Nanofiber-based spectroscopy of organic molecules

This thesis reports on the experimental realization of nanofiber-based spectroscopy of organic molecules. The light guided by subwavelength diameter optical nanfibers exhibits a pronounced evanescent field surrounding the fiber which yields high excitation and emission collection efficiencies for molecules on or near the fiber surface.rnThe optical nanofibers used for the experiments presented in this thesis are realized as thernsub-wavelength diameter waist of a tapered optical fiber (TOF). The efficient transfer of thernlight from the nanofiber waist to the unprocessed part of the TOF depends critically on therngeometric shape of the TOF transitions which represent a nonuniformity of the TOF. Thisrnnonuniformity can cause losses due to coupling of the fundamental guided mode to otherrnmodes which are not guided by the taper over its whole length. In order to quantify the lossrnfrom the fundamental mode due to tapering, I have solved the coupled local mode equationsrnin the approximation of weak guidance for the three layer system consisting of fiber core andrncladding as well as the surrounding vacuum or air, assuming the taper shape of the TOFsrnused for the experiments presented in this thesis. Moreover, I have empirically studied therninfluence of the TOF geometry on its transmission spectra and, based on the results, I haverndesigned a nanofiber-waist TOF with broadband transmission for experiments with organicrnmolecules.rnAs an experimental demonstration of the high sensitivity of nanofiber-based surface spectroscopy, I have performed various absorption and fluorescence spectroscopy measurements on the model system 3,4,9,10-perylene-tetracarboxylic dianhydride (PTCDA). The measured homogeneous and inhomogeneous broadening of the spectra due to the interaction of the dielectric surface of the nanofiber with the surface-adsorbed molecules agrees well with the values theoretically expected and typical for molecules on surfaces. Furthermore, the self-absorption effects due to reasorption of the emitted fluorescence light by circumjacent surface-adsorbed molecules distributed along the fiber waist have been analyzed and quantified. With time-resolved measurements, the reorganization of PTCDA molecules to crystalline films and excimers can be observed and shown to be strongly catalyzed by the presence of water on the nanofiber surface. Moreover, the formation of charge-transfer complexes due to the interaction with localized surface defects has been studied. The collection efficiency of the molecular emission by the guided fiber mode has been determined by interlaced measurements of absorption and fluorescence spectra to be about 10% in one direction of the fiber.rnThe high emission collection efficiency makes optical nanofibers a well-suited tool for experiments with dye molecules embedded in small organic crystals. As a first experimental realization of this approach, terrylene-doped para-terphenyl crystals attached to the nanofiber-waist of a TOF have been studied at cryogenic temperatures via fluorescence and fluorescence excitation spectroscopy. The statistical fine structure of the fluorescence excitation spectrum for a specific sample has been observed and used to give an estimate of down to 9 molecules with center frequencies within one homogeneous width of the laser wavelength on average for large detunings from resonance. The homogeneous linewidth of the transition could be estimated to be about 190MHz at 4.5K.

New ways of looking at synapses

Current concepts of synaptic fine-structure are derived from electron microscopic studies of tissue fixed by chemical fixation using aldehydes. However, chemical fixation with glutaraldehyde and paraformaldehyde and subsequent dehydration in ethanol result in uncontrolled tissue shrinkage. While electron microscopy allows for the unequivocal identification of synaptic contacts, it cannot be used for real-time analysis of structural changes at synapses. For the latter purpose advanced fluorescence microscopy techniques are to be applied which, however, do not allow for the identification of synaptic contacts. Here, two approaches are described that may overcome, at least in part, some of these drawbacks in the study of synapses. By focusing on a characteristic, easily identifiable synapse, the mossy fiber synapse in the hippocampus, we first describe high-pressure freezing of fresh tissue as a method that may be applied to study subtle changes in synaptic ultrastructure associated with functional synaptic plasticity. Next, we propose to label presynaptic mossy fiber terminals and postsynaptic complex spines on CA3 pyramidal neurons by different fluorescent dyes to allow for the real-time monitoring of these synapses in living tissue over extended periods of time. We expect these approaches to lead to new insights into the structure and function of central synapses.

