Direct observation of a long-lived single-atom catalyst chiseling atomic structures in graphene

Fabricating stable functional devices at the atomic scale is an ultimate goal of nanotechnology. In biological processes, such high-precision operations are accomplished by enzymes. A counterpart molecular catalyst that binds to a solid-state substrate would be highly desirable. Here, we report the direct observation of single Si adatoms catalyzing the dissociation of carbon atoms from graphene in an aberration-corrected high-resolution transmission electron microscope (HRTEM). The single Si atom provides a catalytic wedge for energetic electrons to chisel off the graphene lattice, atom by atom, while the Si atom itself is not consumed. The products of the chiseling process are atomic-scale features including graphene pores and clean edges. Our experimental observations and first-principles calculations demonstrated the dynamics, stability, and selectivity of such a single-atom chisel, which opens up the possibility of fabricating certain stable molecular devices by precise modification of materials at the atomic scale.

BETA-GA2O3: A TRANSPARENT CONDUCTIVE OXIDE FOR POTENTIAL RESISTIVE SWITCHING APPLICATIONS

Thesis (Ph.D.)--University of Washington, 2016-08

Dynamic Workload Parallelization and System Calibration on Single-Chip Cloud Computer

Many-core systems are emerging from the need of more computational power and power efficiency. However there are many issues which still revolve around the many-core systems. These systems need specialized software before they can be fully utilized and the hardware itself may differ from the conventional computational systems. To gain efficiency from many-core system, programs need to be parallelized. In many-core systems the cores are small and less powerful than cores used in traditional computing, so running a conventional program is not an efficient option. Also in Network-on-Chip based processors the network might get congested and the cores might work at different speeds. In this thesis is, a dynamic load balancing method is proposed and tested on Intel 48-core Single-Chip Cloud Computer by parallelizing a fault simulator. The maximum speedup is difficult to obtain due to severe bottlenecks in the system. In order to exploit all the available parallelism of the Single-Chip Cloud Computer, a runtime approach capable of dynamically balancing the load during the fault simulation process is used. The proposed dynamic fault simulation approach on the Single-Chip Cloud Computer shows up to 45X speedup compared to a serial fault simulation approach. Many-core systems can draw enormous amounts of power, and if this power is not controlled properly, the system might get damaged. One way to manage power is to set power budget for the system. But if this power is drawn by just few cores of the many, these few cores get extremely hot and might get damaged. Due to increase in power density multiple thermal sensors are deployed on the chip area to provide realtime temperature feedback for thermal management techniques. Thermal sensor accuracy is extremely prone to intra-die process variation and aging phenomena. These factors lead to a situation where thermal sensor values drift from the nominal values. This necessitates efficient calibration techniques to be applied before the sensor values are used. In addition, in modern many-core systems cores have support for dynamic voltage and frequency scaling. Thermal sensors located on cores are sensitive to the core's current voltage level, meaning that dedicated calibration is needed for each voltage level. In this thesis a general-purpose software-based auto-calibration approach is also proposed for thermal sensors to calibrate thermal sensors on different range of voltages.

Symmetry properties of one- and two- electron molecular integrals

The maximum numbers of distinct one- and two-electron integrals that arise in calculating the electronic energy of a molecule are discussed. It is shown that these may be calculated easily using the character table of the symmetry group of the set of basis functions used to express the wave function. Complications arising from complex group representations and from a conflict of symmetry between the basis set and the nuclear configuration are considered and illustrated by examples.

Fast assembly of fock matrices utilising symmetry properties of the basis set

A method of assembling the elements of the Fock matrix is described which is a modification of that due to Dacre. Lists of symmetry equivalent one-electron integrals are used as pointers to abbreviate the process of collecting two-electron integrals into the Fock matrix.

Toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in the developing male Wistar(Han) rat I: no decrease in epididymal sperm count after a single acute dose

