized from 11-undecanoic acid 55 via an acid chloride coupling with triethylene glycol monomethyl ether 58, and isolated in a 72% yield. A number of attempts were made to produce an acyl azide SAM monomer 59, with success finally achieved via the acid chloride coupling of 11,11’-dithiobisundecanoic acid 54 with 5-amino-1,3-benzenedicarbonyl diazide 62 to produce 59 with an isolated yield of ~ 30%. Gold surfaces were prepared on atomically flat silicon wafers using an argon-ion sputterer. SAM films were formed on the gold surfaces via traditional solution based self-assembly methodology. A UV patterning protocol was developed, and a successful patterning trial using the NHS terminated monomer to backfill the UV exposed areas of a dodecane thiol monolayer was achieved and visualized using AFM and fluorescence microscopy after treating the surface with aminofluorescein. The covalent attachment of green fluorescent protein to the monolayer surface via reaction with the NHS terminated monolayer was demonstrated. The fluorescence of the biomolecule was preserved. The formation of a monolayer using the acyl azide monomer 59, was characterised by contact angle and XPS analysis. However, preliminary studies into the activation of the acyl azide surface into the reactive isocyanate were unsuccessful. There is however, significant scope for further investigations into this interesting surface technology. Chapter 3 includes a review on heterobifunctional linker technology with a particular focus on amine and thiol reactive moieties and literature examples of heterobifunctional linkers of this type. Synthesis of heterobifunctional reagents such as 71 and 74 via a two step synthetic methodology involving the coupling of maleic anhydride with the parent amino-acids in acetic acid, followed by a one pot cyclisation and NHS esterification using DCC in DMF were successful, with overall yields of 9% and 32% respectively for the two reaction steps. The one pot extension of 74 with 6-aminohexanoic acid, followed by DCC, facilitated NHS esterification was achieved successfully in a yield of 30%. Attempts to extend 74 with the synthesised amino acid 88 were unsuccessful due to the insolubility of 88 in organic solvents. A different synthetic strategy was devised towards the synthesis of 85 with the coupling of 74 and mono BOC protected ethylene diamine 91 in DCM to give 93 in an isolated yield of 60%. Deprotection of the terminal amine was achieved via reaction with TFA in DCM however all attempts to prepare the free amine were unsuccessful. Subsequent attempts to couple 94 with both succinic anhydride and 92 were unsuccessful. A maleimide functionalized crown ether was synthesised as a molecule for protein modification via the reaction of 74 with 4’-aminobenzo-15-crown-5 97 to produce 98 in an 80% yield. All compounds were fully characterised with crystal structures obtained for 74, 79 and 89.

An important new area of science and engineering relates to nanoscience and nanotechnology, which has been defined as “the emerging capability of human beings to observe and organise matter at the atomic level”. The purpose of this study is to examine a technology enabled learning approach that is informed by perspectives from an embodiment framework of cognition. The study aimed to enhance students’ understanding of challenging nanoscience concepts at the undergraduate level, such as surface area to volume relationships and size dependent properties. Students learned the targeted nanoscience knowledge using two different learning technologies: (a) the experimental group with Agent-Based Models (ABMs) and (b) the comparison group with dynamic visualisations. An empirical study was conducted to compare students in these two groups in terms of learning outcomes and reasoning strategies on assessments of declarative and procedural knowledge as well as solving transfer problems. Given earlier research that proposed ABMs provide an embodied approach for learning, three indicators based on an embodiment framework of cognition were used to compare these two learning approaches: (a) perspective taking, (b) causal inference making, and (c) reasoning strategies. The results of this study revealed no significant differences on declarative knowledge gains between the two groups; however, the ABM group significantly outperformed the dynamic visualisation group on the procedural knowledge and knowledge transfer assessments. Moreover, analyses of the post-test think-aloud video protocols revealed that the majority of the ABM students used first- to third-person perspectives, made causal inferences, and spontaneously used gestures, whereas students in the dynamic visualisation group did not. These results suggest that the ABM students were employing sensorimotor processes and mental simulations associated with an embodiment framework of cognition as they generated their solutions to these problems, while the dynamic visualisation students seemed to rely on memory retrieval of information from the videos. Overall, the findings of this study demonstrate that using ABMs to learn nanoscience phenomena can be more effective than learning with dynamic visualisations. In addition to the superior learning outcomes, students using the ABM approach demonstrated thinking and gestural behaviours that are consistent with an embodied framework of cognition. Given the extensive use of dynamic visualisations in science teaching, further research is needed to determine if ABMs might provide a superior approach for helping students to learn challenging scientific knowledge in nanoscience and other areas. Finally, it is hoped this study might stimulate further interest in research areas the nature of innovative learning experiences for understanding difficult scientific knowledge and their underlying theoretical mechanisms.

Chapter 1 includes a review on dendrimers, their synthesis and applications, with a particular focus on urea-linked dendritic species. The synthetic strategy utilised in this body of work was based on the preparation of a number of branched synthetic building blocks possessing differing terminal functionality. These branched dendrons, bearing three terminal residues and based on the cheap starting material tris(hydroxymethyl)aminomethane (TRIS) 23, involved the coupling of 3.3 equivalents of an appropriately para-substituted benzoic acid chloride with BOC protected TRIS 24 in DCM in the presence of triethylamine. The p-nitro, p-methoxy and p-methyl benzoyl chloride starting materials were obtained commercially, whilst N-(4-carboxyphenyl)maleimide was synthesised according to literature procedures. The BOC protected dendrons (25–27, 34) were synthesized in yields ranging from 50–92%. Deprotection of the BOC protected dendrons 25 and 26 in DCM with TFA, followed by the addition of 1M Na2CO3 afforded the TFA salts 35 and 36, respectively. The corresponding free base amines 37 and 38 were obtained on further treatment of the TFA salts with sodium carbonate. Deprotection of the BOC protected dendrons 27 and 34 afforded the free amines 39 and 48 directly after treatment with sodium carbonate. Synthesis of functionalised branched molecules containing 6- and 9-peripheral functionalities was achieved by refluxing 2 or 3 equivalents of the free amine dendrons with the bi- or tri- functional isocyanate cores, 15 and 45, in refluxing DCM, in most cases the products precipitated from the reaction mixture after 18 h and were isolated simply by filtration, otherwise the removal of the solvent from the reaction mixture afforded the spectroscopically pure product. Conversion of the peripheral nitro functionalised species 14 and 21 to the corresponding amines occurred smoothly via hydrogenation using 5% Pd/C under elevated temperature and pressure (DMF, 55 ºC, 600 psi) and afforded the polyamine 6-mer 51 in 92% yield and the 9-mer 50 in 90% yield, respectively. Similarly, conversion of the methoxy coated 9-mer 42, to the corresponding phenolic compound (AlBr3, dodecane thiol, DCM) afforded the 9-mer polyphenol 52 in an 87% yield. All compounds prepared were fully characterised and crystal structures were obtained for 26 and 35. Chapter 2 includes a review on self-assembled monolayers of organosulfur compounds on gold, applications, patterning techniques and techniques for the characterisation of these surfaces. A number of surface monomers were successfully synthesized, to be used for various surface functionalisations, including the formation of an amine reactive N-hydroxysuccinimide (NHS) disulfide 53, via the DCC coupling of 11,11’-dithiobisundecanoic acid 54 with N-hydroxysuccinimide with an isolated yield of 30%. A novel protein-resistant monomer 58 was also synthesized from 11-undecanoic acid 55 via an acid chloride coupling with triethylene glycol monomethyl ether 58, and isolated in a 72% yield. A number of attempts were made to produce an acyl azide SAM monomer 59, with success finally achieved via the acid chloride coupling of 11,11’-dithiobisundecanoic acid 54 with 5-amino-1,3-benzenedicarbonyl diazide 62 to produce 59 with an isolated yield of ~ 30%. Gold surfaces were prepared on atomically flat silicon wafers using an argon-ion sputterer. SAM films were formed on the gold surfaces via traditional solution based self-assembly methodology. A UV patterning protocol was developed, and a successful patterning trial using the NHS terminated monomer to backfill the UV exposed areas of a dodecane thiol monolayer was achieved and visualized using AFM and fluorescence microscopy after treating the surface with aminofluorescein. The covalent attachment of green fluorescent protein to the monolayer surface via reaction with the NHS terminated monolayer was demonstrated. The fluorescence of the biomolecule was preserved. The formation of a monolayer using the acyl azide monomer 59, was characterised by contact angle and XPS analysis. However, preliminary studies into the activation of the acyl azide surface into the reactive isocyanate were unsuccessful. There is however, significant scope for further investigations into this interesting surface technology. Chapter 3 includes a review on heterobifunctional linker technology with a particular focus on amine and thiol reactive moieties and literature examples of heterobifunctional linkers of this type. Synthesis of heterobifunctional reagents such as 71 and 74 via a two step synthetic methodology involving the coupling of maleic anhydride with the parent amino-acids in acetic acid, followed by a one pot cyclisation and NHS esterification using DCC in DMF were successful, with overall yields of 9% and 32% respectively for the two reaction steps. The one pot extension of 74 with 6-aminohexanoic acid, followed by DCC, facilitated NHS esterification was achieved successfully in a yield of 30%. Attempts to extend 74 with the synthesised amino acid 88 were unsuccessful due to the insolubility of 88 in organic solvents. A different synthetic strategy was devised towards the synthesis of 85 with the coupling of 74 and mono BOC protected ethylene diamine 91 in DCM to give 93 in an isolated yield of 60%. Deprotection of the terminal amine was achieved via reaction with TFA in DCM however all attempts to prepare the free amine were unsuccessful. Subsequent attempts to couple 94 with both succinic anhydride and 92 were unsuccessful. A maleimide functionalized crown ether was synthesised as a molecule for protein modification via the reaction of 74 with 4’-aminobenzo-15-crown-5 97 to produce 98 in an 80% yield. All compounds were fully characterised with crystal structures obtained for 74, 79 and 89.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Biomolecular and Physical Sciences
Full Text