Developmental Changes in the Structure and Composition of the Postsynaptic Density

The development of the brain and its underlying circuitry is dependent on the formation of trillions of chemical synapses, which are highly specialized contacts that regulate the flow of information from one neuron to the next. It is through these synaptic connections that neurons wire together into networks capable of performing specific tasks, and activity-dependent changes in their structural and physiological state is one way that the brain is thought to adapt and store information. At the ultrastructural level, developmental and activity-dependent changes in the size and shape of dendritic spines have been well documented, and it is widely believed that structural changes in spines are a hallmark sign of synapse maturation and alteration of synaptic physiology. While changes in spine structure have been studied extensively, changes in one of its most prominent components, the postsynaptic density (PSD), have largely evaded observation. The PSD is a protein-rich organelle on the cytoplasmic side of the postsynaptic membrane, where it sits in direct opposition to the presynaptic terminal. The PSD functions both to cluster neurotransmitter receptors at the cell surface as well as organize the intracellular signaling molecules responsible for transducing extracellular signals to the postsynaptic cell. Much is known about the chemical composition of the PSD, but the structural arrangement of its molecular components is not well documented. Adding to the difficulty of understanding such a complex mass of protein machinery is the fact that its protein composition is known to change in response to synaptic activity, meaning that its structure is plastic and no two PSDs are identical. Here, immuno-gold labeling and electron tomography of PSDs isolated throughout development was used to track changes in both the structure and molecular composition of the PSD. State-of-the-art cryo-electron tomography was used to study the fine structure of the PSD during development, and provides an unprecedented glimpse into its molecular architecture in an un-fixed, unstained and hydrated state. Through this analysis, large structural and compositional changes are apparent and suggest a model by which the PSD is first assembled as a mesh-like lattice of proteins that function as support for the later recruitment of various PSD components. Spatial analysis of the recruitment of proteins into the PSD demonstrated that its assembly has an underlying order.

Determination of the magnetostrictive atomic enviroments in FeCoB alloys

The atomic environments of Fe and Co involved in the magnetostriction effect in FeCoB alloys have been identified by differential extended x-ray fine structure (DiffEXAFS) spectroscopy. The study, done in amorphous and polycrystalline FeCoB films, demonstrates that the alloys are heterogeneous and that boron plays a crucial role in the origin of their magnetostrictive properties. The analysis of DiffEXAFS in the polycrystalline and amorphous alloys indicates that boron activates magnetostriction when entering as an impurity into octahedral interstitial sites of the Fe bcc lattice, causing its tetragonal distortion. Magnetostriction would be explained then by the relative change in volume when the tetragonal axis of the site is reoriented under an externally applied magnetic field. The experiment demonstrates the extreme sensitivity of DiffEXAFS to characterize magnetostrictive environments that are undetectable in their related EXAFS spectra.

Attachment to the nuclear matrix mediates specific alterations in chromatin structure

The DNA in eukaryotic chromosomes is organized into a series of loops that are permanently attached at their bases to the nuclear scaffold or matrix at sequences known as scaffold-attachment or matrix-attachment regions. At present, it is not clear what effect affixation to the nuclear matrix has on chromatin architecture in important regulatory regions such as origins of replication or the promoter regions of genes. In the present study, we have investigated cell-cycle-dependent changes in the chromatin structure of a well characterized replication initiation zone in the amplified dihydrofolate reductase domain of the methotrexate-resistant Chinese hamster ovary cell line CHOC 400. Replication can initiate at any of multiple potential sites scattered throughout the 55-kilobase intergenic region in this domain, with two subregions (termed ori-β and ori-γ) being somewhat preferred. We show here that the chromatin in the ori-β and ori-γ regions undergoes dramatic alterations in micrococcal nuclease hypersensitivity as cells cross the G1/S boundary, but only in those copies of the amplicon that are affixed to the nuclear matrix. In contrast, the fine structure of chromatin in the promoter of the dihydrofolate reductase gene does not change detectably as a function of matrix attachment or cell-cycle position. We suggest that attachment of DNA to the nuclear matrix plays an important role in modulating chromatin architecture, and this could facilitate the activity of origins of replication.