It has been reported that fetal exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) causes defects in the male reproductive system of the rat. We set out to replicate and extend these effects using a robust experimental design. Groups of 75 (control vehicle) or 55 (50, 200 or 1000 ng of TCDD kg-1 bodyweight) female Wistar(Han) rats were exposed to TCDD on Gestational Day (GD) 15, then allowed to litter. The high dose group dams showed no sustained weight loss compared to control, but four animals had total litter loss. Pups in the high dose group showed reduced body weight up till day 21, and pups in the medium dose group showed reduced body weight in the first week post partum. Balano-preputial separation (BPS) was significantly delayed in the high dose group male offspring. There were no significant effects of treatment when the offspring were subjected to a functional observational battery, or mated with females to assess reproductive capability. 25 males per group were killed on post natal day (PND) 70, and ~60 animals per group (~30 for the high dose group) on PND120 to assess seminology and other endpoints. At PND120, the two highest dose groups showed a statistically significant elevation of sperm counts, compared to control; however, this effect was small (~30%), within the normal range of sperm counts for this strain of rat, was not reflected in testicular spermatid counts nor PND70 data, and is therefore postulated to have no biological significance. Although there was an increase in the proportion of abnormal sperm at PND70, seminology parameters were otherwise unremarkable. Testis weights in the high dose group were slightly decreased at PND 70 and 120, and at PND120, brain weights were decreased in the high dose group, liver to body weight ratios were increased for all three dose groups, with an increase in inflammatory cell foci in the epididymis in the high dose group. These data show that TCDD is a potent developmental toxin after exposure of the developing fetus, but that acute developmental exposure to TCDD on GD15 caused no decrease in sperm counts.

In situ transmission electron microscopy ion irradiations of model iron-chromium alloys

Iron-chromium alloys are used as a model to study the microstructural evolution of defects in irradiated structural steel components of a nuclear reactor. We examine the effects of temperature and chromium concentration on the defect evolution and segregation behavior in the early stages of damage. In situ irradiations are conducted in a transmission electron microscope (TEM) at 300°C and 450°C with 150keV iron ions in single crystal Fe14Cr and Fe19Cr bicrystal to doses of 2E15 ions/cm^2. The microstructures resulting from annealing and irradiation of the alloy are characterized by analysis of TEM micrographs and diffraction patterns and compared with those of irradiated pure iron. We found the irradiation temperature to have little effect on the microstructural development. We also found that the presence of chromium in the sample leads to defect populations with small average loop size and no extended or nested loop structures, in contrast to the populations of large extended loops seen in irradiated pure iron. A very weak dependence was found on the specific chromium content of the alloy. Chromium was shown to suppress defect growth by inhibiting defect mobility in the alloy. While defects in pure iron are highly mobile and able to grow, those in the FeCr alloys remained small and relatively motionless due to the pinning effect of the chromium.

Components and circuits for tunneling diode based high frequency sources

Terahertz (THz) technology has been generating a lot of interest because of the potential applications for systems working in this frequency range. However, to fully achieve this potential, effective and efficient ways of generating controlled signals in the terahertz range are required. Devices that exhibit negative differential resistance (NDR) in a region of their current-voltage (I-V ) characteristics have been used in circuits for the generation of radio frequency signals. Of all of these NDR devices, resonant tunneling diode (RTD) oscillators, with their ability to oscillate in the THz range are considered as one of the most promising solid-state sources for terahertz signal generation at room temperature. There are however limitations and challenges with these devices, from inherent low output power usually in the range of micro-watts (uW) for RTD oscillators when milli-watts (mW) are desired. At device level, parasitic oscillations caused by the biasing line inductance when the device is biased in the NDR region prevent accurate device characterisation, which in turn prevents device modelling for computer simulations. This thesis describes work on I-V characterisation of tunnel diode (TD) and RTD (fabricated by Dr. Jue Wang) devices, and the radio frequency (RF) characterisation and small signal modelling of RTDs. The thesis also describes the design and measurement of hybrid TD oscillators for higher output power and the design and measurement of a planar Yagi antenna (fabricated by Khalid Alharbi) for THz applications. To enable oscillation free current-voltage characterisation of tunnel diodes, a commonly employed method is the use of a suitable resistor connected across the device to make the total differential resistance in the NDR region positive. However, this approach is not without problems as the value of the resistor has to satisfy certain conditions or else bias oscillations would still be present in the NDR region of the measured I-V characteristics. This method is difficult to use for RTDs which are fabricated on wafer due to the discrepancies in designed and actual resistance values of fabricated resistors using thin film technology. In this work, using pulsed DC rather than static DC measurements during device characterisation were shown to give accurate characteristics in the NDR region without the need for a stabilisation resistor. This approach allows for direct oscillation free characterisation for devices. Experimental results show that the I-V characterisation of tunnel diodes and RTD devices free of bias oscillations in the NDR region can be made. In this work, a new power-combining topology to address the limitations of low output power of TD and RTD oscillators is presented. The design employs the use of two oscillators biased separately, but with the combined output power from both collected at a single load. Compared to previous approaches, this method keeps the frequency of oscillation of the combined oscillators the same as for one of the oscillators. Experimental results with a hybrid circuit using two tunnel diode oscillators compared with a single oscillator design with similar values shows that the coupled oscillators produce double the output RF power of the single oscillator. This topology can be scaled for higher (up to terahertz) frequencies in the future by using RTD oscillators. Finally, a broadband Yagi antenna suitable for wireless communication at terahertz frequencies is presented in this thesis. The return loss of the antenna showed that the bandwidth is larger than the measured range (140-220 GHz). A new method was used to characterise the radiation pattern of the antenna in the E-plane. This was carried out on-wafer and the measured radiation pattern showed good agreement with the simulated pattern. In summary, this work makes important contributions to the accurate characterisation and modelling of TDs and RTDs, circuit-based techniques for power combining of high frequency TD or RTD oscillators, and to antennas suitable for on chip integration with high frequency oscillators.

