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Optical, Mechanical, and Electronic Properties of Etched Silicon Nanopillars
Get PDFThis work focuses on the fabrication, characterization and applications of silicon nanopillars. We explain the techniques involved in creating sub 50 nm diameter pillars with aspect ratios of 60:1. Original work encompassed the use of a novel etch mask made of reactive ion sputtered aluminum oxide, 'pseudo-Bosch' inductively coupled reactive ion etching (ICP-RIE) to etch structures on the nanoscale. These methods demonstrate a unique approach to the largely 'bottom-up' technology used in nanowire fabrication.
We also explored the self-terminating oxidation behavior of convex, two-dimension silicon structures. It was found that during the oxidation process, strain built up at the moving Si-SiO2 interface eventually led to a cessation of oxidation. This was used to predictably reduce the diameter of these pillars to 2 nm, making 'nanowhiskers.' We were able to characterize the results of this oxidation non-destructively by utilizing reflection mode transmission electron microscopy (R-TEM).
Using spun-on PMMA and an electron beam to constrict it and bend the pillars, we were able to incorporate as much as 25% strain. More interestingly this deformation appeared to be elastic, as the pillars, once freed from the polymer, would snap back to their upright position.
A consequence of the creation of silicon nanowhiskers was that silicon, a normally poor light emitter due to its indirect bandgap, became photoluminescent. As we reduced the diameter we noticed that the bandgap became direct and the emission peak was blue-shifted. We were able to utilize a tight-binding model (TBM) that was modified by the oxidation induced strain. This modified model predicted the blue-shift in peak emission wavelength with decreasing pillar diameter. The strain induced in the pillar during the oxidation played a significant role in the peak emission wavelength and shape of the bandstructure. By corrugating the pillars with an oscillating etch technique we were able to turn our nanopillars into quantum dots which also proved to photoluminesce.
Finally we look at the possibilities of creating a silicon light emitting diode. By creating a double-gated structure it is possible to overcome the difficulties encountered with sub 5 nm diameter pillars. A possible fabrication process, and the current work done to implement it, is presented as well as a simulation explaining the behavior of this device in the future. </p
An Optimal Transport Approach to Robust Reconstruction and Simplification of 2D Shapes
Get PDFWe present a robust 2D shape reconstruction and simplification algorithm which takes as input a defect-laden point set with noise and outliers. We introduce an optimal-transport driven approach where the input point set, considered as a sum of Dirac measures, is approximated by a simplicial complex considered as a sum of uniform measures on 0- and 1-simplices. A fine-to-coarse scheme is devised to construct the resulting simplicial complex through greedy decimation of a Delaunay triangulation of the input point set. Our method performs well on a variety of examples ranging from line drawings to grayscale images, with or without noise, features, and boundaries
The Importance of Compact-Object Spin in Extreme and Intermediate-Mass Ratio Inspirals
No full textGravitational waves can be produced when a compact object (stellar-mass black hole, neutron star, or white dwarf) spirals towards a massive black hole. For moderate mass ratios of 10-2 - 10-4, these events are known as intermediate mass ratio inspirals (IMRis), whereas for mass ratios below 10-4 they are called extreme mass ratio inspirals (EMRis). These events will be important sources for the proposed gravitational-wave detector LISA (Laser Interferometer Space Antenna) and will provide a precise test
of general relativity in the unexplored regime of strong gravitational fields. To detect
these gravitational waves and reliably measure the parameters of the binary producing
them, highly accurate models of gravitational waveforms are needed. The spin of the
orbiting compact object (CO) introduces forces that affect the orbit and waveform,
but these effects are often ignored. The goal of this thesis is to determine under what
circumstances compact-object spin will significantly alter the waveform as measured
by LISA. To do this, a post-Newtonian waveform model will be used to explore CO
spin effects. It is concluded that neglecting CO spin does not effect the detectability
of EMRis or IMRis. Parameter measurement errors introduced by neglecting CO
spin are typically small unless the binary system happens to be particularly close.
Constraining the value of compact object spin is unlikely but may be possible for a
nearby IMRI. Within the approximations used in this study, it appears CO spin is
marginally important, but that conclusion may change if a more realistic waveform
model is used in future work
Uncovering the Lagrangian from Observations of Trajectories
Get PDFWe approach the problem of automatically modeling a mechanical system from data about its dynamics, using a method motivated by variational integrators. We write the discrete Lagrangian as a quadratic polynomial with varying coefficients, and then use the discrete Euler-Lagrange equations to numerically solve for the values of these coefficients near the data points. This method correctly modeled the Lagrangian of a simple harmonic oscillator and a simple pendulum, even with significant measurement noise added to the trajectories
Progress Toward the Cortistatin A Carbocyclic Core and the Development of the Catalytic Enantioselective Alkylation of 3-Helooxindoles
Get PDFBiologically active natural products often contain interesting and complex structural features and functionalities that make them attractive targets for synthetic chemists. As such, these natural products can serve as inspiration for the development of new reaction methodology.
