Coherent electron-phonon coupling and polaron-like transport in molecular wires

We present a technique to calculate the transport properties through one-dimensional models of molecular wires. The calculations include inelastic electron scattering due to electron-lattice interaction. The coupling between the electron and the lattice is crucial to determine the transport properties in one-dimensional systems subject to Peierls transition since it drives the transition itself. The electron-phonon coupling is treated as a quantum coherent process, in the sense that no random dephasing due to electron-phonon interactions is introduced in the scattering wave functions. We show that charge carrier injection, even in the tunneling regime, induces lattice distortions localized around the tunneling electron. The transport in the molecular wire is due to polaron-like propagation. We show typical examples of the lattice distortions induced by charge injection into the wire. In the tunneling regime, the electron transmission is strongly enhanced in comparison with the case of elastic scattering through the undistorted molecular wire. We also show that although lattice fluctuations modify the electron transmission through the wire, the modifications are qualitatively different from those obtained by the quantum electron-phonon inelastic scattering technique. Our results should hold in principle for other one-dimensional atomic-scale wires subject to Peierls transitions.Comment: 21 pages, 8 figures, accepted for publication in Phys. Rev. B (to appear march 2001

Natural history specimens collected and/or identified and deposited.

Natural history specimen data collected and/or identified by K. Samanta Orellana, <a href="https://orcid.org/0000-0002-4098-5823">https://orcid.org/0000-0002-4098-5823</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>

Growth and Evolution of the Symbiota Portal Network

Symbiota is empowering biodiversity collections communities across the globe to efficiently manage and mobilize their data. Beginning with only a handful of collections in two major portals in the early 2010s (Gries et al. 2014), Symbiota now acts as the primary content management system for over 1,000 collections in more than 50 portals. Over 1,800 collections share data through Symbiota portals, constituting over 90+ million records and 42+ million images. The iDigBio Symbiota Support Hub, a team and cyberinfrastructure based out of Arizona State University and supported by the United States (U.S.) National Science Foundation, hosts 52 Symbiota portals and provides daily help and resources to all Symbiota user communities. The Symbiota codebase is being actively developed in collaboration with several funded projects, including the U.S. National Ecological and Observatory Network (NEON), to support new data types and connections, such as between Symbiota portals and other collections management systems, and to other resources (e.g., Index Fungorum, Global Registry of Scientific Collections, Bionomia, Environmental Data Initiative). Because the Symbiota codebase is open source and shared among portals, new developments in any portal empower the entire network. Here we describe recent expansions of the Symbiota network, including new portals, collaborations, functionalities, and sustainability actions. We look forward to building further collaborations with diverse, international collections data communities

Taxonomic Curation in a Multi-taxa Symbiota Portal

Symbiota is an open-source software that allows the creation of online portals for accessing, managing, and mobilizing biodiversity data (Gries et al. 2014, Symbiota Support Hub 2021). Most of the portals are focused on communities with specific taxonomic interests, which often allows the construction of specialized taxonomic thesauri by portal managers (Gilbert et al. 2020, Pearson 2021a). A portal dedicated to the full range of collections in one country (Portal de Biodiversidad de Guatemala 2022) has represented an interesting challenge for taxonomic management. The Guatemala Biodiversity portal currently allows the digitization and active management of 29 natural history collections in this country, including collections of vertebrates, invertebrates, plants, fungi, lichens, and fossils. Additionally, two institutional observation collections are live managed within the portal (Orellana et al. 2022). This brings up the need to have a suitable taxonomic thesaurus that serves all the collection managers involved. Similar to other Symbiota portals, the Guatemala Biodiversity portal facilitates the incorporation of external catalogs such as Catalog of Life (Bánki et al. 2022), and the World Register of Marine Species (WoRMS Editorial Board 2022), resources which could easily constitute the base of the taxonomic thesaurus of the portal. However, due to the regional focus of this site, it is not ideal to add all the species available in these virtual catalogs. A partial solution has been importing snapshot collections with Guatemalan records from different Symbiota portals, or from the Global Biodiversity Information Facility (GBIF.org 2022). This approach takes advantage of the specimens identified by specialists in different collections around the world, and the taxonomic cleaning tools available in Symbiota portals (Pearson 2021b) allow the curation of the scientific names.Nevertheless, these automated tools are often not enough to maintain the taxonomic thesaurus in understudied regions, such as Guatemala, and the manual curation of species names is still necessary. The curation of the taxonomic thesaurus in this portal is a work in progress, and we are achieving this with the creation of curated checklists within the portal (Orellana 2022, Pearson and Walker 2021), with the incorporation of names in published catalogs (Cano 2006, Cano and Schuster 2012, Camacho et al. 2022), and with the curation of the available names according to institutional catalogs (CECON 2022). Additional information about the conservation status of the species is being added to the taxon profile pages, attaching recent data provided by the Red List of the International Union for Conservation of Nature and publications by local researchers (IUCN 2021, Elías et al. 2022). The availability of a regional curated taxonomic thesaurus in the Guatemala Biodiversity portal is still limited and restricted to groups like vertebrates and certain groups of insects, yet this online resource is useful for researchers who are working in local collections or are compiling information to publish new catalogs and checklists for Guatemala. Continuing with the improvement of this taxonomic resource is necessary not only to advance the knowledge of the biodiversity of Guatemala but to aggregate this information into relevant global catalogs

