abstract: Studying charge transport through single molecules tethered between two metal electrodes is of fundamental importance in molecular electronics. Over the years, a variety of methods have been developed in attempts of performing such measurements. However, the limitation of these techniques is still one of the factors that prohibit one from gaining a thorough understanding of single molecule junctions. Firstly, the time resolution of experiments is typically limited to milli to microseconds, while molecular dynamics simulations are carried out on the time scale of pico to nanoseconds. A huge gap therefore persists between the theory and the experiments. This thesis demonstrates a nanosecond scale measurement of the gold atomic contact breakdown process. A combined setup of DC and AC circuits is employed, where the AC circuit reveals interesting observations in nanosecond scale not previously seen using conventional DC circuits. The breakdown time of gold atomic contacts is determined to be faster than 0.1 ns and subtle atomic events are observed within nanoseconds. Furthermore, a new method based on the scanning tunneling microscope break junction (STM-BJ) technique is developed to rapidly record thousands of I-V curves from repeatedly formed single molecule junctions. 2-dimensional I-V and conductance-voltage (G-V) histograms constructed using the acquired data allow for more meaningful statistical analysis to single molecule I-V characteristics. The bias voltage adds an additional dimension to the conventional single molecule conductance measurement. This method also allows one to perform transition voltage spectra (TVS) for individual junctions and to study the correlation between the conductance and the tunneling barrier height. The variation of measured conductance values is found to be primarily determined by the poorly defined contact geometry between the molecule and metal electrodes, rather than the tunnel barrier height. In addition, the rapid I-V technique is also found useful in studying thermoelectric effect in single molecule junctions. When applying a temperature gradient between the STM tip and substrate in air, the offset current at zero bias in the I-V characteristics is a measure of thermoelectric current. The rapid I-V technique allows for statistical analysis of such offset current at different temperature gradients and thus the Seebeck coefficient of single molecule junctions is measured. Combining with single molecule TVS, the Seebeck coefficient is also found to be a measure of tunnel barrier height. / Dissertation/Thesis / Ph.D. Electrical Engineering 2012

In atomic force microscopy (AFM), the measured force between tip and substrate is used to produce images with subatomic resolution. In this thesis, plausible electrostatic interactions between tip-substrate is studied and compared with the experimental results in the report Vibrations of a molecule in an external force field by Okabayashi et al.. A simplified model gives by hand that the interaction between substrate and tip is dominated by a point charge - point charge relation due to the interatomic distances in AFM. We find that the electrostatic interaction can reproduce the experiment down to a limit of z ~ 3 Å. Further, we find that the tip interacts with the sample as a point charge with an induced dipole moment obtained by the electric field of the substrate. By analyzing electrostatic forces and compare them with the results in the Okabayashi et al. report, the AFM images in the report could be reproduced. / <p>Rättande lärare: Cecilia Holmqvist</p>

Mesenchymal stem cells are the stem cells that replace the bone, fat and cartilage tissues of the human body. In addition, these cells can form muscles, ligaments and neurons. This wide multipotency has made mesenchymal stem cells of particular interest in the fields of tissue engineering and regenerative medicine. Furthermore, mesenchymal stem cells can modulate the immune system by reducing factors that increase inflammation and immune recognition. This immune recognition suppression has resulted in their application as part of bone marrow transplantation in the prevention of 'graft versus host‘ disease. There are hundreds of on-going clinical trials using these cells for the treatment of autoimmune diseases such as type I diabetes, arthritis and multiple sclerosis. The increasing importance of these cells has brought in to focus the culture methods used to for their expansion and manipulation. Currently, animal derived components are used as surfaces for their growth and as components in the culture media. This exposes these cells to animal pathogens and antigens that can be passed to the recipients of these cells. In the first part of this thesis, polymer microarrays were employed to identify alternatives to the biological surfaces currently used for mesenchymal stem cell culture. This platform allowed hundreds of polyacrylates/acrylamides and polyurethanes to be simultaneously scrutinised to identify surfaces that could support their growth and maintain their stem cell characteristics. Identified polymer surfaces were monitored in long-term culture (10 passages) and were shown to retain the cell phenotype and capacity to differentiate, thus providing chemically defined substrates for long-term mesenchymal stem cell culture. In the second part of this thesis, a 'smart‘ polymer microarray of hydrophilic cross-linked polymers (hydrogels) were used to remove another key biological component of culture, trypsin. These 'smart‘ hydrogels modulated their properties depending on the temperature. Hydrogels that could trigger mesenchymal stem cell release after a reduction in temperature were identified. A unique passaging system using a modest temperature reduction for 1h was developed as a passaging method. Cells were maintained and monitored for 10 passages using this novel enzyme free passaging method. Analysis of the mesenchymal stem cell phenotype and differentiation capacity revealed this method superior than conventional culturing methods. In the final part of this thesis, a 'knowledge-based‘ small molecule library was designed, which could potentially yield small molecules to manipulate/enhance the mesenchymal stem cell state without the use of biological components. The key protein pathways that control the stem cell state were examine with the bioinformatics tool GeneGo was used to identify compounds that affected these pathways, resulting in selection of 200 small molecules. The effect of the small molecules on the mesenchymal phenotype was examined and 5 small molecules were identified that enhanced the phenotype of these cells. The anti-inflammatory properties associated with the hit compounds led to the investigation of their effects on key surface proteins associated with the immune-modulatory state of the cells. In this preliminary study, two of the small molecules, estriol and spermine, increased the expression of a key mesenchymal stem cell marker STRO-1 and down regulated ICAM-1, a critical component of the immune modulation capacity of this cell type.