Measurement of target single-spin asymmetry in charged kaon electroproduction on a transversely polarized 3He target

The subject of quark transverse spin and transverse momentum distribution are two current research frontier in understanding the spin structure of the nucleons. The goal of the research reported in this dissertation is to extract new information on the quark transversity distribution and the novel transverse-momentum-dependent Sivers function in the neutron. A semi-inclusive deep inelastic scattering experiment was performed at the Hall A of the Jefferson laboratory using 5.9 GeV electron beam and a transversely polarized ^{3}He target. The scattered electrons and the produced hadrons (pions, kaons, and protons) were detected in coincidence with two large magnetic spectrometers. By regularly flipping the spin direction of the transversely polarized target, the single-spin-asymmetry (SSA) of the semi-inclusive deep inelastic reaction ^{3}He^{uparrow}(e,e'h^{\pm})X was measured over the kinematic range 0.13 < x < 0.41 and 1.3 < Q^{2} < 3.1 (GeV)^{2}. The SSA contains several different azimuthal angular modulations which are convolutions of quarks distribution functions in the nucleons and the quark fragmentation functions into hadrons. It is from the extraction of the various ``moments'' of these azimuthal angular distributions (Collins moment and Sivers moment) that we obtain information on the quark transversity distribution and the novel T-odd Sivers function. In this dissertation, I first introduced the theoretical background and experimental status of nucleon spins and the physics of SSA. I will then present the experimental setup and data collection of the JLab E06-010 experiment. Details of data analysis will be discussed next with emphasis on the kaon particle identification and the Ring-Imaging Cherenkov detector which are my major responsibilities in this experiment. Finally, results on the kaon Collins and Sivers moments extracted from the Maximum Likelihood method will be presented and interpreted. I will conclude with a discussion on the future prospects for this research.

Effects of Exposure to the Sound from Seismic Airguns on Pallid Sturgeon and Paddlefish - Data Set

Dataset for publication in PLOS One

Simulation tools for the analysis of single electronic systems

Developments in theory and experiment have raised the prospect of an electronic technology based on the discrete nature of electron tunnelling through a potential barrier. This thesis deals with novel design and analysis tools developed to study such systems. Possible devices include those constructed from ultrasmall normal tunnelling junctions. These exhibit charging effects including the Coulomb blockade and correlated electron tunnelling. They allow transistor-like control of the transfer of single carriers, and present the prospect of digital systems operating at the information theoretic limit. As such, they are often referred to as single electronic devices. Single electronic devices exhibit self quantising logic and good structural tolerance. Their speed, immunity to thermal noise, and operating voltage all scale beneficially with junction capacitance. For ultrasmall junctions the possibility of room temperature operation at sub picosecond timescales seems feasible. However, they are sensitive to external charge; whether from trapping-detrapping events, externally gated potentials, or system cross-talk. Quantum effects such as charge macroscopic quantum tunnelling may degrade performance. Finally, any practical system will be complex and spatially extended (amplifying the above problems), and prone to fabrication imperfection. This summarises why new design and analysis tools are required. Simulation tools are developed, concentrating on the basic building blocks of single electronic systems; the tunnelling junction array and gated turnstile device. Three main points are considered: the best method of estimating capacitance values from physical system geometry; the mathematical model which should represent electron tunnelling based on this data; application of this model to the investigation of single electronic systems. (DXN004909)

Microfluidics-based single-cell functional proteomics microchip for portraying protein signal transduction networks within the framework of physicochemical principles, with applications in fundamental and translational cancer research

Single-cell functional proteomics assays can connect genomic information to biological function through quantitative and multiplex protein measurements. Tools for single-cell proteomics have developed rapidly over the past 5 years and are providing unique opportunities. This thesis describes an emerging microfluidics-based toolkit for single cell functional proteomics, focusing on the development of the single cell barcode chips (SCBCs) with applications in fundamental and translational cancer research.