Identification, retinoid binding, and x-ray analysis of a human retinol-binding protein

Two cellular retinol-binding proteins (CRBP I and II) with distinct tissue distributions and retinoid-binding properties have been recognized thus far in mammals. Here, we report the identification of a human retinol-binding protein resembling type I (55.6% identity) and type II (49.6% identity) CRBPs, but with a unique H residue in the retinoid-binding site and a distinctively different tissue distribution. Additionally, this binding protein (CRBP III) exhibits a remarkable sequence identity (62.2%) with the recently identified ι-crystallin/CRBP of the diurnal gecko Lygodactylus picturatus [Werten, P. J. L., Röll, B., van Alten, D. M. F. & de Jong, W. W. (2000) Proc. Natl. Acad. Sci. USA 97, 3282–3287 (First Published March 21, 2000; 10.1073/pnas.050500597)]. CRBP III and all-trans-retinol form a complex (Kd ≈ 60 nM), the absorption spectrum of which is characterized by the peculiar fine structure typical of the spectra of holo-CRBP I and II. As revealed by a 2.3-Å x-ray molecular model of apo-CRBP III, the amino acid residues that line the retinol-binding site in CRBP I and II are positioned nearly identically in the structure of CRBP III. At variance with the human CRBP I and II mRNAs, which are most abundant in ovary and intestine, respectively, the CRBP III mRNA is expressed at the highest levels in kidney and liver thus suggesting a prominent role for human CRBP III as an intracellular mediator of retinol metabolism in these tissues.

Alignment of a 1.2-Mb chromosomal region from three strains of Rhodobacter capsulatus reveals a significantly mosaic structure.

High-resolution physical maps of the genomes of three Rhodobacter capsulatus strains, derived from ordered cosmid libraries, were aligned. The 1.2-Mb segment of the SB1003 genome studied here is adjacent to a 1-Mb region analyzed previously [Fonstein, M., Nikolskaya, T. & Haselkorn, H. (1995) J. Bacteriol. 177, 2368-2372]. Probes derived from the ordered cosmid set of R. capsulatus SB1003 were used to link cosmids from the St. Louis and 2.3.1 strain libraries. Cosmids selected this way did not merge into a single contig but formed several unlinked groups. EcoRV restriction maps of the ordered cosmids were then constructed using lambda terminase and fused to derive fragments of the chromosomal map. In order to link these fragments, their ends were transcribed to produce secondary probes for hybridization to gridded cosmid libraries of the same strains. This linking reduced the number of subcontigs to three for the St. Louis strain and one for the 2.3.1 strain. Hybridization of the same probes back to the ordered cosmid set of SB1003 positioned the subcontigs on the high-resolution physical map of SB1003. The final alignment of the restriction maps shows numerous large and small translocations in this 1.2-Mb chromosomal region of the three Rhodobacter strains. In addition, the chromosomes of the three strains, whose fine-structure maps can now be compared over 2.2 Mb, are seen to contain regions of 15-80 kb in which restriction sites are highly polymorphic, interspersed among regions in which the positions of restriction sites are highly conserved.

The chemical structure and mechanical properties of phenolic resins and related polymers

Paper-based phenolic laminates are used extensively in the electrical industry. Many small components are fabricated from these materials by the process known as punching. Recently an investigation was carried out to study the effect of processing variables on the punching properties. It was concluded that further work would be justified and that this should include a critical examination of the resin properties in a more controlled and systematic manner. In this investigation an attempt has been made to assess certain features of the resin structure in terms of thermomechanical properties. The number of crosslinks in the system was controlled using resins based on phenol and para-cresol formulations. Intramolecular hydrogen bonding effects were examined using substituted resins and a synthetically derived phenol based on 1,3-di-(o-hydroxyphenyl) propane.. A resin system was developed using the Friedel Crafts reaction to examine inter-molecular hydrogen bonding at the resin-paper interface. The punching properties of certain selected resins were assessed on a qualitative basis. In addition flexural and dynamic mechanical properties were determined in a general study of the structure-property relationships of these materials. It has been shown that certain features of the resin structure significantly influenced mechanical properties. :F'urther, it was noted that there is a close relationship between punching properties, mechanical damping and flexural strain. This work includes a critical examination of the curing mechanism and views are postulated in an attempt to extend knowledge in this area of the work. Finally, it is argued that future work should be based on a synthetic approach and that dynamic mechanical testing would provide a powerful tool In developing a deeper understanding of the resin fine structure.

