Jeremy Brouillet

We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.

High crystallinity GeSn substitutional alloy thin films with up to 8.7 at.% Sn are directly grown on amorphous SiO2 layers at low crystallization temperatures of 370~470 °C for potential applications in 3D electronic-photonic integration on Si as well as inexpensive virtual substrates for tandem solar cells. The optimal Ge0.913Sn0.087 thin film demonstrates a strong (111) texture and an average gain size of 10 μm, and its grain boundaries are mostly twin and low-angle boundaries with low densities of defect recombination centers. The 8.7 at.% Sn incorporated substitutionally into the Ge lattice far exceeds the ~1 at.% equilibrium solubility limit. Correspondingly, the direct band gap is significantly red-shifted from 0.8 eV for pure Ge to ~0.5 eV for crystalline Ge0.913Sn0.087, right at the verge of the indirect-to-direct gap transition that occurs at 8-10 at.% Sn alloying. Optoelectronic properties are greatly enhanced due to this transition.

Tuning the macroscopic dielectric response on demand holds potential for actively tunable metaphotonics and optical devices. In recent years, graphene has been extensively investigated as a tunable element in nanophotonics. Significant theoretical work has been devoted on the tuning the hyperbolic properties of graphene/dielectric heterostructures; however, until now, such a motif has not been demonstrated experimentally. Here we focus on a graphene/polaritonic dielectric metamaterial, with strong optical resonances arising from the polar response of the dielectric, which are, in general, difficult to actively control. By controlling the doping level of graphene via external bias we experimentally demonstrate a wide range of tunability from a Fermi level of E_F=0 eV to E_F=0.5 eV, which yields an effective epsilon-near-zero crossing and tunable dielectric properties, verified through spectroscopic ellipsometry and transmission measurements.

Highly textured Ge 0.91 Sn 0.09 is obtained on both amorphous SiO 2 /Si and glass substrates at low temperatures <475 o C, which shows grain sizes up to tens of microns. Strikingly, the nucleation center spacing ranges from 0.1 to 1 mm, orders of magnitude larger than common solid state crystallization. This observation indicates an exceedingly high grain growth rate vs. a low nucleation rate. Therefore, we can control nucleation sites and fabricate geometrically confined pseudo single crystalline GeSn grain using patterning techniques, including surface Sn dots/patches, local laser annealing, and nanotaper patterns. Another remarkable result is that ~9 at.% Sn is incorporated substitutionally into Ge, far exceeding the equilibrium solubility limit of ~1 at.%. The high Sn composition, together with ~0.24% thermally induced tensile strain in the film, shifts the GeSn direct band gap to ~0.5 eV (2500nm) and converts it into a direct band gap semiconductor with significantly enhanced optoelectronic properties.

We demonstrate pseudo single crystal, direct-band-gap Ge0.89Sn0.11 crystallized on amorphous layers at <450 °C towards 3D Si photonic integration. We developed two approaches to seed the lateral single crystal growth: (1) utilize the Gibbs-Thomson eutectic temperature depression at the tip of an amorphous GeSn nanotaper for selective nucleation; (2) laser-induced nucleation at one end of a GeSn strip. Either way, the crystallized Ge0.89Sn0.11 is dominated by a single grain >18 μm long that forms optoelectronically benign twin boundaries with others grains. These pseudo single crystal, direct-band-gap Ge0.89Sn0.11 patterns are suitable for monolithic 3D integration of active photonic devices on Si.