Cette thèse décrit dans un premier temps la synthèse entièrement régiosélective de phtalocyanines tétra-(endo-alcoxy)-fonctionnalisées puis la formation de leurs complexes avec des ions métalliques. Dans un second temps sont étudiées leurs propriétés magnétiques, l'induction de mésophases colonnaires dans des gammes de températures convenables et avec des tailles modérées de substituants, ainsi que leur utilisation dans des diodes organiques. L'approche synthétique à suivre est la cyclo-tétramérisation de 3-(2-alkylalcoxy)-phtalonitriles suivie de la coordination d'un ion métallique. La symétrisation des chaînes aliphatiques dans le précurseur 3-alcoxy-phtalonitrile, en allant de 2 butyloctyl à 2-pentylheptyl, maintient la régiosélectivité et le mésomorphisme, tandis que les courtes chaînes 2-butylhexyl mènent à la formation d'un mélange de phtalocyanines régioisomères et à une plus grande tentance à la crystallisation. La combinaison de températures de clarification raisonnables avec un empilement colonnaire à température ambiante et avec une proportion assez importante de centres conjurés au sein de la masse moléculaire rend les deux premières séries de matériaux, c'est-à-dire MPc(OCH2CHBuHex)4, and MPc(OCH2CHPent2)4, potentiellement utiles comme transporteurs de charges uniformément orientables dans des dispositifs électroniques organiques. Nous démontrons que ces matériaux phtalocyanines tétra-α-alcoxy-substitués, représentés par H2Pc(OCH2CHBuHex)4, NiPc(OCH2CHBuHex)4 et CuPc(OCH2CHBuHex)4, mènent à des performances originales des dispositifs quand ils sont utilisés comme couche active organique dans des structures simples de diode ITO/PEDOT :PSS/PC/Al. Un redressement prononcé du courant est obtenu dans des diodes malgré l’alignement planaire prépondérant des colonnes dans les couches. Le ligand Pc tétra-α-alcoxy-substitué très soluble donne des molécules-aimants mononucléaires originales par coordination avec MnIII et DyIII. Remarquablement, l’isomère de symétrie C4h du complexe sandwich octa-alcoxy se forme sélectivement grâce aux subsistants encombrants sur les deux cycles Pc. / This thesis describes the fully regioselective synthesis of symmetric all-endo tetra-alkoxy-functionalized phthalocyanines and their metal ion complexes accompanied by induction of columnar mesophases in convenient temperature ranges at moderate substituent sizes, as well as their use in organic diodes and the study of their magnetic properties. The synthetic approach to follow is lithium-induced macrocyclization of 3-(2-alkylalkoxy)-phthalonitriles prior to transition meatl ion insertion. Symmetrization of the aliphatic chains in the 3-alkoxy-phthalonitrile precursor from 2-butylocytyl to 2-pentylheptyl maintains both the regioisomeric mixture during the cyclo-tetramerization and to a somewhat greater tendency to crystallization. The combination of attainable clearing temperatures with room temperature columnar stacking and with a relatively high content of conjugated core within the molecular mass makes the first two series of materials, i.e. MPc(OCH2CHBuHex)4, and MPc(OCH2CHPent2)4, potentially useful as uniformly orientable charge transposters in organic electronic devices. We establish that these tetra-α-alkoxy substituted phthalocyanine materials, as exemplified with H2Pc(OCH2CHBuHex)4, NiPc(OCH2CHBuHex)4 and CuPc(OCH2CHBuHex)4, lead to original device performances when applied as an active organic layer in simple ITO/PEDOT:PSS/PC/Al diode structures. A pronounced current rectification of the diodes is obtained despite the preponderantly planar alignment of the columns in the films. The highly soluble tetra-α-alkoxy-substituted Pc ligand, when combined with MnIII and DyIII, gives rise to original mononuclear single molecule magnets. Remarkably, the C4h-symmetric isomer of the octa-alkoxy double decker complex is formed selectively due of presence of the bulky substituents on both Pc rings.