Leveraging the Symbiota Support Hub for Biodiversity Data Mobilization

Symbiota is an open source software for managing and mobilizing biodiversity data from physical and virtual collections. Over 700 natural history collections use Symbiota as their primary content management system, and over 600 additional collections use Symbiota portals to mobilize a copy or subsamples of their data for use by specific communities of expertise. For both "live-managed" and "snapshot" collections, Symbiota provides data import, export, and publishing tools to lower data mobilization barriers. For example, collections in Symbiota portals can publish their data directly to the Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio) using Darwin Core Archive protocols for data sharing, obviating the need to install or host local Integrated Publishing Toolkit (IPT) instances. Over 150 institutions currently use this workflow to publish datasets to GBIF. The strengths of Symbiota's approach to mobilization are part technical and part social. Once a collection has data in a portal, using the portal’s built-in data mobilization tools requires little technical expertise, and Symbiota portal managers are typically very accessible and helpful in assisting with the process. With sustained funding of the iDigBio Symbiota Support Hub, we are increasing the capacity of Symbiota to mobilize biodiversity through (1) improved documentation regarding the data mobilization process (https://symbiota.org/docs); (2) increased capacity for individualized attention to users through a larger service team and a robust help desk system; (3) the launch of "Portal Advancement Campaigns"—targeted efforts to promote data quality and mobilization (e.g., publishing to data aggregators); and (4) the development of an API infrastructure to enhance data interoperability and accessibility. We provide an overview of these new technologies and services for promoting and assisting with data mobilization, and we discuss future developments

Symbiota Integrations: Exploration of Historical and Current Methods of Data Sharing Across a Decentralized Portal Network and Goals of Extending Interoperability Globally

Over the last decade, the Symbiota open-source software has been readily available to establish occurrence-based data portals that represent the taxonomic and geographic expertise of a specific community of researchers. Reasons for establishing a data portal vary, but often focus on:data mobilization via the creation of public data access points (e.g., in-house search and export tools, Application Programming Interface (API) access, publication tools pushing data up to aggregators);tools and workflows that support active specimen digitization projectsa method for staging and preparing datasets for analysis to answer specific research questions (e.g., data assessment, correction, augmentation).The software functions as a Content Management System (CMS) allowing any dataset to be collaboratively augmented, modified, and managed online. Currently, the software provides support for over 1000 collection datasets to manage their specimen data directly within a Symbiota portal as a live managed dataset. Portals often include “snapshot” data imported from externally managed systems, which are updated on a regular schedule. Depending on the goals of a project, portals will vary in the composition of live to snapshot collections, though most contain a mixture of both. In this respect, data portals serve as intermediate aggregators, integrating multiple specimen datasets that collectively represent a community-based research perspective.Symbiota portals typically function as mid-level data aggregators that are community driven by a group of researchers with expertise within a specific taxonomic domain. This decentralized approach has been shown to promote the emergence of multiple regionally, taxonomically, or institutionally localized, self-identifying communities of practice. Each community is empowered to control the social and informational design and versioning of their local data infrastructures and signals. The upfront cost of decentralization is more than offset by the long-term benefit of achieving sustained expert engagement, higher-quality data products, and ultimately more societal impact for biodiversity data.In contrast to the vision of pushing data from the source to the global aggregators and ultimately out to the research community, Symbiota records are distributed across a growing array of sub-aggregators. For instance, Arizona State University Vascular Plant Herbarium's specimen data consist of a live managed dataset within SEINet with subsets of their data pushed out to the Portal de Biodiversidad de Guatemala and the Cooperative Taxonomic Resource for American Myrtaceae Symbiota portals as snapshot record sets. Not only does this support research associated with each of the portal communities, it exposes the records to researchers with local and taxonomic expertise to review, correct, and comment on the occurrence data. While the Symbiota portals provide tools for these communities to annotate the distributed snapshot records, the annotations need to be directed back to the source collection. Aside from the technical challenges, there are social negotiations that need to be considered. Collection managers might not want to integrate external edits, or the collection might be understaffed without anyone to approve the information transfer. Issues associated with “round-tripping” back to the source are complicated. Nevertheless, global coordination is feasible through automatable data sharing agreements that enable efficient propagation and translation of biodiversity data across communities.Within this presentation, we will explore ways specimen and annotation data have been shared across the Symbiota portal network, as well as the associated technical and social challenges we have encountered. We will also present recent enhancements in tracking project metadata, data provenance, record annotations, and the establishment of a public API architecture. These developments are leveraged to regulate machine-to-machine annotation propagation to enhance interoperability by providing support for real-time transmission of occurrence annotations across the distributed network of Symbiota portals. By demonstrating methods and challenges associated with data sharing across the Symbiota portal network, we strive to contribute to the global discussion of data sharing, but more importantly, solicit input and direction from the greater community on how we can improve data sharing beyond the Symbiota network