Biomedical Neuroscience
Ph.D.
While combination anti-retroviral therapy (cART) has improved the length and quality of life of individuals living with HIV-1 infection, the prevalence of HIV-associated neurocognitive disorders (HAND) has increased and remains a significant clinical concern. The neuropathogenesis of HAND is not completely understood, however, latent HIV infection in the central nervous system (CNS) and chronic neuroinflammation are believed to play a prominent role. CNS-associated macrophages and resident microglia are significant contributors to CNS inflammation and constitute the chief reservoir of HIV-1 infection in the CNS. Previous studies from our lab suggest monocyte/macrophage invasion of the CNS in HIV may be driven by altered monocyte/macrophage homeostasis. We have reported expansion of a monocyte subset (CD14+CD16+CD163+) in peripheral blood of HIV+ patients that is phenotypically similar to macrophages/microglia that accumulate in the CNS as seen in post-mortem tissue. The factors driving the expansion of this monocyte subset are unknown, however, signaling through cFMS, a type III receptor tyrosine kinase (RTK), may play a role. Macrophage-colony stimulating factor (M-CSF), a ligand of cFMS, has been shown to be elevated in the cerebral spinal fluid (CSF) of individuals with the most severe form of HAND, HIV-associated dementia (HAD). M-CSF promotes a Macrophage-2-like phenotype and increases CD16 and CD163 expression in cultured monocytes. M-CSF has also been shown to increase the susceptibility of macrophages to HIV infection and enhance virus production. These findings, in addition to the known function of M-CSF in promoting macrophage survival, supports a role for M-CSF in the development and maintenance of macrophage viral reservoirs in tissues where these cells accumulate, including the CNS. Interestingly, a second ligand for cFMS, IL-34, was recently identified and reported to share some functions with M-CSF, suggesting that both ligands may contribute to HIV-associated CNS injury and AIDS pathogenesis. Through immunohistochemical studies using a relevant animal model of HIV infection, SIV infected rhesus macaques, we reported the presence of M-CSF and IL-34 in the brains of seronegative and SIV+ animals, for the first time, and identified spatial differences in the expression of these ligands. Important to our interest in viral persistence in the CNS, we observed the predominance of M-CSF expression in brain to be by cells that comprise perivascular cuffs and nodular lesions, which contain monocytes/ macrophages that have migrated into the CNS. IL-34 appeared to be a tissue-specific ligand expressed by resident microglia. Like M-CSF, we found that IL-34 also increased the frequency of CD16+CD163+ monocytes in vitro. We further investigated the potential of cFMS inhibition as a means to abrogate macrophage-2-like immune polarization using the small molecule tyrosine kinase inhibitor (TKI), GW2580. The addition of GW2580 abolished cFMS ligand-mediated increases in CD16+CD163+ monocyte frequency in human peripheral blood mononuclear cells (PBMC) as well as virus production in HIV infected primary human microglia. Furthermore, we found cFMS-mediated upregulation of CD16 and CD163 to be relevant to an additional disease process, high-grade astrocytomas, suggesting that M-CSF and IL-34 may be mediators of other neuroinflammatory diseases, as well. We hope these findings will provide insight into the role of altered monocyte/macrophage homeostasis in HIV disease and identify a novel strategy for targeting long-lived cellular reservoirs of HIV infection through restored immune homeostasis.
Temple University--Theses

Lateral diffusion of membrane components (lipids and proteins) is an important membrane property to measure since the essential process of absorption of anti-cancer and other drugs -some of which are not soluble in lipids and therefore would not be able to penetrate the cell membrane through passive diffusion- lies on it. In particular, the procedure of diffusion into the cell cytoplasm is reliant on free volumes in the membrane (passive diffusion) as well as carrier proteins (facilitated diffusion). By enhancing the mobility of lipids and/or proteins, the possibility of the carrier protein to "encapsulate" pharmacological components maxim- izes, as a "scanning" of the proteins gets performed due to the fluid phase of a biological membrane. At the same time, the increased mobility of the lipids facilitates the passage of lipid-soluble molecules into the cell. Thus, given that the success of anticancer treatments heavily depends on their absorption by the cell, a significant enhancement of the cell mem- brane permeability (permeabilisation) is rendered vital to the applicability of the technique. For this reason, there is augmented interest in combined methods such as Nanotechnology based drug delivery that is focused on the development of optimally designed therapeutic agents along with the application of shock waves to enhance the membrane permeability to the agents. This study examines the impact of shock waves on a numerical model of a biological membrane. Cont/d.

Un effort mondial existe actuellement dans le but de réaliser un ordinateur quantique. Un tel dispositif permettrait d'implémenter des algorithmes plus rapides que les algorithmes classiques pour certaines tâches (recherche dans des bases de données, factorisation d'entiers). Il permettrait également de simuler des systèmes quantiques de manière beaucoup plus efficace qu'un ordinateur classique. L'obtention de ce gain en puissance nécessite d'intriquer un grand nombre de bits quantiques (qubits). Celle ci suppose de pouvoir déplacer un qubit d'un point à un autre de l'espace. Dans cette thèse, nous démontrons une première étape vers le déplacement d'un qubit de spin électronique : un électron unique est déplacé, à la demande, entre deux boîtes quantiques distantes de quelques microns. Le transport est réalisé à l'aide d'une onde acoustique de surface qui entraîne l'électron. Le transfert a été réalisé avec une efficacité de 90 % et déclenché à la nanoseconde. Ces résultats ouvrent la voie à la réalisation d'expériences d'optique quantique électronique avec une détection évènement par évènement. L'envoi d'un électron sur deux initialement présents ouvre la voie à la génération de paires d'électrons distants et intriqués.

