ASU Scholarship Showcase

Plasmonic and metamaterial based nano/micro-structured materials enable spectrally selective resonant absorption, where the resonant bandwidth and absorption intensity can be engineered by controlling the size and geometry of nanostructures. Here, we demonstrate a simple, lithography-free approach for obtaining a resonant and dynamically tunable broadband absorber based on vanadium dioxide (VO2) phase transition. Using planar layered thin film structures, where top layer is chosen to be an ultrathin (20 nm) VO2 film, we demonstrate broadband IR light absorption tuning (from similar to 90% to similar to 30% in measured absorption) over the entire mid-wavelength infrared spectrum. Our numerical and experimental results indicate that the bandwidth of the absorption bands can be controlled by changing the dielectric spacer layer thickness. Broadband tunable absorbers can find applications in absorption filters, thermal emitters, thermophotovoltaics, and sensing.

Background: Blindness has evolved repeatedly in cave-dwelling organisms, and many hypotheses have been proposed to explain this observation, including both accumulation of neutral loss-of-function mutations and adaptation to darkness. Investigating the loss of sight in cave dwellers presents an opportunity to understand the operation of fundamental evolutionary processes, including drift, selection, mutation, and migration.

Results: Here we model the evolution of blindness in caves. This model captures the interaction of three forces: (1) selection favoring alleles causing blindness, (2) immigration of sightedness alleles from a surface population, and (3) mutations creating blindness alleles. We investigated the dynamics of this model and determined selection-strength thresholds that result in blindness evolving in caves despite immigration of sightedness alleles from the surface. We estimate that the selection coefficient for blindness would need to be at least 0.005 (and maybe as high as 0.5) for blindness to evolve in the model cave-organism, Astyanax mexicanus.

Conclusions: Our results indicate that strong selection is required for the evolution of blindness in cave-dwelling organisms, which is consistent with recent work suggesting a high metabolic cost of eye development.

The most common evolutionary events at the molecular level are single-base substitutions, as well as insertions and deletions (indels) of short DNA segments. A large body of research has been devoted to develop probabilistic substitution models and to infer their parameters using likelihood and Bayesian approaches. In contrast, relatively little has been done to model indel dynamics, probably due to the difficulty in writing explicit likelihood functions. Here, we contribute to the effort of modeling indel dynamics by presenting SpartaABC, an approximate Bayesian computation (ABC) approach to infer indel parameters from sequence data (either aligned or unaligned). SpartaABC circumvents the need to use an explicit likelihood function by extracting summary statistics from simulated sequences. First, summary statistics are extracted from the input sequence data. Second, SpartaABC samples indel parameters from a prior distribution and uses them to simulate sequences. Third, it computes summary statistics from the simulated sets of sequences. By computing a distance between the summary statistics extracted from the input and each simulation, SpartaABC can provide an approximation to the posterior distribution of indel parameters as well as point estimates. We study the performance of our methodology and show that it provides accurate estimates of indel parameters in simulations. We next demonstrate the utility of SpartaABC by studying the impact of alignment errors on the inference of positive selection. A C ++ program implementing SpartaABC is freely available in http://spartaabc.tau.ac.il.

Under models of isolation-by-distance, population structure is determined by the probability of identity-by-descent between pairs of genes according to the geographic distance between them. Well established analytical results indicate that the relationship between geographical and genetic distance depends mostly on the neighborhood size of the population which represents a standardized measure of gene flow. To test this prediction, we model local dispersal of haploid individuals on a two-dimensional landscape using seven dispersal kernels: Rayleigh, exponential, half-normal, triangular, gamma, Lomax and Pareto. When neighborhood size is held constant, the distributions produce similar patterns of isolation-by-distance, confirming predictions. Considering this, we propose that the triangular distribution is the appropriate null distribution for isolation-by-distance studies. Under the triangular distribution, dispersal is uniform over the neighborhood area which suggests that the common description of neighborhood size as a measure of an effective, local panmictic population is valid for popular families of dispersal distributions. We further show how to draw random variables from the triangular distribution efficiently and argue that it should be utilized in other studies in which computational efficiency is important.

