Electromagnetic properties of anisotropic plasmonic metamaterials

In this dissertation we study the electromagnetic properties of plasmonic metamaterials. We develop an analytical description to solve the fundamental problem of free-space scattering in planar plasmonic systems by utilizing anisotropic metamaterials. We show with exact numerical simulations that these manufactured materials do completely eliminate the scattering, and even in the case of fabrication defects the scattering is greatly minimized. We further show that the standard effective medium theory calculations for the cases of anisotropic metamaterials constructed of metal-dielectric layers fails to account for nonlocal effects in the cases where the constituent materials have large differences in permittivity. We show how it is possible to construct a plasmon waveguide out of such a structure and describe a new naming scheme based on the bulk plasmon modes that are supported. Finally, we study the effective medium theory applied to the case of plasmonic wires embedded in a dielectric host. We describe the effect the geometric properties of the structure has on effective permittivities. For example, we show that a 10% stretching/compression of the distance between nanowires can change the sign of elements of the permittivity tensor. These results can be applied to high-performance optical sensing, optical polarizers, novel lenses including the hyper- and superlenses, and subdiffraction imaging

The Plant Ontology facilitates comparisons of plant development stages across species

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution

Renormalization Group Approach to Interacting Fermions

The stability of nonrelativistic fermionic systems to interactions is studied within the Renormalization Group framework. A brief introduction to $\phi^4$ theory in four dimensions and the path integral formulation for fermions is given. The strategy is as follows. First, the modes on either side of the Fermi surface within a cut-off $\Lambda$ are chosen and a path integral is written to describe them. An RG transformation which eliminates a part of these modes, but preserves the action of the noninteracting system is identified. Finally the possible perturbations of this free-field fixed point are classified as relevant, irrelevant or marginal. A $d=1$ warmup calculation involving a system of fermions shows how, in contrast to mean-field theory, the RG correctly yields a scale invariant system (Luttinger liquid) In $d=2$ and 3, for rotationally invariant Fermi surfaces, {\em automatically} leads to Landau's Fermi liquid theory, which appears as a fixed point characterized by an effective mass and a Landau function $F$, with the only relevant perturbations being of the superconducting (BCS) type The functional flow equations for the BCS couplings are derived and separated into an infinite number of flows, one for each angular momentum. It is shown that similar results hold for rotationally non-invariant (but time-reversal invariant) Fermi surfaces also, A study of a nested Fermi surface shows an additional relevant flow leading to charge density wave formation. For small $\Lambda / K_F$, a 1/N expansion emerges, with $N = K_F/ \Lambda$, which explains why one is able to solve the narrow cut-off theory. The search for non-Fermi liquids in $d=2$Comment: 191 pages, Latex, Yale, July 1993; 18 EPS figures appende

The Gene Ontology knowledgebase in 2023

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

FragariaCyc: A metabolic pathway database for woodland strawberry Fragaria vesca

FragariaCyc is a strawberry-specific cellular metabolic network based on the annotated genome sequence of Fragaria vesca L. ssp. vesca, accession Hawaii 4. It was built on Pathway-Tools platform using MetaCyc as the reference. The experimental evidences from published literature were used for supporting/editing existing entities and for the addition of new pathways, enzymes, reactions, compounds, and small molecules in the database. To date, FragariaCyc comprises 66 super-pathways, 488 unique pathways, 2,348 metabolic reactions, 3,507 enzymes, and 2,134 compounds. In addition to searching and browsing FragariaCyc, researchers can compare pathways across various plant metabolic networks and analyze their data using Omics Viewer tool. We view FragariaCyc as a resource for the community of researchers working with strawberry and related fruit crops. It can help understanding the regulation of overall metabolism of the strawberry plant during development and in response to diseases and abiotic stresses. FragariaCyc is available online at http://pathways.cgrb.oregonstate.edu