Local luminous infrared galaxies. I. Spatially resolved observations with the Spitzer infrared spectrograph

We present results from the Spitzer Infrared Spectrograph spectral mapping observations of 15 local luminous infrared galaxies (LIRGs). In this paper, we investigate the spatial variations of the mid-IR emission which includes fine structure lines, molecular hydrogen lines, polycyclic aromatic features (PAHs), continuum emission, and the 9.7 μm silicate feature. We also compare the nuclear and integrated spectra. We find that the star formation takes place in extended regions (several kpc) as probed by the PAH emission, as well as the [Ne II]12.81 μm and [Ne III]15.56 μm emissions. The behavior of the integrated PAH emission and 9.7 μm silicate feature is similar to that of local starburst galaxies. We also find that the minima of the [Ne III]15.56 μm/[Ne II]12.81 μm ratio tends to be located at the nuclei and its value is lower than that of H II regions in our LIRGs and nearby galaxies. It is likely that increased densities in the nuclei of LIRGs are responsible for the smaller nuclear [Ne III]15.56 μm/[Ne II]12.81 μm ratios. This includes the possibility that some of the most massive stars in the nuclei are still embedded in ultracompact H II regions. In a large fraction of our sample, the 11.3 μm PAH emission appears more extended than the dust 5.5 μm continuum emission. We find a dependency of the 11.3 μm PAH/7.7 μm PAH and [Ne II]12.81 μm/11.3 μm PAH ratios with the age of the stellar populations. Smaller and larger ratios, respectively, indicate recent star formation. The estimated warm (300 K

The Evolution of Massive Young Stellar Objects in the Large Magellanic Cloud

This thesis presents an analysis of the largest catalog to date of infrared spectra of massive young stellar objects in the Large Magellanic Cloud. Evidenced by their very different spectral features, the luminous objects span a range of evolutionary states from those most embedded in their natal molecular material to those that have dissipated and ionized their surroundings to form compact HII regions and photodissociation regions. We quantify the contributions of the various spectral features using the statistical method of principal component analysis. Using this analysis, we classify the YSO spectra into several distinct groups based upon their dominant spectral features: silicate absorption (S Group), silicate absorption and fine-structure line emission (SE), polycyclic aromatic hydrocarbon (PAH) emission (P Group), PAH and fine-structure line emission (PE), and only fine-structure line emission (E). Based upon the relative numbers of sources in each category, we are able to estimate the amount of time massive YSOs spend in each evolutionary stage. We find that approximately 50% of the sources have ionic fine-structure lines, indicating that a compact HII region forms about half-way through the YSO lifetime probed in our study. Of the 277 YSOs we collected spectra for, 41 have ice absorption features, indicating they are surrounded by cold ice-bearing dust particles. We have decomposed the shape of the ice features to probe the composition and thermal history of the ice. We find that most the CO2 ice is embedded a polar ice matrix that has been thermally processed by the embedded YSO. The amount of thermal processing may be correlated with the luminosity of the YSO. Using the Australia Telescope Compact Array, we imaged the dense gas around a subsample of our sources in the HII complexes N44, N105, N113, and N159 using HCO+ and HCN as dense gas tracers. We find that the molecular material in star forming environments is highly clumpy, with clumps that range from subparsec to ~2 parsecs in size and with masses between 10^2 to 10^4 solar masses. We find that there are varying levels of star formation in the clumps, with the lower-mass clumps tending to be without massive YSOs. These YSO-less clumps could either represent an earlier stage of clump to the more massive YSO-bearing ones or clumps that will never form a massive star. Clumps with massive YSOs at their centers have masses larger than those with massive YSOs at their edges, and we suggest that the difference is evolutionary: edge YSO clumps are more advanced than those with YSOs at their centers. Clumps with YSOs at their edges may have had a significant fraction of their mass disrupted or destroyed by the forming massive star. We find that the strength of the silicate absorption seen in YSO IR spectra feature is well-correlated with the on-source HCO+ and HCN flux densities, such that the strength of the feature is indicative of the embeddedness of the YSO. We estimate that ~40% of the entire spectral sample has strong silicate absorption features, implying that the YSOs are embedded in circumstellar material for about 40% of the time probed in our study.

