A DNA molecule passing through a nanopore in a liner and sequential fashion allows for unprecedented interrogation of the polymer. Adding transverse electrodes that are comparable in size and sensitive to the DNA molecule, can further the attempts to rapidly sequence DNA. Carbon nanotubes are comparable in size and interact strongly with the DNA molecule. This makes them an excellent choice for integration with nanopores. Only the section of the carbon nanotube in immediate proximity to the nanopore should be sensitive to the DNA molecules. Atomic layer deposition of metal-oxides passivates the sections of the carbon nanotube that are not to interact with the DNA molecule. The coating also protects the thin film interconnects leading to the carbon nanotube. Hafnium oxide is superior to aluminum oxide in chemical resistance and electrical insulation but leads to a high failure rate of the carbon nanotube across nanopore devices. Aluminum oxide, combined with gold thin film interconnects to the carbon nanotube, produced the first functioning devices in electrolyte. These devices had concurrently functioning ionic (current across the nanopore) and transverse (current through the carbon nanotube) channels. No concurrent DNA translocation signal was recorded on the ionic and nanotube current traces. Analyzing the translocation events recorded on the ionic channel indicated that double-stranded DNA (dsDNA) passed through the carbon nanotube articulated nanopore an order of magnitude slower than it would have through a comparable unarticulated nanopore. The slower translocation observed is a necessary condition for sequencing. Investigating dsDNA translocation under various experimental conditions led to the discovery of a new interaction between the molecule and small nanopores. A dsDNA molecule is trapped when the electric field near the nanopore attracts and immobilizes a non-end segment of the molecule at the nanopore orifice without inducing folded translocation. In this work, the expression “trapped dsDNA” will exclusively refer to the immobilization of a dsDNA molecule at the orifice of the nanopore. The ionic current through the nanopore decreases when the dsDNA molecule is trapped by the nanopore. By contrast, a translocating dsDNA molecule under the same conditions causes an ionic current increase. Finite element modeling results predict this behavior for the conditions of the experiment. / Physics

This is a summary report on some existing results and methods regarding the problem of determining the basins of attraction of dynamical systems (in particular, two-dimensional diffeomorphisms) when there is a coexistence of attractors. Based on the work of Helena Nusse and James Yorke, it presents existence and characterization results for a certain kind of basin boundaries (namely, the Wada boundaries). The key feature of their approach is to redefine the idea of a basin boundary by introducing the notion of a `basin cell', which bypasses the problem of exactly locating the attractor of a system, which is often either not well-defined or hard to locate in practice. Moreover, the basin cells and their boundaries are characterized by utilizing the stable and unstable manifolds of the system, which are easier to locate by numerical methods, and thus their method provides both numerically verifiable characteristics and algorithms for computation. / text

Organic thin film transistors (TFTs) based on the field effect transistor architecture provide a methodology for sensing by exhibiting a change in the transport properties such as shifts in mobility, threshold voltage and conductivity. Chemical recognition is achievable by various methods including the two processes, which we are studying, direct analyte interactions with the semiconductor and specific receptor molecules on the semiconducting surface. Previous work demonstrates the effects of carrier concentration, grain size (surface morphology), and channel length on the sensing response to analytes such as alcohols, which exhibit a moderate dipole moment. When the alcohol interacts with the organic channel the addition of a trap and a positive charge occurs at the grain boundaries. At low carrier concentrations the added charge has the effect of producing an increase in current for the sensing response. At higher carrier concentrations the occurrence of trapping overwhelms the effect of the positive charge and you see and reduction in current. Typically the mobility shifts, which occur during sensing are correlated with trapping for polar analytes. The magnitude of the mobility decreases are dependent on the dipole moment of the polar analyte. Another aspect of organic materials is the fine-tuning of the chemical sensitivity by modifying the surface with receptor sites to increase the partition coefficient. In our study we pull the polarization, molecular dipole moment, transport and trapping, and partition coefficient concepts together to produce a model, which describes how an OFET based sensor interacts with an analyte with and without receptor molecules and under aqueous conditions. / text

No description available.