Les composés polyaromatiques polysoufrés représentent une classe de molécules peu étudiées, malgré leurs propriétés intéressantes. La présence du soufre influence les propriétés redox, photophysiques et de complexation. Nous avons préparé une série de ces composés par des réactions de substitution nucléophile aromatique. Ceux-ci peuvent être fonctionnalisés par des unités polyaromatiques, tels que l’anthracène ou le pyrène, ou par des glycosides. Leurs propriétés de luminescence ont été étudiées en particulier sous l’angle de l’émission induite par l’agrégation, où les composés deviennent émissifs lorsqu’ils sont immobilisés en phase solide ou fortement refroidis. Ils permettent également de stabiliser des nanoparticules de fer/platine, où une forte densité d’atomes de soufre divalent joue un rôle important en nanosciences. Les dérivés glycosylés ont été testés chez différentes lectines comme ConA, PAIL, PAIIL et Bc2lA, les trois dernières étant impliquées dans les infections bactériennes chez les patients atteints de mucoviscidose. Les études comprennent les propriétés photophysiques, de réticulation et des mesures d’affinité par des méthodes biophysiques (SPR, ITC et HIA). Ceci a ammené à la production de nouveaux biocapteurs ou sondes luminescentes basés sur des interactions sélectives lectine-sucre dans l’éventualité future de dispositifs de diagnostics et de détection à partir d’expression de lectines (ex. cancer, infections bactériennes, etc.).Une autre classe de composés polyaromatiques a été étudiée, les hélicènes. Ces molécules hélicoïdales chirales sont retrouvées sous deux formes énantiomériques, selon le pas d’hélice. Nous présentons ici une nouvelle méthode de synthèse des hélicènes par une voie organométallique de réactions d’annulation et d’insertions C-H. Une étude poussée des conditions réactionnelles a été réalisée. Nous avons préparé des hélicènes fonctionnalisés. Les dérivés bromés et cyanés du [5]-hélicène ont été déposés sur la surface de Suzuki, afin d’étudier par nc-AFM les propriétés de structuration de ces produits sur une surface isolante. Le [5]-hélicène a aussi été fonctionnalisé par des unités mannosylés, dans les mêmes perspectives que pour les astérisques soufrés glycosylés. Ces hélicènes glycosylés sont les premiers de la sorte décrit dans la littérature. Ils ont présenté des propriétés convenables vers des sondes luminescentes chirales et d’autres biocapteurs, qui sont basés sur les interactions lectine-sucre
Polysulfurated polyaromatic compounds represent a class of molecules that are not extensively studied, despite their interesting properties. The presence of sulfur affects their redox, photophysical and complexation properties. We prepared a series of these compounds by using some aromatic nucleophilic substitutions. They can be further functionalized by some polyaromatic units, such as anthracene or pyrene, or by some glycosides.Their luminescence properties have been especially studied for their agregation induced emission properties, where the emission of the compounds is turned on when they are immobilized in solid phase or strongly cooled. These compounds can also be used to stabilize iron/platinum nanoparticles, where a high density of divalent sulfur atoms play an important role in nanosciences. Glycosylated derivatives have been tested with different lectins like ConA, PAIL, PAIIL and Bc2lA, the last three being involved in bacterial infections found in patient suffering from cystic fibrosis. Studies include photophysical and reticulation properties, and also affinitiy assays by using biophysical methods (SPR, ITC, and HIA). It provided some novel biosensors or luminescent sensors based on some selective lectin-carbohydrate interactions, in the event of future diagnostic devices and biological detection originating from lectins expressions (ex. cancer, bacterial infection, etc.).Another class of polyaromatic compounds has been studied, the helicenes,. Those chiral helical molecules can be found under two enantiomeric forms, according to the sense of the helical pitch.We herein present a new synthetic method of helicenes based on an organometallic route for some annulation reactions and C-H insertions. An exhaustive study of reaction conditions has been performed. We have prepared some functionnalized helicenes. Brominated and cyanated [5]-helicene derivatives have been deposited on a Suzuki surface, in order to study their structuration properties by nc-AFM on a non conductive surface. [5]-helicene was further functionnalized with some mannosylated units, with the same perspectives as for the glycosylated sulfurated asterisks. Those glycosylated helicenes are the first of their kind described in the literature. They provided some adequate properties toward new chiral and luminescent sensors, as well as other biosensors, which are based on lectin-carbohydrate interactions

Les composés polyaromatiques polysoufrés représentent une classe de molécules peu étudiées, malgré leurs propriétés intéressantes. La présence du soufre influence les propriétés redox, photophysiques et de complexation. Nous avons préparé une série de ces composés par des réactions de substitution nucléophile aromatique. Ceux-ci peuvent être fonctionnalisés par des unités polyaromatiques, tels que l’anthracène ou le pyrène, ou par des glycosides. Leurs propriétés de luminescence ont été étudiées en particulier sous l’angle de l’émission induite par l’agrégation, où les composés deviennent émissifs lorsqu’ils sont immobilisés en phase solide ou fortement refroidis. Ils permettent également de stabiliser des nanoparticules de fer/platine, où une forte densité d’atomes de soufre divalent joue un rôle important en nanosciences. Les dérivés glycosylés ont été testés chez différentes lectines comme ConA, PAIL, PAIIL et Bc2lA, les trois dernières étant impliquées dans les infections bactériennes chez les patients atteints de mucoviscidose. Les études comprennent les propriétés photophysiques, de réticulation et des mesures d’affinité par des méthodes biophysiques (SPR, ITC et HIA). Ceci a ammené à la production de nouveaux biocapteurs ou sondes luminescentes basés sur des interactions sélectives lectine-sucre dans l’éventualité future de dispositifs de diagnostics et de détection à partir d’expression de lectines (ex. cancer, infections bactériennes, etc.).Une autre classe de composés polyaromatiques a été étudiée, les hélicènes. Ces molécules hélicoïdales chirales sont retrouvées sous deux formes énantiomériques, selon le pas d’hélice. Nous présentons ici une nouvelle méthode de synthèse des hélicènes par une voie organométallique de réactions d’annulation et d’insertions C-H. Une étude poussée des conditions réactionnelles a été réalisée. Nous avons préparé des hélicènes fonctionnalisés. Les dérivés bromés et cyanés du [5]-hélicène ont été déposés sur la surface de Suzuki, afin d’étudier par nc-AFM les propriétés de structuration de ces produits sur une surface isolante. Le [5]-hélicène a aussi été fonctionnalisé par des unités mannosylés, dans les mêmes perspectives que pour les astérisques soufrés glycosylés. Ces hélicènes glycosylés sont les premiers de la sorte décrit dans la littérature. Ils ont présenté des propriétés convenables vers des sondes luminescentes chirales et d’autres biocapteurs, qui sont basés sur les interactions lectine-sucre
Polysulfurated polyaromatic compounds represent a class of molecules that are not extensively studied, despite their interesting properties. The presence of sulfur affects their redox, photophysical and complexation properties. We prepared a series of these compounds by using some aromatic nucleophilic substitutions. They can be further functionalized by some polyaromatic units, such as anthracene or pyrene, or by some glycosides.Their luminescence properties have been especially studied for their agregation induced emission properties, where the emission of the compounds is turned on when they are immobilized in solid phase or strongly cooled. These compounds can also be used to stabilize iron/platinum nanoparticles, where a high density of divalent sulfur atoms play an important role in nanosciences. Glycosylated derivatives have been tested with different lectins like ConA, PAIL, PAIIL and Bc2lA, the last three being involved in bacterial infections found in patient suffering from cystic fibrosis. Studies include photophysical and reticulation properties, and also affinitiy assays by using biophysical methods (SPR, ITC, and HIA). It provided some novel biosensors or luminescent sensors based on some selective lectin-carbohydrate interactions, in the event of future diagnostic devices and biological detection originating from lectins expressions (ex. cancer, bacterial infection, etc.).Another class of polyaromatic compounds has been studied, the helicenes,. Those chiral helical molecules can be found under two enantiomeric forms, according to the sense of the helical pitch.We herein present a new synthetic method of helicenes based on an organometallic route for some annulation reactions and C-H insertions. An exhaustive study of reaction conditions has been performed. We have prepared some functionnalized helicenes. Brominated and cyanated [5]-helicene derivatives have been deposited on a Suzuki surface, in order to study their structuration properties by nc-AFM on a non conductive surface. [5]-helicene was further functionnalized with some mannosylated units, with the same perspectives as for the glycosylated sulfurated asterisks. Those glycosylated helicenes are the first of their kind described in the literature. They provided some adequate properties toward new chiral and luminescent sensors, as well as other biosensors, which are based on lectin-carbohydrate interactions