xii, 112 p. : ill. (some col.) / Biological molecular motors exist in an interesting regime of physics where momentum is unimportant and diffusive motion is large. While only exerting small forces, these motors still manage to achieve directed motion and do work. Brownian motors induce directed motion of diffusive particles and are used as models for biological and artificial molecular motors. A flashing ratchet is a Brownian motor that rectifies thermal fluctuations of diffusive particles through the use of a time-dependent, periodic, and asymmetric potential. It has been predicted that a feedback-controlled flashing ratchet has a center of mass speed as much as one order of magnitude larger than the optimal periodically flashing ratchet. We have successfully implemented the first experimental feedback ratchet and observed the predicted order of magnitude increase in velocity. We experimentally compare two feedback algorithms for small particle numbers and find good agreement with Langevin dynamics simulations. We also find that existing algorithms can be improved to be more tolerant to feedback delay times. This experiment was implemented by a scanning line optical trap system. In a bottom-up approach to understanding molecular motors, a synthetic protein-based molecular motor, the "tumbleweed", is being designed and constructed. This design uses three ligand dependent DNA repressor proteins to rectify diffusive motion of the construct along a DNA track. To predict the behavior of this artificial motor one needs to understand the binding and unbinding kinetics of the repressor proteins at a single-molecule level. An assay, similar to tethered particle motions assays, has been developed to measure the unbinding rates of these three DNA repressor proteins. In this assay the repressor is immobilized to a surface in a microchamber. Long DNA with the correct recognition sequence for one of the repressors is attached to a microsphere. As the DNA-microsphere construct diffuses through the microchamber it will sometimes bind to the repressor protein. Using brightfield microscopy and a CCD camera the diffusive motion of the microsphere can be characterized and bound and unbound states can be differentiated. This method is tested for feasibility and shown to have sufficient resolution to measure the unbinding rates of the repressor proteins. / Committee in charge: Dr. Raghu Parthasarathy, Chair; Dr. Heiner Linke, Research Advisor; Dr. Dan Steck; Dr. John Toner; Dr. Brad Nolan

SMFD techniques offer genuine detection possibilities which are often inaccessible using ensemble methods. This was demonstrated in three projects investigating translocation activity of CHD4 protein, analysis of MS2 phage capsid assembly and in-cell characterization of DNA structure. In other projects, binding interactions between two fluorescent probes and a short oligonucleotide were characterized and all optical depth of focus extended microscope configuration for imaging of individual molecules inside bacterial cells was developed and tested.

ROLE ASOVÉ 'KÁLY INTERAKCE SYSTÉM-LÁZE VE FOTOSYNTETICKÉM P ENOSU EXCITANÍ ENERGIE Tato práce se věnuje vlivu rychlého a pomalého molekulárno pohybu na přenos excitační energie ve fotosyntetick- ých světlosběrných komplexech. Vyvinuli jsme nový teoretický popis vnitromolekulárních vibračních mod· a zjistili jsme, že jejich resonance s energetickými rozdíly mezi fotosyntetickými pigmenty m·že vést ke zrychlení přenosu energie. Použitím jednomolekulární spektroskopie jsme pozorovali jak pomalé změny bílkovinné konformace mohou zcela změnit stav světlosběrného komplexu LHCII vyšších rostlin. Také jsme vyvinuli novou experimentální techniku, dvoupulzní ultrarychlou jednomolekulární spektroskopii. S její pomocí m·žeme pozorovat jak pomalý pohyb bílkoviny bakteriální antény LH2 ovlivňuje ultrarychlou relaxaci energie uvnitř komplexu. Konstrukcí jednotného modelu pro ultrarychlé objemové a jednomolekulární experimenty se nám podařilo zakomponovat rychlou a pomalou časovou škálu molekulárního pohybu do jednoho pohledu na fotosyntetický sběr světla.