Mesenchymal stem cells and nano-structured surfaces

Mesenchymal stem cells (MSCs) represent multipotent stromal cells that can differentiate into a variety of cell types, including osteoblasts (bone cells), chondrocytes (cartilage cells), and adipocytes (fat cells). Their multi-potency provides a great promise as a cell source for tissue engineering and cell-based therapy for many diseases, particularly bone diseases and bone formation. To be able to direct and modulate the differentiation of MSCs into the desired cell types in situ in the tissue, nanotechnology is introduced and used to facilitate or promote cell growth and differentiation. These nano-materials can provide a fine structure and tuneable surface in nanoscales to help the cell adhesion and promote the cell growth and differentiation of MSCs. This could be a dominant direction in future for stem cells based therapy or tissue engineering for various diseases. Therefore, the isolation, manipulation, and differentiation of MSCs are very important steps to make meaningful use of MSCs for disease treatments. In this chapter, we have described a method of isolating MSC from human bone marrow, and how to culture and differentiate them in vitro. We have also provided research methods on how to use MSCs in an in vitro model and how to observe MSC biological response on the surface of nano-scaled materials.

A new single-phase frequency adaptive Phase-Locked Loop (PLL) for harmonic measurement

The paper presents an improved Phase-Locked Loop (PLL) for measuring the fundamental frequency and selective harmonic content of a distorted signal. This information can be used by grid interfaced devices and harmonic compensators. The single-phase structure is based on the Synchronous Reference Frame (SRF) PLL. The proposed PLL needs only a limited number of harmonic stages by incorporating Moving Average Filters (MAF) for eliminating the undesired harmonic content at each stage. The frequency dependency of MAF in effective filtering of undesired harmonics is also dealt with by a proposed method for adaptation to frequency variations of input signal. The method is suitable for high sampling rates and a wide frequency measurement range. Furthermore, an extended model of this structure is proposed which includes the response to both the frequency and phase angle variations. The proposed algorithm is simulated and verified using Hardware-in-the-Loop (HIL) testing.

ESR study of exchange coupled pairs in copper diethyldithiocarbamate—explanation of the low temperature hyperfine anomaly

A study of the hyperfine interaction in the ESR of Cu-Cu pairs in single crystals of copper diethyldithiocarbamate as a function of temperature has shown distinct differences in the hyperfine structure in the two fine structure transitions at 20 K, the spectrum not having the same hyperfine intensity pattern in the low field fine structure transition in contrast to that of the high field transition. The details of the structure of both the fine structure transitions in the 20 K spectrum have now been explained by recognizing the fact that the mixing of the nuclear spin states caused by the anisotropic hyperfine interaction affects the electron spin states | + 1 > and | −> differently. This has incidentally led to a determination of the sign ofD confirming the earlier model. The anomalous hyperfine structure is found to become symmetric at 77 K and 300 K. It is proposed that the reason for this lies in the dynamics of spin-lattice interaction which limits the lifetime of the spin states in each of the electronic levels | − 1 >, | 0 > and | + 1 > The estimate of spin-lattice relaxation time agrees with those indicated from other studies. The model proposed here for the hyperfine interaction of pairs in the electronic triplet state is of general validity.

Surface-mediated selective photocatalytic aerobic oxidation reactions on TiO2 nanofibres

N-doped TiO2 nanofibres were observed to possess lower aerobic oxidation activity than undoped TiO2 nanofibres in the selective photocatalytic aerobic oxidation of enzylamine and 4-methoxybenzyl alcohol. This was attributed to the reduction free energy of O2 adsorption in the vicinity of nitrogen dopant sites, as indicated by density functional theory (DFT) calculations when three-coordinated oxygen atoms are substituted by nitrogen atoms. It was found that the activity recovered following a controlled calcination of the N-doped NFs in air. The dependence of the conversion of benzylamine and 4-methoxybenzyl alcohol on the intensity of light irradiation confirmed that these reactions were driven by light. Action spectra showed that the two oxidation reactions are responsive to light from the UV region through to the visible light irradiation range. The extended light absorption wavelength range in these systems compared to pure TiO2 materials was found to result from the formation of surface complex species following adsorption of reactants onto the catalysts' surface, evidenced by the in situ IR experiment. Both catalytic and in situ IR results reveal that benzaldehyde is the intermediate in the aerobic oxidation of benzylamine to N-benzylidenebenzylamine process.