We have developed a high density lipoprotein (HDL)-based platform for transport and delivery of hydrophobic gold nanoparticles (AuNP). The ability of apolipoprotein E3 (apoE3) to act as a ligand for the low-density lipoprotein receptor (LDLr) was exploited to gain entry of HDL with AuNP into glioblastoma cells. AuNP of 3, 10 and 17 nm diameter, the latter two synthesized by phase transfer process, were solubilized by integration into reconstituted HDL (rHDL). Absorption spectroscopy indicated the presence of stable particles with signature surface plasmon bands, while electron microscopy revealed AuNP embedded in rHDL core. The rHDL-AuNP complexes displayed robust binding to the LDLr, were internalized by the glioblastoma cells, and appeared as aggregated AuNP in the endosomal-lysosomal compartments. The rHDL-AuNP generated little cytotoxicity and were able to cross the blood brain barrier. The findings bear significance since they offer an effective means of delivering AuNP across tumor cell membrane.

This thesis describes the synthesis of water-soluble dendron-conjugated gold nanoparticles (Den-AuNPs) with various average core sizes and the evaluation of stability, cytotoxicity, and cell permeability and uptake of these materials. The characterization of Den-AuNPs using various instruments including transmission electron microscopy (TEM), matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS), 1H NMR, FT-IR, and UV-vis spectroscopy confirms the dendron conjugation to the glutathione-capped gold nanoparticles (AuNPs). The stability of AuNPs and Den-AuNPs in solutions of different pH and salt concentration was determined by monitoring changes in surface plasmon bands of gold using UV-vis spectroscopy. The Den-AuNPs were found to be more stable than the precursor AuNPs maintaining their solubility at the pHs higher than 4 and with the salt concentrations of up to 100 mM. The improved stability of Den-AuNPs suggests that the post-functionalization of thiol-capped gold nanoparticle surfaces with dondrons can further improve the physiological stability and biocompatibility of gold nanoparticle-based materials. Cytotoxicity studies with AuNPs and Den-AuNPs with and without flourophores were also performed by examining cell viability for 3T3 fibroblasts using a MTT cell proliferation assay. The conjugation of dendrons to the AuNPs with flourophores was able to decrease the cytotoxicity brought about by the flourophores. The successful uptake of Den-AuNPs in mouse fibroblast 3T3 cells shows the physiological viability of the hybrid materials.

Natural manganese oxides are generally formed in surficial environments that are near ambient temperature and water-rich, and may be exposed to wet-dry cycles and a variety of adsorbate species that influence dramatically their level of hydration. Manganese oxide minerals are often poorly crystalline, nanophase, and hydrous. In the near-surface environment they are involved in processes that are important to life, such as water column oxygen cycling, biomineralization, and transport of minerals/nutrients through soils and water. These processes, often involving transformations among manganese oxide polymorphs, are governed by a complex interplay between thermodynamics and kinetics. Manganese oxides are also used in technology as catalysts, and for other applications.

The major goal of this dissertation is to examine the energetics of bulk and nanophase manganese oxide phases as a function of particle size, composition, and surface hydration. Careful synthesis and characterization of manganese oxide phases with different surface areas provided samples for the study of enthalpies of formation by high temperature oxide melt solution calorimetry and of the energetics of water adsorption on their surfaces. These data provide a quantitative picture of phase stability and how it changes at the nanoscale.

The surface energy of the hydrous surface of Mn₃O₄ is 0.96 ± 0.08 J/m², of Mn₂O₃ is 1.29 ± 0.10 J/m², and of MnO₂ is 1.64 ± 0.10 J/m². The surface energy of the anhydrous surface of Mn₃O₄ is 1.62 ± 0.08 J/m ², of Mn₂O₃ is 1.77 ± 0.10 J/m ², and of MnO₂ is 2.05 ± 0.10 J/m². Supporting preliminary findings (Navrotsky et al., 2010), the spinel phase (Mn₃O₄) has a lower surface energy (more stabilizing) than bixbyite, while the latter has a smaller surface energy than pyrolusite. These differences significantly change the positions in oxygen fugacity—temperature space of the redox couples Mn₃O₄-Mn₂O ₃ and Mn₂O₃-MnO₂ favoring the lower surface enthalpy phase (the spinel Mn₃O₄) for smaller particle size and in the presence of surface hydration.

Chemisorption of water onto anhydrous nanophase Mn₂O ₃ surfaces promotes rapidly reversible redox phase changes at room temperature as confirmed by calorimetry, X-ray diffraction, and titration for manganese average oxidation state. Water adsorption microcalorimetry (in situ) at room temperature measured the strongly exothermic integral enthalpy of water adsorption (-103.5 kJ/mol) and monitored the energetics of the redox phase transformation. Hydration-driven redox transformation of anhydrous nanophase Mn(III) ₂O₃, (high surface enthalpy of anhydrous surfaces 1.77 ± 0.10 J/m²) to Mn(II,III)₃O₄ (lower surface enthalpy 0.96 ± 0.08 J/m²) occurred during the first few doses of water vapor. Surface reduction of nanoparticle bixbyite (Mn ₂O₃) to hausmannite (Mn₃O₄) occurs under conditions where no such reactions are seen or expected on grounds of bulk thermodynamics in coarse-grained materials.

Layered structure manganese oxides contain alkali or alkaline earth cations and water, are generally fine-grained, and have considerable thermodynamic stability. The surface enthalpies (SE) of layered and tunnel structure complex manganese oxides are significantly lower than those of the binary manganese oxide phases. The SE for hydrous surfaces and overall manganese average oxidation state (AOS) (value in parentheses) are: cryptomelane 0.77 ± 0.10 J/m ² (3.78), sodium birnessite 0.69 ± 0.13 J/m² (3.56), potassium birnessite 0.55 ± 0.11 J/m² (3.52), and calcium birnessite 0.41 ± 0.11 J/m² (3.50). Surface enthalpies of hydrous surfaces of the calcium manganese oxide nanosheets are: δCa _0.39MnO_2.3nH₂O 0.75 ± 0.10 J/m² (3.89) and δCa_0.43MnO_2.3nH₂O 0.57 ± 0.12 J/m² (3.68). The surface enthalpy of the complex manganese oxides appears to decrease with decreasing manganese average oxidation state, that is, with greater mixed valence manganese (Mn ^3+/4+). Low surface energy suggests loose binding of H₂O on the internal and external surfaces and may be critical to catalysis in both natural and technological settings.