Made available in DSpace on 2014-06-11T19:25:29Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-12-12Bitstream added on 2014-06-13T20:33:08Z : No. of bitstreams: 1 furtadoneto_a_me_guara.pdf: 575510 bytes, checksum: 6a1a49e71ce6fbc8113435f66d99a240 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O foco deste trabalho é o espectro de inversão da molécula de amônia, resultado do fenômeno do tunelamento quântico. Para isso, usamos um modelo simpli cado, uni- dimensional, suscetível a uma análise teórica rigorosa usando a mecânica quântica não- relativística. Dentre as diversas funções hamiltonianas já estudadas para este modelo, zemos uma rápida apreciação dos trabalhos de Cohen, Dennison-Uhlenbeck, Manning, Merzbacher e Rosen-Morse. Para um estudo mais profundo, usamos o potencial do poço duplo nito que, posteriormente, descobrimos já fora analisado por Peacock-López. Re- zemos a análise deste potencial usando um caminho diferente do realizado por aquele autor. Analisamos os casos limites para este potencial e notamos que realmente, nesses regimes, ele tende para um poço nito único ou dois poços nitos separados. Então, de- senvolvemos um software grá co centrado no pacote MINUIT, desenvolvido pelo CERN, para analisar e ajustar os parâmetros aos dados experimentais da amônia e, ao nal, comparamos os resultados obtidos com aqueles encontrados na literatura. No ajuste dos parâmetros à amônia, houve uma melhoria acentuada quando passamos de uma fórmula mais simples da massa reduzida para outra mais so sticada. No caso especí co do po- tencial de Peacock-López, a comparação revela que os nossos resultados, de uma maneira geral, são mais precisos. Nossa análise se soma àquelas que contêm uma discussão quan- titativa do potencial de poço duplo. Como parte integrante deste trabalho, uma versão unidimensional simétrica do potencial de Morse foi exatamente resolvida em termos de funções de Kummer e um par de equações transcendentes para as autoenergias. A tentativa de ajustar este resultado à molécula de amônia, porém, mostrou que os padrões de poço duplo deste potencial... / The focus of this work is the inversion spectrum of the ammonia molecule, a result of the phenomenon of quantum tunneling. For this, we use a simpli ed, one-dimensional model, amenable to a rigorous theoretical analysis using the non-relativistic quantum me- chanics. Among the various Hamiltonian functions previously studied for this model, we made a quick appraisal of the work of Cohen, Dennison-Uhlenbeck, Manning, Merzbacher and Rosen-Morse. For a deeper study, we used the nite double-well potential which, as we later discovered, had been considered by Peacock-López. We redid the analysis of this potential using a di¤erent path made by that author. We analyze the limiting cases for this potential and actually noticed that in these schemes, it tends to one nite well or two separate nite wells. So, we developed a graphical software centered on the MINUIT pack- age, developed by CERN, to analyze and adjust the parameters to the experimental data of ammonia and at the end, we compared the results with those found in the literature. In setting the parameters of ammonia, there was a marked improvement when we move from a simpler formula for the reduced mass to a more sophisticated one. In the speci c case of the potential of Peacock-López, the comparison shows that our results, in general, are more accurate and precise. Our analysis adds to those that contain a quantitative discussion of the double-well potential. As part of this work, a symmetric one-dimensional version of the Morse potential is exactly solved in terms of the Kummer functions and a pair of transcendental equations for the eigenenergies. Attempting to adjust this result to the ammonia molecule, however, showed that the double-well patterns of this potential well are irreconcilable with the energy spectrum of ammonia: Close pairs separated by long intervals