In the past decades, numerous single-molecule techniques have been developed to investigate individual bio-molecules and cellular machines. While a lot is known about the structure, localization, and interaction partners of such molecules, much less is known about their mechanical properties. To investigate the weak, non-covalent interactions that give rise to the mechanics of and between proteins, an instrument capable of resolving sub-nanometer displacements and piconewton forces is necessary. One of the most prominent biophysical tool with such capabilities is an optical tweezers. Optical tweezers is a non-invasive all-optical technique in which typically a dielectric microsphere is held by a tightly focused laser beam. This microsphere acts like a microscopic, three-dimensional spring and is used as a handle to study the biological molecule of interest. By interferometric detection methods, the resolution of optical tweezers can be in the picometer range on millisecond time scales. However, on a time scale of seconds—at which many biological reactions take place—instrumental noise such as thermal drift often limits the resolution to a few nanometers. Such a resolution is insufficient to resolve, for example, the ångstrom-level, stepwise translocation of DNA-binding enzymes corresponding to distances between single basepairs of their substrate. To reduce drift and noise, differential measurements, feedback-based drift stabilization techniques, and ‘levitated’ experiments have been developed. Such methods have the drawback of complicated and expensive experimental equipment often coupled to a reduced throughput of experiments due to a complex and serial assembly of the molecular components of the experiments. We developed a high-resolution optical tweezers apparatus capable of resolving distances on the ångstrom-level over a time range of milliseconds to 10s of seconds in surface-coupled assays. Surface-coupled assays allow for a higher throughput because the molecular components are assembled in a parallel fashion on many probes. The high resolution was a collective result of a number of simple, easy-to-implement, and cost-efficient noise reduction solutions. In particular, we reduced thermal drift by implementing a temperature feedback system with millikelvin precision—a convenient solution for biological experiments since it minimizes drift in addition to enabling the control and stabilization of the experiment’s temperature. Furthermore, we found that expanding the laser beam to a size smaller than the objective’s exit pupil optimized the amount of laser power utilized in generating the trapping forces. With lower powers, biological samples are less susceptible to photo-damage or, vice versa, with the same laser power, higher trapping forces can be achieved. With motorized and automated procedures, our instrument is optimized for high-resolution, high-throughput surface-coupled experiments probing the mechanics of individual biomolecules. In the future, the combination of this setup with single-molecule fluorescence, super-resolution microscopy or torque detection will open up new possibilities for investigating the nanomechanics of biomolecules.

By shining a precisely tuned laser through an atomic vapor, we can determine local mag- netic field strength in scalar form and in a way that is not affected by temperature changes. This technology has been used in space many times before on missions flown by NASA and ESA, such as SWARM, Øersted, and CHAMP to calibrate accompanying vector mag- netometers which are subject to offsets caused by temperature changes. The device we constructed is a small, low-cost application of this scientific principle and opens up new areas of scientific possibility for cubesats and the ability to define geomagnetic field struc- tures on a small (<10km) scale as part of the ANDESITE cubesat mission being developed at Boston University. Previously, magnetic sensors in orbit have been flown individually on a single spacecraft or in very small groups such as the International Sun-Earth Exporers (ISEE) and SWARM which each used three separate spacecraft. This method of analyzing the geomagnetic field cannot provide a spatial or time resolution smaller than that of the separation between magnetic field readings. This project has focused on producing a tabletop demonstra- tion of a compact sensor head which could enable measurements on unprecedented small scales. Toward this end we have accomplished the construction and preliminary testing of a compact sensor head which contains all necessary elements to function as a scalar atomic magnetometer.