We present a versatile biosensing strategy that uses nucleic acids programmed to undergo an isothermal toehold mediated strand displacement in the presence of analyte. This rearrangement results in a double biotinylated duplex formation that induces the rapid aggregation of streptavidin decorated quantum dots (QDs). As biosensor reporters, QDs are advantageous to organic fluorophores and fluorescent proteins due to their enhanced spectral and fluorescence properties. Moreover, the nanoscale regime aids in an enhanced surface area that increase the number of binding of macromolecules, thus making cross-linking possible. The biosensing transduction response, in the current approach, is dictated by the analysis of the natural single particle phenomenon known as fluorescence intermittency, or blinking is the stochastic switching of fluorescence intensity ON (bright) and OFF (dark) states observed in single QD or other fluorophores. In contrast to binary blinking that is typical for single QDs, aggregated QDs exhibit quasi-continuous emission. This change is used as an output for the novel biosensing techniques developed by us. Analysis of blinking traces that can be measured by laser scanning confocal microscopy revealed improved detection of analytes in the picomolar ranges. Additionally, this unique biosensing approach does not require the analyte to cause any fluorescence intensity or color changes. Lastly, this biosensing method can be coupled with therapeutics, such as RNA interference inducers, that can be conditionally released and thus used as a theranostic probes.

Nanofabrication through multiphoton absorption has generated considerable interest because of its unique ability to generate 2D and 3D structures in a single laser-direct-write step as well as its ability to generate feature sizes well below the diffraction limited laser spot size. The majority of multiphoton fabrication has been used to create 3D structures of photopolymers which have applications in a wide variety of fields, but require additional post-processing steps to fabricate conductive structures. It has been shown that metal ions can also undergo multiphoton absorption, which reduces the metal ions to stable atoms/nanoparticles which are formed at the laser focal point. When the focus is located at the substrate surface, the reduced metal is deposited on the surface, which allows arbitrary 2D patterning as well as building up 3D structures from this first layer. Samples containing the metal ions can be prepared either in a liquid solution, or in a polymer film. The polymer film approach has the benefit of added support for the 3D metallic structures; however it is difficult to remove the polymer after fabrication to leave a free standing metallic structure. With the ion solution method, free standing metallic structures can be fabricated but need to be able to withstand surface tension forces when the remaining unexposed solution is washed away.

So far, silver nanowires with resistivity on the order of bulk silver have been fabricated, as well as a few small 3D structures. This research focuses on the surfactant assisted multiphoton reduction of silver ions in a liquid solution. The experimental setup consists of a Coherent Micra 10 Ultrafast laser with 30fs pulse length, 80MHz repetition rate, and a wavelength centered at 800nm. This beam is focused into the sample using a 100x objective with a N.A. of 1.49. Silver structures such as nanowires and grid patterns have been produced with minimum linewidth of 180nm. Silver nanowires with resistivity down to 6x bulk silver have been fabricated. Three-dimensional structures have also been fabricated with up to a 10µm height at a thickness of 500nm. This method can fabricate structures with the possible applications in plasmonic metamaterials, photonic crystals, MEMS/NEMS and micro/nanocircuitry.

As a class of carbon-based nanomaterials, single-walled carbon nanotubes (SWNT) have many structural variations, called chiralities, each with different properties. Many potential applications of SWNT require the properties of a single chirality, but current synthesis methods can only produce single chiralities at prohibitive costs, or mixtures of chiralities at more affordable prices. Post-synthesis chirality separations provide a solution to this problem, and hydrogel separations are one such method.

Despite much work in this field, the underlying interactions between SWNT and hydrogel are not fully understood. During separation, large quantities of SWNT are irretrievably lost due to irreversible adsorption to the hydrogel, posing a major problem to separation efficiency, while also offering an interesting scientific problem concerning the interaction of SWNT with hydrogels and surfactants.

This thesis explores the problem of irreversible adsorption, offering an explanation for the process from a mechanistic viewpoint, opening new ways for improvement in separation. In brief, this work concludes adsorption follows three pathways, two of which lead to irreversible adsorption, both mediated by the presence of surfactants and limited by characteristics of the hydrogel surface. These findings stand to increase the general understanding of hydrogel SWNT separations, leading to improvements in separation, and bringing the research field closer to the many potential applications of single-chirality SWNT.

With the technological advances of today, comes the increasing need for device miniaturization. This thesis focuses on the construction of nanostructures, approached from both bottom-up (synthesis) and top-down (lithography) methods. First, a bottom-up method to construct cadmium selenide semiconductor nanoparticles under mild conditions in reverse micelles is described and investigated. A detailed spectroscopic study of nanoparticle growth is provided, whereby the growth was monitored over a period of up to a year. The nanoparticles were removed from the surfactant using ethanol precipitation and were subjected to surface derivatization in order to stabilize them. Secondly, photoreversible cycloaddition of an anthracene derivative is studied for use in double-exposure lithography. The system was found to be adequately reversible, though possible side photoreactions were investigated. Spectroscopic studies were also conducted and photophysical pathways of the compound were examined. The compound was found to have a cleaving quantum yield of 0.67 +/- 0.04 and was established as an actinometer to assess the efficacy of future candidate compounds.

Apoptosis (programmed cell-death) is a common final pathway through which cells die in retinal degenerative diseases. The purpose of this project was to develop biodegradable nanoparticles that quickly deliver XIAP, an inhibitor of apoptosis, to retinal cells following acute insults. In vitro protein release profiles from different formulations were established, and two cell types were incubated with nanoparticles to assess cellular uptake. Subretinal injections were carried out in rats to assess in vivo localization and possible toxicity. In vitro studies showed an initial burst of protein followed by sustained release, with overall low levels of protein release. Cell culture experiments suggest that particles are mostly membrane-bound, and some may be internalized. In vivo experiments revealed no signs of toxicity, and protein localized within the photoreceptor layer. In conclusion, nanoparticles may provide a good delivery system for XIAP; however higher levels of protein release are needed for neuroprotection, warranting further investigation.

Direct coagulation printing (DCP) is a new approach to extrusion-based additive manufacturing, developed during this thesis project using alumina nanopowder. The fabrication of complex ceramic parts, sintered to full density, was achieved and the details of this invention are described. With the use of additive manufacturing, complex features can be generated that are either very difficult or unattainable by conventional subtractive manufacturing methods. Three unique approaches were taken to create a slurry suitable for extrusion 3D-printing. Each represented a different method of suspending alumina nanopowder in a liquid; a bio-polymer gel based on chitosan, a synthetic polymer binder using poly-vinyl acetate (PVA), and electrostatic stabilization with the dispersant tri-ammonium citrate (TAC). It was found that TAC created a slurry with viscosity and coagulation rate that were tuneable through pH adjustment with nitric acid. This approach led to the most promising printing and sintering results, and is the basis of DCP. Taguchi and fractional factorial design of experiments models were used to optimize mixing of the alumina slurry, rheological properties, print quality, and sinterability. DCP was characterized by measuring the mechanical properties and physical characteristics of printed parts. Features as small as ~450 ?m in width were produced, in parts with overhangs and enclosed volumes, in both linear and radial geometries. After sintering, these parts exhibited little to no porosity, with flexural modulus and hardness comparing favorably with conventionally manufactured alumina parts. A remarkable aspect of DCP is that it is a completely binderless process, requiring no binder removal step. In addition, DCP can employ nanopowders, allowing for enhanced mechanical properties as observed in nano-grained materials. Perhaps most importantly, any material that acquires a surface charge when in aqueous media has the potential to be used in DCP, making it a method of additive manufacturing using many metals and ceramics other than alumina.

III-V optoelectronic device integration in a CMOS post-process compatible manner is important for the intimate integration of silicon-based electronic and photonic integrated circuits. The low temperature, self-catalyzed growth of high crystalline quality Wurtzite-phase InP nanopillars directly on silicon presents a viable approach to integrate high performance nano-optoelectronic devices.