Mutation is the ultimate source of all genetic variation and is, therefore, central to evolutionary change. Previous work on Paramecium tetraurelia found an unusually low germline base-substitution mutation rate in this ciliate. Here, we tested the generality of this result among ciliates using Tetrahymena thermophila. We sequenced the genomes of 10 lines of T. thermophila that had each undergone approximately 1,000 generations of mutation accumulation (MA). We applied an existing mutation-calling pipeline and developed a new probabilistic mutation detection approach that directly models the design of an MA experiment and accommodates the noise introduced by mismapped reads. Our probabilistic mutation-calling method provides a straightforward way of estimating the number of sites at which a mutation could have been called if one was present, providing the denominator for our mutation rate calculations. From these methods, we find that T. thermophila has a germline base-substitution mutation rate of 7.61 × 10 ^-12 per-site, per cell division, which is consistent with the low base-substitution mutation rate in P. tetraurelia. Over the course of the evolution experiment, genomic exclusion lines derived from the MA lines experienced a fitness decline that cannot be accounted for by germline base-substitution mutations alone, suggesting that other genetic or epigenetic factors must be involved. Because selection can only operate to reduce mutation rates based upon the "visible" mutational load, asexual reproduction with a transcriptionally silent germline may allow ciliates to evolve extremely low germline mutation rates.

The strong light-matter interaction and the valley selective optical selection rules make monolayer (ML) MoS₂ an exciting 2D material for fundamental physics and optoelectronics applications. But, so far, optical transition linewidths even at low temperature are typically as large as a few tens of meV and contain homogeneous and inhomogeneous contributions. This prevented in-depth studies, in contrast to the better-characterized ML materials MoSe₂ and WSe₂. In this work, we show that encapsulation of ML MoS₂ in hexagonal boron nitride can efficiently suppress the inhomogeneous contribution to the exciton linewidth, as we measure in photoluminescence and reflectivity a FWHM down to 2 meV at T = 4 K. Narrow optical transition linewidths are also observed in encapsulated WS₂, WSe₂, and MoSe₂ MLs. This indicates that surface protection and substrate flatness are key ingredients for obtaining stable, high-quality samples. Among the new possibilities offered by the well-defined optical transitions, we measure the homogeneous broadening induced by the interaction with phonons in temperature-dependent experiments. We uncover new information on spin and valley physics and present the rotation of valley coherence in applied magnetic fields perpendicular to the ML.

The valley degree of freedom in two-dimensional (2D) crystals recently emerged as a novel information carrier in addition to spin and charge. The intrinsic valley lifetime in 2D transition metal dichalcogenides (TMD) is expected to be markedly long due to the unique spin-valley locking behavior, where the intervalley scattering of the electron simultaneously requires a large momentum transfer to the opposite valley and a flip of the electron spin. However, the experimentally observed valley lifetime in 2D TMDs has been limited to tens of nanoseconds thus far. We report efficient generation of microsecond-long-lived valley polarization in WSe₂/MoS₂ heterostructures by exploiting the ultrafast charge transfer processes in the heterostructure that efficiently creates resident holes in the WSe₂ layer. These valley-polarized holes exhibit near-unity valley polarization and ultralong valley lifetime: We observe a valley-polarized hole population lifetime of more than 1 μs and a valley depolarization lifetime (that is, intervalley scattering lifetime) of more than 40 μs at 10 K. The near-perfect generation of valley-polarized holes in TMD heterostructures, combined with ultralong valley lifetime, which is orders of magnitude longer than previous results, opens up new opportunities for novel valleytronics and spintronics applications.