Hydrogen embrittlement (HE), which results in an unpredictable failure of metals, has been a major limitation in the design of critical components for a wide range of engineering applications, given the near-ubiquitous presence of hydrogen in their service environments. However, the exact mechanisms that underpin HE failure remain poorly understood. It is known that hydrogen, when free to diffuse in these materials, can tend to concentrate at a crack tip front. In turn, this facilitates crack propagation. Hence one of the proposed strategies for mitigating HE is to limit the content of freely diffusing hydrogen within the metal atomic lattice via the introduction of microstructural hydrogen traps. Further, it is empirically known that the introduction of finely-dispersed distribution of nano-sized carbide hydrogen traps in ferritic steel matrix can improve resilience to HE. This resilience has been attributed to the effective hydrogen trapping of the carbides. However, conclusive atomic-scale experimental evidence is still lacking as to the manner by which these features can impede the movement of the hydrogen. This lack of insight limits the further progress for the optimisation of the microstructural design of this type of HE-resistant steel. In order to further understand the hydrogen trapping phenomenon of the nano-sized carbide in steel, an appropriate characterisation method is required. Atom probe tomography (APT) has been known for its powerful combination of high 3D spatial and chemical resolution for the analysis of very fine precipitates. Furthermore, previous studies have shown that the application of isotopic hydrogen (²H) loading techniques, combined with APT, facilitates the hydrogen signal associated to fine carbides to be unambiguously identified. However, the considerable experimental requirements as utilised by these previous studies, particularly the instrumental capability necessary for retention of the trapped hydrogen in the needle-shaped APT specimen, limits the study being reproduced or extended. In this APT study, a model ferritic steel with finely dispersed V-Mo-Nb carbides of 10-20 nm is investigated. Initially, existing specialised instrumentation formed the basis of a cryogenic specimen chain under vacuum, so as to retain loaded hydrogen after an electrolytic charging treatment for APT analysis. This work confirms the importance of cryogenic treatment for the retention of trapped hydrogen in APT specimen. The quality of the obtained experimental data allows a quantitative analysis on the hydrogen trapping mechanism. Thus, it is conclusively determined that interior of the carbides studied in this steel acts as the hydrogen trapping site as opposed to the carbide/matrix interface as commonly expected. This result supports the theoretical investigations proposing that the hydrogen trapping within the carbide interior is enabled by a network of carbon vacancies. Based on the established importance of the specimen cold chain in these APT experiments, this work then successfully develops a simplified approach to cryo-transfer which requires no instrumental modification. In this approach there is no requirement for the charged specimen to be transferred under vacuum conditions. The issue of environmental-induced ice contamination on the cryogenic sample surface in air transfer is resolved by its sublimation in APT vacuum chamber. Furthermore, the temperature of the transferred sample is able to be determined independently by both monitoring changes to vacuum pressure in the buffer chamber and also the thermal response of the APT sample stage in the analysis chamber. This simplified approach has the potential to open up a range of hydrogen trapping studies to any commercial atom probe instrument. Finally, as an example of the use of this simplified cryo-transfer technique, targeted studies for determining the source of hydrogen adsorption during electropolishing and electrolytic loading process are demonstrated. This research provides a critical verification of hydrogen trapping mechanism of fine carbides as well as an achievable experimental protocol for the observation of the trapping of individual hydrogen atoms in alloy microstructures. The methods developed here have the potential to underpin a wide range of possible experiments which address the HE problem, particularly for the design of new mitigation strategies to prevent this critical issue.

Developing effective conservation strategies requires an empirical understanding of species' responses to human-mediated disturbances. Observable responses are typically limited to dramatic changes such as wildlife population declines or range shifts. However, preceding these obvious responses, more subtle responses may signal larger-scale future change, including changes in species' behaviours and interspecific interactions. Disturbance-induced shifts to species' diel activity patterns may disrupt mechanisms of niche partitioning along the 24-hour time axis, altering community structure via altered competitive interactions. I investigate the main questions and methods of analysis applicable to camera-trap data for furthering our understanding of temporal dynamics in animal communities. I apply these methods to evaluate the impacts of human-mediated disturbance on species' activity patterns and temporal niche partitioning in two separate studies, focusing on responses in the mammalian carnivore community. In the Canadian Rocky Mountain carnivore guild, species alter diel activities in relation to anthropogenic landscape development, although these shifts may be manifesting through indirect biotic effects instead of direct responses to human disturbance. Mesocarnivore species on a mixed-use landscape featuring anthropogenic land-use and introduced free-ranging dogs (Canis familiaris) shift activities in relation to spatiotemporal dog activity. Native carnivores partition diel activities differently on open landscapes of enhanced predation risk but abundant prey resources. Detecting shifts in species' temporal behaviours and competitive interactions may enable identification of potential precursors of population declines and shifting community assemblages, providing us with opportunities to pre-emptively manage against such biodiversity losses on human-modified landscapes. / Graduate