For the optical transmitter side of the photonic link, InGaAs quantum wells have been grown in a core-shell manner within InP nanopillars. Position-controlled growth with varying pitch is used to systematically control emission wavelength across the same growth substrate. These nanopillars have been fabricated into electrically-injected quantum well in nanopillar LEDs operating within the silicon transparent 1400–1550 nm spectral window and efficiently emitting micro-watts of power. A high quality factor (Q ~ 1000) undercut cavity quantum well nanolaser is demonstrated, operating in the silicon-transparent wavelength range up to room temperature under optical excitation.

We also demonstrate an InP nanopillar phototransistor as a sensitive, low-capacitance photoreceiver for the energy-efficient operation of a complete optical link. Efficient absorption in a compact single nanopillar InP photo-BJT leads to a simultaneously high responsivity of 9.5 A/W and high 3dB-bandwidth of 7 GHz.

For photovoltaic energy harvesting, a sparsely packed InP nanopillar array can absorb ~90% of the incident light because of the large absorption cross section of these near-wavelength nanopillars. Experimental data based on wavelength and angle resolved integrating sphere measurements will be presented to discuss the nearly omnidirectional absorption properties of these nanopillar arrays.

This dissertation reports the synthesis and characterization of nanoscale coordination polymers (NCPs) for anticancer drug delivery. Nanoparticles have been explored in order to address the limitations of small molecule chemotherapeutics. NCPs have been investigated as drug delivery vehicles as they can exhibit the same beneficial properties as the bulk metal-organic frameworks as well as interesting characteristics that are unique to nanomaterials.

Gd-MTX (MTX = methotrexate) NCPs with a MTX loading of 71.6 wt% were synthesized and stabilized by encapsulation within a lipid bilayer containing anisamide (AA), a small molecule that targets sigma receptors which are overexpressed in many cancer tissues. Functionalization with AA allows for targeted delivery and controlled release to cancer cells, as shown by enhanced efficacy against leukemia cells. The NCPs were doped with Ru(bpy)₃²⁺ (bpy = 2,2'-bipyridine), and this formulation was utilized as an optical imaging agent by confocal microscopy.

NCPs containing the chemotherapeutic pemetrexed (PMX) were synthesized using different binding metals. Zr-based materials could not be stabilized by encapsulation with a lipid bilayer, and Gd-based materials showed that PMX had degraded during synthesis. However, Hf-based NCPs containing 19.7 wt% PMX were stabilized by a lipid coating and showed in vitro efficacy against non-small cell lung cancer (NSCLC) cell lines. Enhanced efficacy was observed for formulations containing AA.

Additionally, NCP formulations containing the cisplatin prodrug disuccinatocisplatin were prepared; one of these formulations could be stabilized by encapsulation within a lipid layer. Coating with a lipid layer doped with AA rendered this formulation an active targeting agent. The resulting formulation proved more potent than free cisplatin in NSCLC cell lines. Improved NCP uptake was demonstrated by confocal microscopy and competitive binding assays.

Finally, a Pt(IV) oxaliplatin prodrug was synthesized and incorporated in different NCPs using various binding metals. A moderate drug loading of 44.9 wt% was determined for Zr-based NCPs. This drug loading, along with a diameter less than 200 nm, make these particles promising candidates for further stabilization via lipid encapsulation.

Nanoscopic pores in biological systems – cells, for example – are responsible for regulating the transport of ionic and molecular species between physiologically distinct compartments maintained by thin plasma membranes. These biological pores are proteinaceous structures: long, contorted chains of chemical building blocks called amino acids. Protein pores have evolved to span a staggering range of shapes, sizes and chemical properties, each crucial to a pore's unique functionality.

Protein pores have extremely well-defined jobs. For instance, pores called ion channels only transport ions. Within this family, there are pores designated to selectively transport specific ions, such as sodium channels for sodium, chloride channels for chloride and so on. Further subdivisions exist within each type of ion channel, resulting in a pantheon of specialized proteins pores.

Specificity and selectivity are bestowed upon a pore through its unique incorporation and arrangement of its amino acids, which in turn have their own unique chemical and physical properties. With hundreds of task-specific pores, deciphering the precise relationship between form and function in these protein channels is a critical, but daunting task. In this thesis, we examine an alternative for probing the fundamental mechanisms responsible for transport on the nanoscale.

Solid-state membranes offer well-defined structural surrogates to directly address the science underlying pore functionality. Numerous protein pores rely on electronic interactions, size exclusion principles and hydrophobic effects to fulfill their duties, regardless of their amino acid sequence. Substituting an engineered and well-characterized pore, we strive to achieve and, thus, understand the hallmarks of biological pore function: analyte recognition and selective transport.

While we restrict our study to only two readily available membrane materials – one a polymer and the other a ceramic – nanofabrication techniques give us access to a virtually limitless combination of pore shapes and sizes. Exploiting this, we investigate the role of pore geometry in mediating the electrostatic and steric interactions responsible for transport on the nanoscale. Through targeted chemical modifications of our homogenous pores, we easily tailor their surface properties to investigate the role of hydrophobic effects in confined environments. Unbound by the physiological limitations of protein structures (such as sensitivity to electrolyte composition and fragility to external forces), our report concludes with the fusion of fabrication and modification considerations to design robust components for nanofluidic circuitry and nanoscopic biosensors.

Magnetic nanostructures have widespread applications in many areas of physics and engineering, and nanosphere lithography has recently emerged as promising tool for the fabrication of such nanostructures. The goal of this research is to explore the magnetic properties of a thin film of ferromagnetic material deposited onto a hexagonally close-packed monolayer array of polystyrene nanospheres, and how they differ from the magnetic properties of a typical flat thin film. The first portion of this research focuses on determining the optimum conditions for depositing a monolayer of nanospheres onto chemically pretreated silicon substrates (via drop-coating) and the subsequent characterization of the deposited nanosphere layer with scanning electron microscopy. Single layers of permalloy (Ni80Fe20) are then deposited on top of the nanosphere array via DC magnetron sputtering, resulting in a thin film array of magnetic nanocaps. The coercivities of the thin films are measured using a home-built magneto-optical Kerr effect (MOKE) system in longitudinal arrangement. MOKE measurements show that for a single layer of permalloy (Py), the coercivity of a thin film deposited onto an array of nanospheres increases compared to that of a flat thin film. In addition, the coercivity increases as the nanosphere size decreases for the same deposited layer. It is postulated that magnetic exchange decoupling between neighboring nanocaps suppresses the propagation of magnetic domain walls, and this pinning of the domain walls is thought to be the primary source of the increase in coercivity.

Colloidally prepared nanocrystals of transparent conducting oxide (TCO) semiconductors have emerged in the past decade as an exciting new class of plasmonic materials. In recent years, there has been tremendous progress in developing synthetic methods for the growth of these nanocrystals, basic characterization of their properties, and their successful integration into optoelectronic and electrochemical devices. However, many fundamental questions remain about the physics of localized surface plasmon resonance (LSPR) in these materials, and how their optoelectronic properties derive from their underlying structural properties. In particular, the influence of the concentration and distribution of dopant ions and compensating defects on the optoelectronic properties of TCO nanocrystals has seen little investigation.

Indium tin oxide (ITO) is the most widely studied and commercially deployed TCO. Herein we investigate the role of the distribution of tin dopants on the optoelectronic properties of colloidally prepared ITO nanocrystals. Owing to a high free electron density, ITO nanocrystals display strong LSPR absorption in the near infrared. Depending on the particular organic ligands used, they are soluble in various solvents and can readily be integrated into densely packed nanocrystal films with high conductivities. Using a combination of spectroscopic techniques, modeling and simulation of the optical properties of the nanocrystals using the Drude model, and transport measurements, it is demonstrated herein that the radial distribution of tin dopants has a strong effect on the optoelectronic properties of ITO nanocrystals.