Cortistatin A contains a unique rearranged steroidal core and possesses potent anti-angiogenic activity. These features have made cortistatin A the target of many synthetic efforts, including ours. The progress toward the synthesis of the cortistatin A carbocyclic core via an enyne-ene metathesis is discussed. Our studies towards the construction of the cortistatin A carbocyclic core yielded an interesting result, wherein an attempted SN2 inversion of a secondary mesylate afforded product with retention of stereochemistry.
Oxindole derived motifs are also prevalent in biologically active molecules. More specifically, 3,3-disubstituted oxindoles can be used to access pyrrolidinylspirooxindole and pyrrolidinoindoline cores. Herein, the development of a catalytic enantioselective malonate alkylation of 3-halooxindoles to access enantiopure 3,3-disubstituted oxindoles is detailed. We then demonstrate that the enantiopure 3,3-disubstituted oxindoles derived from this novel transformation can be used towards the construction of pyrrolidinylspirooxindole and pyrrolidinoindoline cores.</p
Neurometrically Informed Mechanism Design and the Role of Visual Fixations in Simple Choice
Get PDFThe young field of neuroeconomics has already produced many important insights into the neurobiological underpinnings of decision making. However, at this early stage it is still unclear how much influence the field will have on mainstream economics. Here, I show how a neuroeconomics approach can shed light on two classic economic problems.
First, I show that it is possible to predict individuals’ values for public goods, using functional magnetic resonance imaging (fMRI)-based pattern classification. With such predictions in hand, I demonstrate that it is possible to solve the free-rider problem, by taxing individuals based both on the values that they themselves report and on the predicted values (using fMRI). I go on to more generally prove that by using any informative signal of value, it is possible to overcome classic impossibility results in mechanism design. This allows us to construct mechanisms that simultaneously satisfy dominant strategy incentive compatibility, voluntary participation, budget-balance and social efficiency. Such mechanisms were previously thought to be impossible. I demonstrate how to construct such mechanisms, and test them in three different public goods experiments.
Second, I show that individuals’ looking patterns are critical to the decision making process. When people make choices between options, they tend to look back and forth between them. One might think that these “fixations” are an unimportant by-product of the choice process, but I demonstrate that they are in fact intimately tied to the comparison process. By using a variant of the drift-diffusion models from the perceptual decision making literature, I find that fixations seem to bias the accumulation of evidence towards the item that is being looked at. Therefore, if one spends more time looking at one item over the other, then one is more likely to choose that item. Critically, I am able to show that this effect is not due to subjects looking longer at preferred items. The model has deep implications for how looking patterns (treated as exogenous) should bias choices, and I confirm these predictions using eye-tracking data from subjects choosing between snack foods
Dynamics of Long-Term Sea-Level Change and Vertical Motion of Continents
Get PDFWe formulate and apply dynamic models to better understand mantle processes and evolution, the vertical motion of continents, and regional and global sea-level change since 100 Ma. We show that evolving mid-to-upper mantle upwellings explain observed anomalously shallow bathymetry, the negative geoid, and the low seismic shear velocity anomalies in the Ross Sea region of Antarctica. These upwellings create a long-lived dynamic topography high, and the Campbell plateau of New Zealand experienced excess subsidence as it moved away from this upwelling. We then use instantaneous models globally to demonstrate that upper-to-mid mantle upwellings, located in the Indian Ocean, Ross Sea, northeast Pacific, and west Atlantic, are the primary cause of high-amplitude geoid minima that are localized within the longer wavelength geoid trough created by Mesozoic slabs. We propose that these upwellings constitute an unrecognized mode of mantle upwellings, potentially developed in response to the ancient subduction zones.
In an alternative approach, we apply inverse models to North America (NAM), and find that the vertical motion and relative sea level were controlled by Farallon slab subduction. The Farallon slab was flat-to-shallow lying in the Late Cretaceous and in turn controlled the marine inundation of the western NAM. During the Cenozoic, the Farallon slab sank into the lower mantle, while NAM moved westward in a mantle reference frame, resulting in the dynamic uplift of the western half and dynamic subsidence of the eastern half of NAM. We then use dynamic models and hypsometric analysis to show that the proposed dynamic subsidence potentially explains discrepancies between low-amplitude of sea-level fall inferred from subsidence analysis of New Jersey boreholes compared to sea-level curves based on global data sets.