The microchip designed to simultaneously quantify a panel of secreted, cytoplasmic and membrane proteins from single cells will be discussed at the beginning, which is the prototype for subsequent proteomic microchips with more sophisticated design in preclinical cancer research or clinical applications. The SCBCs are a highly versatile and information rich tool for single-cell functional proteomics. They are based upon isolating individual cells, or defined number of cells, within microchambers, each of which is equipped with a large antibody microarray (the barcode), with between a few hundred to ten thousand microchambers included within a single microchip. Functional proteomics assays at single-cell resolution yield unique pieces of information that significantly shape the way of thinking on cancer research. An in-depth discussion about analysis and interpretation of the unique information such as functional protein fluctuations and protein-protein correlative interactions will follow.

The SCBC is a powerful tool to resolve the functional heterogeneity of cancer cells. It has the capacity to extract a comprehensive picture of the signal transduction network from single tumor cells and thus provides insight into the effect of targeted therapies on protein signaling networks. We will demonstrate this point through applying the SCBCs to investigate three isogenic cell lines of glioblastoma multiforme (GBM).

The cancer cell population is highly heterogeneous with high-amplitude fluctuation at the single cell level, which in turn grants the robustness of the entire population. The concept that a stable population existing in the presence of random fluctuations is reminiscent of many physical systems that are successfully understood using statistical physics. Thus, tools derived from that field can probably be applied to using fluctuations to determine the nature of signaling networks. In the second part of the thesis, we will focus on such a case to use thermodynamics-motivated principles to understand cancer cell hypoxia, where single cell proteomics assays coupled with a quantitative version of Le Chatelier's principle derived from statistical mechanics yield detailed and surprising predictions, which were found to be correct in both cell line and primary tumor model.

The third part of the thesis demonstrates the application of this technology in the preclinical cancer research to study the GBM cancer cell resistance to molecular targeted therapy. Physical approaches to anticipate therapy resistance and to identify effective therapy combinations will be discussed in detail. Our approach is based upon elucidating the signaling coordination within the phosphoprotein signaling pathways that are hyperactivated in human GBMs, and interrogating how that coordination responds to the perturbation of targeted inhibitor. Strongly coupled protein-protein interactions constitute most signaling cascades. A physical analogy of such a system is the strongly coupled atom-atom interactions in a crystal lattice. Similar to decomposing the atomic interactions into a series of independent normal vibrational modes, a simplified picture of signaling network coordination can also be achieved by diagonalizing protein-protein correlation or covariance matrices to decompose the pairwise correlative interactions into a set of distinct linear combinations of signaling proteins (i.e. independent signaling modes). By doing so, two independent signaling modes – one associated with mTOR signaling and a second associated with ERK/Src signaling have been resolved, which in turn allow us to anticipate resistance, and to design combination therapies that are effective, as well as identify those therapies and therapy combinations that will be ineffective. We validated our predictions in mouse tumor models and all predictions were borne out.

In the last part, some preliminary results about the clinical translation of single-cell proteomics chips will be presented. The successful demonstration of our work on human-derived xenografts provides the rationale to extend our current work into the clinic. It will enable us to interrogate GBM tumor samples in a way that could potentially yield a straightforward, rapid interpretation so that we can give therapeutic guidance to the attending physicians within a clinical relevant time scale. The technical challenges of the clinical translation will be presented and our solutions to address the challenges will be discussed as well. A clinical case study will then follow, where some preliminary data collected from a pediatric GBM patient bearing an EGFR amplified tumor will be presented to demonstrate the general protocol and the workflow of the proposed clinical studies.

Metastability and dynamics of stem cells: from direct observations to inference at the single cell level

Organismal development, homeostasis, and pathology are rooted in inherently probabilistic events. From gene expression to cellular differentiation, rates and likelihoods shape the form and function of biology. Processes ranging from growth to cancer homeostasis to reprogramming of stem cells all require transitions between distinct phenotypic states, and these occur at defined rates. Therefore, measuring the fidelity and dynamics with which such transitions occur is central to understanding natural biological phenomena and is critical for therapeutic interventions.

While these processes may produce robust population-level behaviors, decisions are made by individual cells. In certain circumstances, these minuscule computing units effectively roll dice to determine their fate. And while the 'omics' era has provided vast amounts of data on what these populations are doing en masse, the behaviors of the underlying units of these processes get washed out in averages.