ITO nanocrystals were synthesized in both surface-segregated and uniformly distributed dopant profiles. Temperature dependent measurements of optical absorbance were first combined with Drude modeling to extract the internal electrical properties of the ITO nanocrystals, demonstrating that they are well-behaved degenerately doped semiconductors displaying finite conductivity at low temperature and room temperature conductivity reduced by one order of magnitude from that of high-quality thin film ITO.

Synchrotron based x-ray photoelectron spectroscopy (XPS) was then employed to perform detailed depth profiling of the elemental composition of ITO nanocrystals, confirming the degree of dopant surface-segregation. Based on free carrier concentrations extracted from Drude fitting of LSPR absorbance, an inverse correlation was found between surface segregation of tin and overall dopant activation. Furthermore, radial distribution of dopants was found to significantly affect the lineshape and quality factor of the LSPR absorbance. ITO nanocrystals with highly surface segregated dopants displayed symmetric LSPRs with high quality factors, while uniformly doped ITO nanocrystals displayed asymmetric LSPRs with reduced quality factors. These effects are attributed to damping of the plasmon by Coulombic scattering off ionized dopant impurities.

Finally, the distribution of dopants is also found to influence the conductivity of ITO nanocrystal films. Films made from nanocrystals with a high degree of surface segregation demonstrated one order of magnitude higher conductivity than those based on uniformly doped crystals. However, no evidence was found for differences in the surface electronic structure from one type of crystal to the other based on XPS and the exact mechanism for this difference is still not understood.

Several future studies to further illuminate the influence of dopant distribution on ITO nanocrystals are suggested. Using synchrotron radiation, detailed photoelectron spectroscopy on clean ITO nanocrystal surfaces, single-nanoparticle optical measurements, and hard x-ray structural studies will all be instructive in elucidating the interaction between oscillating free electrons and defect scattering centers when a plasmon is excited. In addition, measurements of temperature and surface treatment-dependent conductivity with carefully controlled atmosphere and surface chemistry will be needed in order to better understand the transport properties of ITO nanocrystal films. Each of these studies will enable better fundamental knowledge of the plasmonic properties of nanostructures and improve the development of nanocrystal based plasmonic devices.

I discuss the design, fabrication and measurement at millikelvin-temperatures of Al/AlO_x/Al Josephson junction-based transmon qubits coupled to superconducting thin-film lumped element microwave resonators made of aluminum on sapphire. The resonators had a center frequency of around 6GHz, and a total quality factor ranging from 15,000 to 70,000 for the various devices. The area of the transmon junctions was about 150 nm × 150 nm and with Josephson energy E_J such that 10GHz ≤ E_J ≤ 30 GHz. The charging energy of the transmons arising mostly from the large interdigital shunt capacitance, was E_c/h ≈ 300MHz.

I present microwave spectroscopy of the devices in the strongly dispersive regime of circuit quantum electrodynamics. In this limit the ac Stark shift due to a single photon in the resonator is greater than the linewidth of the qubit transition. When the resonator is driven coherently using a coupler tone, the transmon spectrum reveals individual "photon number'' peaks, each corresponding to a single additional photon in the resonator. Using a weighted average of the peak heights in the qubit spectrum, I calculated the average number of photons n¯ in the resonator. I also observed a nonlinear variation of n¯ with the applied power of the coupler tone P_rf. I studied this nonlinearity using numerical simulations and found good qualitative agreement with data.

In the absence of a coherent drive on the resonator, a thermal population of 5.474 GHz photons in the resonator, at an effective temperature of 120 mK resulted in a weak n = 1 thermal photon peak in the qubit spectrum. In the presence of independent coupler and probe tones, the n = 1 thermal photon peak revealed an Autler-Townes splitting. The observed effect was explained accurately using the four lowest levels of the dispersively dressed Jaynes-Cummings transmon-resonator system, and numerical simulations of the steady-state master equation for the coupled system.

I also present time-domain measurements on transmons coupled to lumped-element resonators. From T₁ and Rabi oscillation measurements, I found that my early transmon devices (called design LEv5) had lifetimes (T₁ ∼ 1 μs) limited by strong coupling to the 50 Ω transmission line. This coupling was characterized by the the rate of change of the Rabi oscillation frequency with the change in the drive voltage (df_Rabi /dV) – also termed the Rabi coupling to the drive. I studied the design of the transmon-resonator system using circuit analysis and microwave simulations with the aim being to reduce the Rabi coupling to the drive. By increasing the resonance frequency of the resonator ω_r/2π from 5.4 GHz to 7.2 GHz, lowering the coupling of the resonator to the transmission line and thereby increasing the external quality factor Q_e from 20,000 to 70,000, and reducing the transmon-resonator coupling g/2π from 70 MHz to 40 MHz, I reduced the Rabi coupling to the drive by an order of magnitude (∼ factor of 20). The T ₁ ∼ 4 μs of devices in the new design (LEv6) was longer than that of the early devices, but still much shorter than the lifetimes predicted from Rabi coupling, suggesting the presence of alternative sources of noise causing qubit relaxation. Microwave simulations and circuit analysis in the presence of a dielectric loss tangent tan δ ≃ 5 × 10 ^-6 agree reasonably well with the measured T ₁ values, suggesting that surface dielectric loss may be causing relaxation of transmons in the new designs.

The vast majority of optical components and devices in use today can be grouped under the umbrella of ``bulk optics''; i.e. they generally have a non-negligible thickness compared to the wavelength of light. This is true of components from lenses to wave plates to Fabry-Perot etalons, all of which need sufficient thickness such that light waves can accumulate an appropriate amount of phase upon propagation through the structure. In this thesis, we develop and explore a variety of optical components that are thin compared to the wavelength of light and lie at the interface between two materials (i.e. a substrate and air). We explore approaches to filter, absorb, redirect, and re-shape light with flat, ultra-thin structures which are easy to fabricate with modern micro- and nanofabrication techniques.
Engineering and Applied Sciences

Glutathione-capped gold nanoparticles of size 1, 3, and 10 nm, CTAB-stabilized gold nanorods, as well as ro-carboxylate-functionalized palladium nanoparticles were synthesized and self-assembled onto graphene oxide to study their coarsening or reshaping behaviors upon heating at different temperatures ranging from 50 °C to 300 °C. These engineered nanoparticle- or nanorod-graphene oxide hybrid materials were studied by transmission electron microscopy (TEM), thermogravimetric analysis (TGA), Fourier-transform infrared (FTIR) spectroscopy, and UV-Vis spectroscopy.

The spherical nanoparticles would undergo coalescence to become larger particles and the nanorods would undergo reshaping to spherical particles. UV-Vis results show that the plasmonic band of gold nanoparticles at 520 nm would shift to higher wavelength indicating the coarsening into larger particles upon heating. Transmission electron microscopy results were generally in good agreements with the UV-Vis results and would be used as a direct tool to observe the structural changes of gold nanoparticles upon heat treatments.

Without the presence of graphene oxide, the nanoparticle coalescence began at the temperature between 150 and 200 °C for all three nanoparticles with different core sizes. But with the presence of graphene oxide, nanoparticles start to coalesce at the temperature below 150 °C. The gold nanorods have two plasmonic bands at ∼780 and ∼520 nm. The bands at ∼780 nm for gold nanorods would disappear when the gold nanorods-graphene oxide is heated at 50 °C indicating the complete reshaping of nanorods even at such a low temperature. Gold nanorods themselves are more stable and do not undergo the reshaping completely until the sample is heated above 150 °C. Since graphene oxide is an excellent thermal conductor, we propose that graphene oxide could transfer heat to the nanoparticles and nanorods efficiently, disrupt the interaction of stabilizing ligands, and make them to either coalesce or undergo reshaping at a lower temperature.

