Lattice Engineering with Surface Acoustic Waves

Quantum simulators are special purpose quantum computers designed to examine problems that are impossible to test with classical computers. They can be used to simulate problems in atomic physics, condensed matter physics, cosmology, high energy physics, nuclear physics and quantum chemistry, among other topics. In condensed matter physics, the simulators are composed of particles and a lattice structure containing the particles. This thesis considers the use of exciton-polaritons as particles and surface acoustic waves to form the lattice potential. Exciton-polaritons are quasiparticles formed by the coherent mixture of photons and excitons in a semiconductor, with properties that are a combination of both components. Lattices of exciton-polaritons can be made by controlling the potential landscape for either the excitons or the photons. This thesis covers two main topics: Surface acoustic waves are mechanical waves that propagate along the surface of a material. They can be simply generated via the inverse piezoelectric effect with interdigital transducers (IDTs) and can be designed to operate at frequencies, from several MHz to several GHz. They modulate the bandgap of the underlying material through the strain field that they carry, which can be used to trap excitons. The formation of potential landscapes for exciton-polaritons with surface acoustic waves has been demonstrated by another group, although their lattices were limited in scope. 1) I designed IDT layouts used to produce lattices that have not been previously demonstrated with surface acoustic waves. Numerical calculations were used to verify the validity of the design. Several pieces of test equipment both for the electrical and optical measurements were designed and built. 2) The designed devices were fabricated using both electron-beam and optical lithography and the quality of the resulting IDTs was quantified by S-parameter measurements. Observation of the lattices formed by the designed devices and the next steps required in implementing a quantum simulator are discussed

Structural Characterization of Pandoraea pnomenusa B-356 Biphenyl Dioxygenase Reveals Features of Potent Polychlorinated Biphenyl-Degrading Enzymes

The oxidative degradation of biphenyl and polychlorinated biphenyls (PCBs) is initiated in Pandoraea pnomenusa B-356 by biphenyl dioxygenase $(BPDO_{B356})$. $BPDO_{B356}$, a heterohexameric $(αβ)_3$ Rieske oxygenase (RO), catalyzes the insertion of dioxygen with stereo- and regioselectivity at the 2,3-carbons of biphenyl, and can transform a broad spectrum of PCB congeners. Here we present the X-ray crystal structures of $BPDO_{B356}$ with and without its substrate biphenyl 1.6-Å resolution for both structures. In both cases, the Fe(II) has five ligands in a square pyramidal configuration: H233 Nε2, H239 Nε2, D386 Oδ1 and Oδ2, and a single water molecule. Analysis of the active sites of $BPDO_{B356}$ and related ROs revealed structural features that likely contribute to the superior PCB-degrading ability of certain BPDOs. First, the active site cavity readily accommodates biphenyl with minimal conformational rearrangement. Second, M231 was predicted to sterically interfere with binding of some PCBs, and substitution of this residue yielded variants that transform 2,2′-dichlorobiphenyl more effectively. Third, in addition to the volume and shape of the active site, residues at the active site entrance also apparently influence substrate preference. Finally, comparison of the conformation of the active site entrance loop among ROs provides a basis for a structure-based classification consistent with a phylogeny derived from amino acid sequence alignments

Curation of characterized glycoside hydrolases of Fungal origin

Fungi produce a wide range of extracellular enzymes to break down plant cell walls, which are composed mainly of cellulose, lignin and hemicellulose. Among them are the glycoside hydrolases (GH), the largest and most diverse family of enzymes active on these substrates. To facilitate research and development of enzymes for the conversion of cell-wall polysaccharides into fermentable sugars, we have manually curated a comprehensive set of characterized fungal glycoside hydrolases. Characterized glycoside hydrolases were retrieved from protein and enzyme databases, as well as literature repositories. A total of 453 characterized glycoside hydrolases have been cataloged. They come from 131 different fungal species, most of which belong to the phylum Ascomycota. These enzymes represent 46 different GH activities and cover 44 of the 115 CAZy GH families. In addition to enzyme source and enzyme family, available biochemical properties such as temperature and pH optima, specific activity, kinetic parameters and substrate specificities were recorded. To simplify comparative studies, enzyme and species abbreviations have been standardized, Gene Ontology terms assigned and reference to supporting evidence provided. The annotated genes have been organized in a searchable, online database called mycoCLAP (Characterized Lignocellulose-Active Proteins of fungal origin). It is anticipated that this manually curated collection of biochemically characterized fungal proteins will be used to enhance functional annotation of novel GH genes

mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support

Enzymes active on components of lignocellulosic biomass are used for industrial applications ranging from food processing to biofuels production. These include a diverse array of glycoside hydrolases, carbohydrate esterases, polysaccharide lyases and oxidoreductases. Fungi are prolific producers of these enzymes, spurring fungal genome sequencing efforts to identify and catalogue the genes that encode them. To facilitate the functional annotation of these genes, biochemical data on over 800 fungal lignocellulose-degrading enzymes have been collected from the literature and organized into the searchable database, mycoCLAP (http://mycoclap.fungalgenomics.ca). First implemented in 2011, and updated as described here, mycoCLAP is capable of ranking search results according to closest biochemically characterized homologues: this improves the quality of the annotation, and significantly decreases the time required to annotate novel sequences. The database is freely available to the scientific community, as are the open source applications based on natural language processing developed to support the manual curation of mycoCLAP. Database URL: http://mycoclap.fungalgenomics.ca