Therefore, in order to understand the behavior of a sample of cells, it is critical to reveal how its underlying components, or mixture of cells in distinct states, each contribute to the overall phenotype. As such, we must first define what states exist in the population, determine what controls the stability of these states, and measure in high dimensionality the dynamics with which these cells transition between states.

To address a specific example of this general problem, we investigate the heterogeneity and dynamics of mouse embryonic stem cells (mESCs). While a number of reports have identified particular genes in ES cells that switch between 'high' and 'low' metastable expression states in culture, it remains unclear how levels of many of these regulators combine to form states in transcriptional space. Using a method called single molecule mRNA fluorescent in situ hybridization (smFISH), we quantitatively measure and fit distributions of core pluripotency regulators in single cells, identifying a wide range of variabilities between genes, but each explained by a simple model of bursty transcription. From this data, we also observed that strongly bimodal genes appear to be co-expressed, effectively limiting the occupancy of transcriptional space to two primary states across genes studied here. However, these states also appear punctuated by the conditional expression of the most highly variable genes, potentially defining smaller substates of pluripotency.

Having defined the transcriptional states, we next asked what might control their stability or persistence. Surprisingly, we found that DNA methylation, a mark normally associated with irreversible developmental progression, was itself differentially regulated between these two primary states. Furthermore, both acute or chronic inhibition of DNA methyltransferase activity led to reduced heterogeneity among the population, suggesting that metastability can be modulated by this strong epigenetic mark.

Finally, because understanding the dynamics of state transitions is fundamental to a variety of biological problems, we sought to develop a high-throughput method for the identification of cellular trajectories without the need for cell-line engineering. We achieved this by combining cell-lineage information gathered from time-lapse microscopy with endpoint smFISH for measurements of final expression states. Applying a simple mathematical framework to these lineage-tree associated expression states enables the inference of dynamic transitions. We apply our novel approach in order to infer temporal sequences of events, quantitative switching rates, and network topology among a set of ESC states.

Taken together, we identify distinct expression states in ES cells, gain fundamental insight into how a strong epigenetic modifier enforces the stability of these states, and develop and apply a new method for the identification of cellular trajectories using scalable in situ readouts of cellular state.

Efeito do tratamento por plasma na proliferação de fibroblastos e esterilização de membranas de quitosana

Chitosan is being studied for use as dressing due their biological properties. Aiming to expand the use in biomedical applications, chitosan membranes were modified by plasma using the following gases: nitrogen (N2), methane (CH4), argon (Ar), oxygen (O2) and hydrogen (H2). The samples were characterized by scanning electron microscopy (SEM), atomic force microscopy (AFM), contact angle, surface energy and water absorption test. Biological Tests were also performed, such as: test sterilization and proliferation of fibroblasts (3T3 line). Through SEM we observed morphological changes occurring during the plasma treatment, the formation of micro and nano-sized valleys. MFA was used to analyze different roughness parameters (Ra, Rp, Rz) and surface topography. It was found that the treated samples had an increase in surface roughness and sharp peaks. Methane plasma treatment decreased the hydrophilicity of the membranes and also the rate of water absorption, while the other treatments turned the membranes hydrophilic. The sterilization was effective in all treatment times with the following gases: Ar, N2 and H2. With respect to proliferation, all treatments showed an improvement in cell proliferation increased in a range 150% to 250% compared to untreated membrane. The highlights were the treatments with Ar 60 min, O2 60 min, CH4 15 min. Observing the results of the analyzes performed in this study, it appears that there is no single parameter that influences cell proliferation, but rather a set of ideal conditions that favor cell proliferation

Urban Identity and tourism:different looks, one single place

‘Urban identity’ is high on the policy agenda and pervades the discourse of the planning community on the value of historical city centres. Unfortunately, there seems to be, until today, no proposal in scholarly literature of any unified conceptual framework or any tools to make identity operational. ‘Tourism’ takes advantage of this process, by seeking the qualities of the place, its authenticity and its perceived uniqueness that is grounded on the physical features as well as on the presence of local communities – their way of living and investing in the place. The interdependence between identity as perceived by tourists (external observer) and the identity of the residents rooted in the relationship with the place (in-group) are key to addressing the identity of historic urban areas. These issues are addressed in the context of the growing attractiveness of Lisbon, Portugal, using a historic neighbourhood as a case study. The findings, which are on a set of interviews with different groups of users, showed the points of convergence and divergence between the different groups’ views of the neighbourhood’s identity. This actor-oriented approach is pivotal to understanding the process and to produce knowledge for informed action.