Nanoparticle- and nanorod-graphene oxide hybrid materials were also used to study the effect of covalent and non-covalent interactions between gold nanoparticles or nanorods and graphene oxide during coarsening or reshaping, respectively. Non-covalent interactions were studied by directly adding graphene oxide to aqueous solutions containing water-soluble metal nanoparticles or nanorods, and covalent interactions were achieved by the self-assembly of the same nanoparticles onto thiolated graphene oxide that was prepared by coupling L-cystine using 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and N-hydroxysuccinimide (NHS). When nanoparticles and nanorods are attached to graphene oxide through additional -covalent bonds, they are more strongly immobilized and therefore would undergo less coalescence and slower reshaping upon heating.

At present modulators in communications industry utilize non-linear materials like indium tin oxide (ITO) and DLD-164 as a dielectric, which makes the fabrication process cumbersome and expensive. This thesis discusses the possibility of using only gold and air as conductor and dielectric to characterize a signal modulating device. Both electro-absorption modulation (EAM) and phase change driven modulation is possible with the design. For the change in phase a length of 2.992 µm for the modulating arm of a Mach-Zehnder modulator (MZM) was achieved for operation at 525 nm. High absorptions of electromagnetic (EM) waves was seen at the 480 nm mark allowing a length of just 4.95 µm for EAM. The results suggest that an all plasmonic noble metal modulator utilizing air as a dielectric is possible for operation in the visible 400 nm to 700 nm range. The concept is supported by proof-of-principle based simulations.

This thesis proposes a novel idea of an all plasmonic modulator driven by changes in free carrier concentration in gold and surface plasmon polariton (SPP) excitations under an applied potential. The prototype model is simulated using a commercial finite difference time domain solver. The simulation enviro nment allows Maxwell’s equations to be solved in the time domain to investigate light propagation and absorption characteristics under an externally applied electric potential. The free carrier concentration dependent permittivity of gold is exploited to investigate possible applications in nano-photonics and optical communications.

Second cervical segment spinal cord hemisection (C2Hx) results in ipsilateral hemidiaphragm paralysis. However, the intact latent crossed phrenic pathway can restore function spontaneously over time or immediately following drug administration.

WGA bound fluorochromes were administered to identify nuclei associated with diaphragm function in both the acute and chronic C2Hx models. WGA is unique in that it undergoes receptor mediated endocytosis and is transsynaptically transported across select physiologically active synapses. Comparison of labeling in the acutely injured to the chronically injured rat provided an anatomical map of spinal and supraspinal injury induced synaptic plasticity. The plasticity occurs over time in the chronic C2Hx model in an effort to adapt to the loss of hemidiaphragm function.

Utilizing the selectivity of WGA, a nanoconjugate was developed to target drug delivery to nuclei involved in diaphragm function post C2Hx in an effort to restore lost function. Theophylline was selected due to its established history as a respiratory stimulant. Theophylline was attached to gold nanoparticles by a transient bond designed to degrade intracellularly. The gold nanoparticles were then permanently attached to WGA-HRP. Following intradiaphragmatic injection, the WGA portion was identified in the ipsilateral phrenic nuclei and bilaterally in the rVRGs. The location of WGA should reflect the location of the AuNP since the peptide bond between them is permanent.

The effectiveness of the nanoconjugate was verified with EMG analysis of the diaphragm and recordings from the phrenic nerves. All doses administered in the acute C2Hx model resulted in resorted hemidiaphragm and phrenic nerve activity. A dose of 0.14mg/kg had a significantly higher percent recovery on day 3, whereas 0.03mg/kg was significantly higher on day 14. The change in most effective dose over time is likely due to the availability or concentration of the drug and location of drug release. Administration of the nanoconjugate was also characterized in the chronically C2Hx model. The dose 0.06mg/kg resulted in significant recovery when injected 12 weeks post-C2Hx. This data suggests that WGA bound nanoconjugates are able to undergo endocytosis. In addition, the theophylline bound nanoconjugate is capable of restoring hemidiaphragm and phrenic nerve activity.

Mesoporous silicate have widespread potential applications, such as drug delivery, supports for catalysis, selective adsorption and host to guest molecules. Most important in the area of scientific research and industrial applications is their demand due to its extremely high surface areas (> 800m ²g⁻¹) and larger pores with well defined structures.

Mesoporous silicate (MCM-41) samples were prepared by hydrothermal method under various chemo-physical conditions and various experimental methods such as small angle X-rays scattering (SAXS), Nitrogen adsorption-desorption analysis at 77 K, Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) were employed to investigate the changes in the structural morphology and subtle lattice parameter changes. With regards to the subtle changes in the structural characteristics of the synthesized mesoporous silicate, we seek to understand the electron density function changes as the synthesis parameter are varied from low molar concentration of ATAB/Si to higher concentration, the system becoming more acidity due to increase in the hydrolysis time of pH regulator as a result of increased production of ethanol and acetic acid and the changes due to extended reaction time.

This Ph.D. research tries to understand the influence of various parameters like surfactant-Si molar ratio, reaction time, and the hydrolysis of the pH regulator on the orderliness/disorderliness of the lattice order, lattice spacing and electron density function. The stages during synthesis are carefully selected to better understand where the greater influence on the overall structural morphology exist so as to be able to ne tune this parameter for any desired specification and application.

The SAXS measurement were conducted on a HECUS S3-Micro X-ray system at Rensselaer Polytechnic Institute, Troy, NY. while the data evaluation and visualization were carried in 3DView 4.2 and EasySWAXS software. The electron density functions were generated with a proprietary software called edens.

In this dissertation, the following observations have been revealed resulting from SAXS measurement.

1. As one increases the hydrolysis duration of ethyl acetate, a gradual collapse of the lattice spacing of the mesoporous silcate MCM-41 is observed. We found from SAXS that there is a slight right shift of the spectra toward the higher q-values indicating that we are gradually losing orderliness in the lattice spacing and hexagonal structure of the mesoporous silica. Also, the intensity of the peak of second and third peaks are diminutive when compared to sample with shorter hydrolysis time.

2. A comparison of the SAXS spectra for the different molar concentration sample reveals that the 0:5M samples shows a deteriorating structural characteristics as compared to the 0:25 and 0:75M samples respectively and a clear decrease in the (100) reflection planes. Also noticed is the slight rightward shift in the overall spectrum prole. This observation suggest that further analysis is needed so as to better understand the result.

3. We establish that during MCM-41 synthesis, longer reaction time is needed to produce quality sample with well defined structurally characteristic for its intended application because according to spectrum for the sample with a longer reaction time (aging), a shift towards the lower q-values indicates that a sample with a larger lattice parameter and wall thickness but the intensities of its peak are diminishing when compared to the other of relatively shorter reaction time.

Other complementary techniques were used to corroborated the result obtained from SAXS. Nitrogen adsorption-desorption analysis at 77K was used to generate the isotherms while B.E.T method was used in conjunction with the isotherms to obtained the very important surface area information. SEM provide a visual structural morphology of the samples and FTIR gave the fingerprint detail of the bonds and vibration types between particle present.

There are many unexplained phenomena that have been observed via atomic force microscopy (AFM) experiments. Understanding the cause of these phenomena is important to perform more accurate quantitative imaging using contact-resonance AFM and other contact-mode AFM techniques at higher scan speeds. This thesis presents evidence to confirm the existence of a scan speed dependent contact-mode AFM phenomenon and applies a squeeze film hydrodynamic lubrication model to explain it. Contact-resonance spectroscopy is used to investigate the phenomenon in which, above a critical scan speed, there is a monotonic decrease in the measured contact-resonance frequency with increasing scan speed. The observed phenomenon was replicated on a mica sample in a randomized set of AFM experiments performed at the National Institute for Standards and Technology (NIST). A literature review revealed that there is a thin water film that exists on mica under certain relative humidity (RH) conditions that has dynamic properties. The squeeze film hydrodynamic lubrication model predicts the general trend observed in the experimental data. However, there exists a higher order model that can be used to investigate the scan speed phenomenon more completely.