Doctor of Philosophy / Department of Chemistry / Takashi Ito / This dissertation describes single-molecule tracking (SMT) measurements for the quantitative characterization of one-dimensional (1D) nanostructures in 200 nm-thick surfactant-templated mesoporous silica (STMS) and cylinder-forming polystyrene-poly(ethylene oxide) diblock copolymer (CF-PS-b-PEO) films with a μm-scale thickness. SMT is advantageous for the characterization of nanomaterials over conventional methods because it permits the simultaneous and quantitative assessment of the nanoscale and microscale morphologies, and mass-transport properties of the materials with a high nanometer-scale resolution under ambient conditions. It offers a unique means for the assessment and evaluation of the μm-scale nanostructure alignment in polymer films induced by vertical spin-coating (for STMS films), directional solution flow and solvent-vapor penetration (SVP) methods (both for CF-PS-b-PEO films), highly crucial for many potential technological applications using the materials. Through this work, we have identified suitable sample preparation conditions (e.g. solvent, temperature or solution flow rate) for obtaining highly-ordered mesoporous and microdomain structures over a long-range (> 5 μm). For the quantitative assessment of the 1D SMT data, orthogonal regression analysis was employed, providing assessment of the in-plane orientation and size of individual nanostructures with nanometer-scale precision. The analysis of the 1D trajectory data allowed the radius (ca. 11 nm) of cylindrical PEO microdomains to be estimated, yielding results consistent with the AFM results (ca. 14 nm). The distribution of the trajectory angles offered the estimation of the average orientation and order of the nanostructures in domains/grains for a μm-wide region of the polymer films, revealing the higher efficiency of SVP in the nanostructure alignment as compared to the spin coating and solution flow approaches. Systematic SMT measurements across the film depth and along lateral mm-scale distances afforded valuable insights into the shear- and solvent-evaporation-based alignment mechanisms induced by solution flow and SVP/spin coating approaches, respectively. Fluorescence recovery after photobleaching (FRAP) measurements in a SVP-aligned CF-PS-b-PEO film permitted the longer-range mass-transport properties to be probed, reflecting the effective continuity of the aligned cylindrical nanostructures over > 100 μm in length. In this dissertation, FRAP and more importantly SMT methods have provided a unique and useful means for the in-depth characterization of morphology and mass-transport characteristics in thin polymer films under ambient conditions, in confined spaces, and with a nanometer-scale resolution.

Doctor of Philosophy / Department of Chemistry / Daniel A. Higgins / This dissertation describes single-molecule tracking (SMT) studies for the quantitative characterization of one-dimensional (1D) nanostructures in surfactant-templated mesoporous silica monoliths prepared within microfluidic channels. Single molecule diffusion of fluorescent probe molecules within the cylindrical mesopores reflects microscopic morphologies and mass-transport properties of the materials with high temporal and spatial resolution. The pore organization and materials order are initially investigated as a function of sol aging prior to loading into the microfluidic channels. Mesopores in these materials are templated by Cetyltrimethylammonium bromide (CTAB). Wide-field fluorescence videos depict 1D motion of the dyes within the individual mesopores. Orthogonal regression analysis of these motions provides a measure of the mesopore orientation. Channels filled prior to gelation of the sol produce monoliths incorporating large monodomains with highly aligned mesopores. In contrast, channels filled close to or after gelation yield monoliths with misaligned pores that are also more disordered. Two-dimensional (2D) small angle X-ray scattering (SAXS) experiments support the results obtained by SMT. These studies help to identify conditions under which highly aligned mesoporous monoliths can be obtained and also demonstrate the utility of SMT for characterization of mesopore order. The non-ionic surfactant Pluronic F127 is also utilized as the structural-directing agent. The diffusive motions of PDI dyes that are uncharged, cationic and anionic are explored by SMT and fluorescence correlation spectroscopy (FCS). The SMT studies for the uncharged dye show development of 1D diffusion along the flow direction while charged dyes exhibit predominant isotropic diffusion, with each of these behaviors becoming more prevalent as a function of aging time after filling of the microfluidic channels. SMT studies from silica-free F127 gels suggest that partitioning plays a important role in governing the diffusion behavior of the PDI dyes within the surfactant-filled mesopores. FCS results exhibit similar mean diffusion coefficients for all three dyes that suggest these dyes diffuse through similar sample regions. These studies demonstrate that the silica pore walls in the mesoporous silica monoliths remain permeable after gelation and that partitioning of solute species to different regions within the pores plays an important role in restricting the dimensionality of their diffusive motion