Modulated reflectance (contactless electroreflectance (CER), photoreflectance (PR), and piezoreflectance (PzR)) has been applied to study direct optical transitions in bulk MoS₂, MoSe₂, WS₂, and WSe₂. In order to interpret optical transitions observed in CER, PR, and PzR spectra, the electronic band structure for the four crystals has been calculated from the first principles within the density functional theory for various points of Brillouin zone including K and H points. It is clearly shown that the electronic band structure at H point of Brillouin zone is very symmetric and similar to the electronic band structure at K point, and therefore, direct optical transitions at H point should be expected in modulated reflectance spectra besides the direct optical transitions at the K point of Brillouin zone. This prediction is confirmed by experimental studies of the electronic band structure of MoS₂, MoSe₂, WS₂, and WSe₂ crystals by CER, PR, and PzR spectroscopy, i.e., techniques which are very sensitive to critical points of Brillouin zone. For the four crystals besides the A transition at K point, an A_H transition at H point has been observed in CER, PR, and PzR spectra a few tens of meV above the A transition. The spectral difference between A and A_H transition has been found to be in a very good agreement with theoretical predictions. The second transition at the H point of Brillouin zone (B_H transition) overlaps spectrally with the B transition at K point because of small energy differences in the valence (conduction) band positions at H and K points. Therefore, an extra resonance which could be related to the B_H transition is not resolved in modulated reflectance spectra at room temperature for the four crystals.

Inbreeding in hermaphroditic plants can occur through two different mechanisms: biparental inbreeding, when a plant mates with a related individual, or self-fertilization, when a plant mates with itself. To avoid inbreeding, many hermaphroditic plants have evolved self-incompatibility (SI) systems which prevent or limit self-fertilization. One particular SI system—homomorphic SI—can also reduce biparental inbreeding. Homomorphic SI is found in many angiosperm species, and it is often assumed that the additional benefit of reduced biparental inbreeding may be a factor in the success of this SI system. To test this assumption, we developed a spatially-explicit, individual-based simulation of plant populations that displayed three different types of homomorphic SI. We measured the total level of inbreeding avoidance by comparing each population to a self-compatible population (NSI), and we measured biparental inbreeding avoidance by comparing to a population of self-incompatible plants that were free to mate with any other individual (PSI).

Because biparental inbreeding is more common when offspring dispersal is limited, we examined the levels of biparental inbreeding over a range of dispersal distances. We also tested whether the introduction of inbreeding depression affected the level of biparental inbreeding avoidance. We found that there was a statistically significant decrease in autozygosity in each of the homomorphic SI populations compared to the PSI population and, as expected, this was more pronounced when seed and pollen dispersal was limited. However, levels of homozygosity and inbreeding depression were not reduced. At low dispersal, homomorphic SI populations also suffered reduced female fecundity and had smaller census population sizes. Overall, our simulations showed that the homomorphic SI systems had little impact on the amount of biparental inbreeding in the population especially when compared to the overall reduction in inbreeding compared to the NSI population. With further study, this observation may have important consequences for research into the origin and evolution of homomorphic self-incompatibility systems.

Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects. The control and eventual elimination of P. vivax are global health priorities. Genomic research contributes to this objective by improving our understanding of the biology of P. vivax and through the development of new genetic markers that can be used to monitor efforts to reduce malaria transmission. Here we analyze whole-genome data from eight field samples from a region in Cordóba, Colombia where malaria is endemic. We find considerable genetic diversity within this population, a result that contrasts with earlier studies suggesting that P. vivax had limited diversity in the Americas. We also identify a selective sweep around a substitution known to confer resistance to sulphadoxine-pyrimethamine (SP). This is the first observation of a selective sweep for SP resistance in this species. These results indicate that P. vivax has been exposed to SP pressure even when the drug is not in use as a first line treatment for patients afflicted by this parasite. We identify multiple non-synonymous substitutions in three other genes known to be involved with drug resistance in Plasmodium species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America.