Resumo: Neste trabalho de tese exploramos a sugestão de Barge e Sommeria (1995) de captura de partículas em vórtices anticiclônicos que se formam devido a instabilidades na nebulosa proto-planetária. O problema dinâmico foi estudado através de simulações de um disco kepleriano bidimensional e incompressível. Examinamos o processo de concentração de partículas dentro de grandes vórtices através das equações do movimento para partículas individuais (com tamanho de 50 cm e 2,12 m) submetidas à gravidade solar e ao arrasto do gás nebular. Os vórtices levam à captura de um grande número de partículas. Mostramos que a eficácia das capturas não depende somente do valor do arrasto gasoso e da elongação do vórtice mas também do modelo do disco proto-planetário escolhido. Um achado muito importante nesse trabalho de tese pode começar a responder à questão sobre a formação planetária: colapso gravitacional ou coagulação? Quando incluímos a auto-gravidade, os resultados que obtivemos mostram que a acumulação das partículas dentro do vórtice é bem mais rápida. É um ponto muito importante na formação dos núcleos planetários até hoje bastante discutido. De fato, a formação dos núcleos planetários dos planetas gigantes precisa da acumulação de material maior que 1MÅ em muito pouco tempo para que o colapso ocorra antes do efeito gravitacional dentro do vórtice começar a expulsar os planetesimais A auto-gravidade até então bastante negligenciada por muitos autores pode ser uma ferramenta essencial a ser incluída no modelo de formação planetária para explicar tal fato. Outro resultado interessante que obtivemos foi que o crescimento por auto-sedimentação das partículas com tamanho sub-métrico, não é muito eficiente para formar planetesimais. Parece que os vórtices capturam partículas com um tamanho preferencial para formar planetesimais ou núcleos planetários. / Abstract: In this thesis, we explore the suggestion of Barge & Sommeria (1995) of dust-trapping in anticyclonic vortices forming due to instabilities in the protoplanetary nebula. The dynamical problem is studied through numerical simulations of a two-dimensional incompressible Keplerian disc. We examine the process of particle concentration inside large vortex through a non-collisional N body's code for individual particles (with sizes of 50 cm and 2,12 m) subject to the solar gravity and the nebular gas drag. The vortices tend to capture a large number of particles. We show that the effectiveness of these captures depend not only on the value of the gaseous drag and the elongation of the vortices but also on the model of the protoplanetary disc chosen. A very important finding in this thesis can start to answer the question of the planetary formation: gravitational collapse or coagulation? When we include the self-gravity, the results that we found show that the accumulation of particles inside the vortices is faster. It is a very important point in the formation of planetary embryo until today highly discussed. In fact, the formation of the giant planets embryo need the accumulation of more material than 1MÅ in a very short time such that the collapse occurs before the gravitational effect inside the vortices start to eject the planetesimals. Self-gravity, until now neglected by many authors could be an essential tool to be included in planetary formation model to explain such fact. Another interesting result that we got was that the growth for auto-sedimentation of particles with sub-metric size, is not very efficient to form planetesimal. It seems that vortices capture particles with a preferential size to form planetesimals or planetary cores. / Orientador: Othon Cabo Winter / Coorientador: Masayoshi Tsuchida / Banca: Ernesto Vieira Neto / Banca: Tadashi Yokoyama / Banca: Rodney da Silva Gomes / Banca: Fernando Virgilio Roig / Doutor

Neste trabalho reportamos a produção da primeira armadilha magneto-ótica que confina simultaneamente duas espécies atômicas distintas: Sódio e Potássio. Para podermos realizar este aprisionamento, foi necessário vencer algumas dificuldades técnicas que justificam, inclusive, a escolha dos elementos utilizados. Nossa armadilha também foi utilizada para realizar o primeiro estudo de colisões frias entre átomos de espécies diferentes. Experimentalmente, as informações sobre essas colisões são obtidas através da medida da dinâmica de perdas da armadilha de S6dio em presença e ausência de átomos frios de Potássio. Observamos que o efeito de colisões heteronucleares e dez vezes menor do que as homonucleares. Esta diferença já era esperada devido ao menor alcance dos potenciais de interação entre átomos no caso de espécies distintas. Nossos resultados são comparados a uma teoria semi-clássica simples e se encontram em bom acordo com as previsões. Introduzimos uma nova técnica que consiste em mudar repentinamente a intensidade do laser aprisionador e observar a variação do número de átomos aprisionados. Medimos a taxa de perdas por colisão entre átomos de Potássio frios como função da intensidade do laser aprisionador. Essa técnica nos permite alcançar o regime de baixas intensidades, inclusive abaixo da intensidade de saturação, sem as limitações da técnica tradicional. Aplicamos essa técnica ao aprisionamento simultâneo e medimos a taxa de perdas por colisão do sódio na presença e ausência de potássio. Com essa medida somos capazes de estimar a seção e choque entre sódio e potássio ambos no estado fundamental / In this thesis we report the production of the first magneto-optical trap that confines simultaneously two atomic species, sodium and potassium. In order to realize this experiment we had to overcome some technical difficulties that justified our choice of these two elements. This trap was used to study cold collisions between two different species. The information about these collisions is obtained experimentally from the dynamics of the sodium trap loss process in the presence and absence of potassium atoms. We observed that the heteronuclear effect is ten times smaller than the homonuclear one. This difference is explained by the smaller range of the interaction potentials between different species. Our results are compared with the theoretical predictions of the semi-classical theory and show a good agreement with the predictions. We have introduced a new technique which consists of a sudden decrease of the laser intensity, after which we observe the temporal variation in the number of trapped atoms. We have measured the loss rate coefficient between cold potassium atoms as a function of light intensity of the trapping laser. This technique allowed us to reach the very low intensity regime, as low as 30% of the saturation intensity, without compromising the loading process. We applied this technique to the simultaneous trapping and measured the loss rate coefficient between cold sodium atoms in the presence and absence of cold potassium atoms. With this measurement we can estimate the value of the cross section between sodium and potassium in the ground state