Finally, we formulate dynamic models based on a hybrid approach, accounting for long-term sea-level change factors self-consistently. We infer the relative importance of dynamic topography versus other factors in controlling regional sea level and relative large-scale vertical motions, and calculate a global sea-level curve. We find that the eustatic sea-level fall since the Late Cretaceous is driven by changes in the age of the ocean floor, but is partially offset by dynamic topography.</p
Hydrogenases and Hydrogen Sensors in the Symbiotic Microbial Communities of Wood-Feeding Termites
Get PDFThe termite gut is an ideal ecosystem for studying hydrogen ecophysiology. Hydrogen is central to the obligate mutualism between termites and their gut microbes and is turned over at rates as high as 33 m3 H2 per m3 hindgut volume daily and maintained near saturation in some species. Acetogenic bacteria use hydrogen to produce up to 1/3 of the total flux of the termite’s primary carbon and energy source, acetate. We have taken a three-fold approach to investigate the hydrogen ecophysiology of the termite gut. In our first approach (Chapter 2) we completed a bioinformatic analysis of [FeFe] hydrogenase-like (H domain) proteins encoded in the genomes of three termite gut treponemes. Treponemes are among the most highly represented groups of gut bacteria. The remarkable diversity of H domain proteins encoded accentuates the importance of hydrogen to their physiology. Moreover, they encoded a poorly understood class hydrogen sensing H domain proteins and thereby present a unique opportunity for their further study. In our second approach (Chapters 3 and 4) we analyzed molecular inventories prepared from termite gut microbiomes of a class of [FeFe] hydrogenases found highly represented in a termite hindgut metagenome. The libraries of peptide sequences clustered with one another in a manner congruent with termite host phylogeny suggesting co-evolution. Interestingly, we observed that higher termite guts may harbor higher sequence diversity than lower termites. In our third approach (Chapter 5) we used microfluidic digital PCR to identify bacteria in the gut of Reticulitermes tibialis encoding [FeFe] hydrogenases. The majority of the 16S rRNA gene phylotypes observed to co-amplify with hydrogenase sequences were treponemal, and the only observed instances of the same 16S rRNA-hydrogenase gene pair co-amplifying in multiple microfluidic chambers corresponded to treponemal phylotypes. Therefore, treponemes may be an important or predominant bacterial group encoding an important family of [FeFe] hydrogenases in the termite gut. The above results provide support for an important role for treponemes in mediating hydrogen metabolism in the termite gut and accentuate the intimacy and stability of the association termites have maintained over the course of their evolution with their gut microbial communities
DNA Directed Self-Assembly of Carbon Nanotube Structures
Get PDFProduction of pure carbon nanotube species and organization of nanoscale structure are two fundamental barriers to the utilization of CNTs in nanoelectronics. We have developed new methods to characterize double walled carbon nanotube (DWNT) structure by Raman spectroscopy and organize single walled carbon nanotube (SWNT) constructs using DNA.
First, using atomistic force fields calculations, we have shown that the radial breathing modes (RBM) of double walled carbon nanotubes can be accurately modeled as two uniform concentric cylindrical elastic shells coupled by a van der Waals interaction. This model leads to a simple equation which can be solved to give accurate RBMs (given diameters) or diameters (given RBMs).
Secondly, we have developed a method for using DNA origami to template the assembly of complex SWNT structures. In this process, SWNTs are modified with non-covalently attached DNA linkers that present duplex labeling domains for base pairing to complementary single stranded hooks on customized DNA origami. We show that the SWNTs attach at positions and in orientations specified by their labeling sequence, and that nanotube cross-junctions assembled from two different SWNTs in this manner can behave as field effect transistors.
Finally, we have devised a method for using DNA linkers to organize arrays of parallel SWNTs with uniform and selectable inter-nanotube separation of <20 nm. SWNTs are first dispersed in aqueous solution with DNA linkers-spacers that non-covalently anchor onto their sidewalls. When the modified SWNTs are then deposited on mica or polar lipid bilayers and allowed to diffuse on the surface, they form parallel arrays of SWNTs in which different domains of the DNA linker-spacers act to maintain array cohesion and enforce uniform separation. Thus, the use of 7 bp, 20 bp, and 60 bp DNA spacer domains result in ~3 nm, ~8.5 nm, and ~22 nm inter-nanotube separations. We further use the spacer domains as rigid scaffolds for the positioning of Streptavidin proteins between adjacent nanotubes, and give a simple method for transfer of intact arrays onto adhesive glass substrates. Further development of this technology could lead to wafer scale organization of dense parallel SWNT decorated with heterogeneous nanoscale objects.</p
Biochemical and Genetic Studies of Genomic Stability
Get PDFGenomes face a constant barrage of threats from endogenous and exogenous sources. The need to maintain fidelity while replicating the entire genome during each cell division necessitates a dynamic cadre of proteins and protein complexes that participate in the DNA replication process. Furthermore, DNA can be damaged during all phases of the cell’s life and that damage must be recognized and repaired in a way that preserves genetic information. These studies focus on one enzyme at the nexus of DNA replication and DNA repair, the helicase/nuclease Dna2. We show that Dna2 possesses a novel ATP/Mn2+ dependent flap endo/exonuclease activity and a DNA end-independent endonuclease activity that is inhibited by Replication Protein A. The regulation of Dna2 activity in the context of the global DNA damage response is of great interest. To that end, we explored the relationship of Dna2 and the DNA damage sensor kinase Mec1. We find that Dna2 is phosphorylated by Mec1 following DNA damage in its N-terminal domain. We then extended these studies from yeast to higher eukaryotes utilizing the Xenopus cell free extract system. Using simulated double strand breaks (DSBs), we constructed a timeline of protein processing steps required for homologous recombination mediated repair. This strategy using Xenopus extracts also place Dna2 on chromatin during DNA replication, physically interacting with other proteins involved in lagging strand replication. Taken together, these biochemical and genetic studies elucidate the multiple roles the Dna2 enzyme plays in order to ensure genomic stability