Identification of a conserved transcriptional activator-repressor module controlling the expression of genes involved in tannic acid degradation and gallic acid utilization in aspergillus niger

Microbial Biotechnolog

Carbohydrate esterase family 16 contains fungal hemicellulose acetyl esterases (HAEs) with varying specificity

Acetyl esterases are an important component of the enzymatic machinery fungi use to degrade plant biomass and are classified in several Carbohydrate Esterase families of the CAZy classification system. Carbohydrate Esterase family 16 (CE16) is one of the more recently discovered CAZy families, but only a small number of its enzyme members have been characterized so far, revealing activity on xylan-derived oligosaccharides, as well as activity related to galactoglucomannan. The number of CE16 genes differs significantly in the genomes of filamentous fungi. In this study, four CE16 members were identified in the genome of Aspergillus niger NRRL3 and it was shown that they belong to three of the four phylogenetic Clades of CE16. Significant differences in expression profiles of the genes and substrate specificity of the enzymes were revealed, demonstrating the diversity within this family of enzymes. Detailed characterization of one of these four A. niger enzymes (HaeA) demonstrated activity on oligosaccharides obtained from acetylated glucuronoxylan, galactoglucomannan and xyloglucan, thus establishing this enzyme as a general hemicellulose acetyl esterase. Their broad substrate specificity makes these enzymes highly interesting for biotechnological applications in which deacetylation of polysaccharides is required.Peer reviewe

Screening of novel fungal Carbohydrate Esterase family 1 enzymes identifies three novel dual feruloyl/acetyl xylan esterases

Feruloyl esterases (FAEs) and acetyl xylan esterases (AXEs) are important enzymes for plant biomass degradation and are both present in Carbohydrate Esterase family 1 (CE1) of the Carbohydrate-Active enZymes database. In this study, ten novel fungal CE1 enzymes from different subfamilies were heterologously produced and screened for their activity towards model and complex plant biomass substrates. CE1_1 enzymes possess AXE activity, while CE1_5 enzymes showed FAE activity. Two enzymes from CE1_2 and one from CE1_5 possess dual feruloyl/acetyl xylan esterase (FXE) activity, showing expansion of substrate specificity. The new FXEs from CE1 can efficiently release both feruloyl and acetyl residues from feruloylated xylan, making them particularly interesting novel components of industrial enzyme cocktails for plant biomass degradation

Two-kind boson mixture honeycomb Hamiltonian of Bloch exciton-polaritons

H.P., M.P., and N.Y.K. are supported by Industry Canada and the Ontario Ministry of Research & Innovation through Early Researcher Awards. This research was undertaken thanks in part to funding from the Canada First Research Excellence Fund (CFREF). H.P. thanks Z. Xie for the travel support to visit IQC. M.P. is a recipient of the Richard and Elizabeth Master Graduate Entrance Scholarship and Natural Sciences and Engineering Research Council (NSERC) Canada Graduate Scholarships-Master’s Program. K.W., A.S., M.M., M.K., S.K., C.S., and S.H. received support from the State of Bavaria.The electronic band structure of a solid is a collection of allowed bands separated by forbidden bands, revealing the geometric symmetry of the crystal structures. Comprehensive knowledge of the band structure with band parameters explains intrinsic physical, chemical, and mechanical properties of the solid. Here we report the artificial polaritonic band structures of two-dimensional honeycomb lattices for microcavity exciton-polaritons using GaAs semiconductors in the wide-range detuning values, from cavity photonlike (red-detuned) to excitonlike (blue-detuned) regimes. In order to understand the experimental band structures and their band parameters, such as gap energies, bandwidths, hopping integrals, and density of states, we originally establish a polariton band theory within an augmented plane wave method with two-kind bosons, cavity photons trapped at the lattice sites, and freely moving excitons. In particular, this two-kind band theory is absolutely essential to elucidate the exciton effect in the band structures of blue-detuned exciton-polaritons, where the flattened excitonlike dispersion appears at larger in-plane momentum values captured in our experimental access window. We reach an excellent agreement between theory and experiments in all detuning values.Publisher PDFPeer reviewe

Semantic text mining support for lignocellulose research

Biofuels produced from biomass are considered to be promising sustainable alternatives to fossil fuels. The conversion of lignocellulose into fermentable sugars for biofuels production requires the use of enzyme cocktails that can efficiently and economically hydrolyze lignocellulosic biomass. As many fungi naturally break down lignocellulose, the identification and characterization of the enzymes involved is a key challenge in the research and development of biomass-derived products and fuels. One approach to meeting this challenge is to mine the rapidly-expanding repertoire of microbial genomes for enzymes with the appropriate catalytic properties. Semantic technologies, including natural language processing, ontologies, semantic Web services and Web-based collaboration tools, promise to support users in handling complex data, thereby facilitating knowledge-intensive tasks. An ongoing challenge is to select the appropriate technologies and combine them in a coherent system that brings measurable improvements to the users. We present our ongoing development of a semantic infrastructure in support of genomics-based lignocellulose research. Part of this effort is the automated curation of knowledge from information on fungal enzymes that is available in the literature and genome resources. Working closely with fungal biology researchers who manually curate the existing literature, we developed ontological natural language processing pipelines integrated in a Web-based interface to assist them in two main tasks: mining the literature for relevant knowledge, and at the same time providing rich and semantically linked information