Localization of interacting electrons in quantum dot arrays driven by an ac-field

We investigate the dynamics of two interacting electrons moving in a one-dimensional array of quantum dots under the influence of an ac-field. We show that the system exhibits two distinct regimes of behavior, depending on the ratio of the strength of the driving field to the inter-electron Coulomb repulsion. When the ac-field dominates, an effect termed coherent destruction of tunneling occurs at certain frequencies, in which transport along the array is suppressed. In the other, weak-driving, regime we find the surprising result that the two electrons can bind into a single composite particle -- despite the strong Coulomb repulsion between them -- which can then be controlled by the ac-field in an analogous way. We show how calculation of the Floquet quasienergies of the system explains these results, and thus how ac-fields can be used to control the localization of interacting electron systems.Comment: 7 pages, 6 eps figures V2. Minor changes, this version to be published in Phys. Rev.

On distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes

Automated genome annotation is essential for extracting biological information from sequence data. The identification and annotation of tRNA genes is frequently performed by the software package tRNAscan-SE, the output of which is listed for selected genomes in the Genomic tRNA database (GtRNAdb). Here, we highlight a pervasive error in prokaryotic tRNA gene sets on GtRNAdb: the miscategorization of partial, non-canonical tRNA genes as standard, canonical tRNA genes. Firstly, we demonstrate the issue using the tRNA gene sets of 20 organisms from the archaeal taxon Thermococcaceae. According to GtRNAdb, these organisms collectively deviate from the expected set of tRNA genes in 15 instances, including the listing of eleven putative canonical tRNA genes. However, after detailed manual annotation, only one of these eleven remains; the others are either partial, noncanonical tRNA genes resulting from the integration of genetic elements or CRISPR-Cas activity (seven instances), or attributable to ambiguities in input sequences (three instances). Secondly, we show that similar examples of the mis-categorization of predicted tRNA sequences occur throughout the prokaryotic sections of GtRNAdb. While both canonical and non-canonical prokaryotic tRNA gene sequences identified by tRNAscan-SE are biologically interesting, the challenge of reliably distinguishing between them remains. We recommend employing a combination of (i) screening input sequences for the genetic elements typically associated with non-canonical tRNA genes, and ambiguities, (ii) activating the tRNAscan-SE automated pseudogene detection function, and (iii) scrutinizing predicted tRNA genes with low isotype scores. These measures greatly reduce manual annotation efforts, and lead to improved prokaryotic tRNA gene set predictions

On distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes

Automated genome annotation is essential for extracting biological information from sequence data. The identification and annotation of tRNA genes is frequently performed by the software package tRNAscan-SE, the output of which is listed for selected genomes in the Genomic tRNA database (GtRNAdb). Here, we highlight a pervasive error in prokaryotic tRNA gene sets on GtRNAdb: the miscategorization of partial, non-canonical tRNA genes as standard, canonical tRNA genes. Firstly, we demonstrate the issue using the tRNA gene sets of 20 organisms from the archaeal taxon Thermococcaceae. According to GtRNAdb, these organisms collectively deviate from the expected set of tRNA genes in 15 instances, including the listing of eleven putative canonical tRNA genes. However, after detailed manual annotation, only one of these eleven remains; the others are either partial, noncanonical tRNA genes resulting from the integration of genetic elements or CRISPR-Cas activity (seven instances), or attributable to ambiguities in input sequences (three instances). Secondly, we show that similar examples of the mis-categorization of predicted tRNA sequences occur throughout the prokaryotic sections of GtRNAdb. While both canonical and non-canonical prokaryotic tRNA gene sequences identified by tRNAscan-SE are biologically interesting, the challenge of reliably distinguishing between them remains. We recommend employing a combination of (i) screening input sequences for the genetic elements typically associated with non-canonical tRNA genes, and ambiguities, (ii) activating the tRNAscan-SE automated pseudogene detection function, and (iii) scrutinizing predicted tRNA genes with low isotype scores. These measures greatly reduce manual annotation efforts, and lead to improved prokaryotic tRNA gene set predictions

On distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes

Automated genome annotation is essential for extracting biological information from sequence data. The identification and annotation of tRNA genes is frequently performed by the software package tRNAscan-SE, the output of which is listed for selected genomes in the Genomic tRNA database (GtRNAdb). Here, we highlight a pervasive error in prokaryotic tRNA gene sets on GtRNAdb: the mis-categorization of partial, non-canonical tRNA genes as standard, canonical tRNA genes. Firstly, we demonstrate the issue using the tRNA gene sets of 20 organisms from the archaeal taxon Thermococcaceae. According to GtRNAdb, these organisms collectively deviate from the expected set of tRNA genes in 15 instances, including the listing of eleven putative canonical tRNA genes. However, after detailed manual annotation, only one of these eleven remains; the others are either partial, non-canonical tRNA genes resulting from the integration of genetic elements or CRISPR-Cas activity (seven instances), or attributable to ambiguities in input sequences (three instances). Secondly, we show that similar examples of the mis-categorization of predicted tRNA sequences occur throughout the prokaryotic sections of GtRNAdb. While both canonical and non-canonical prokaryotic tRNA gene sequences identified by tRNAscan-SE are biologically interesting, the challenge of reliably distinguishing between them remains. We recommend employing a combination of (i) screening input sequences for the genetic elements typically associated with non-canonical tRNA genes, and ambiguities, (ii) activating the tRNAscan-SE automated pseudogene detection function, and (iii) scrutinizing predicted tRNA genes with low isotype scores. These measures greatly reduce manual annotation efforts, and lead to improved prokaryotic tRNA gene set predictions

The Geology of Western Ireland: A Record of the ‘Birth’ and ‘Death’ of the Iapetus Ocean

This chapter reviews the evidence found in the remarkable and varied geology of western Ireland (Fig. 1) for the opening and the closing of the Iapetus Ocean adjacent to the Laurentian margin. The geology visited is briefly reviewed along with a short summary of its likely tectonic significance

Sinopse das espécies nativas e subespontâneas de Andropogoneae Dumort. (Poaceae) na Ilha de Santa Catarina, Brasil A synopsis of the Andropogoneae Dumort. (Poaceae) native and subspontaneous to the Island of Santa Catarina, Florianópolis, SC, Brazil

O presente trabalho consiste no levantamento dos táxons da tribo Andropogoneae (Panicoideae - Poaceae) ocorrentes na Ilha de Santa Catarina, Florianópolis, Brasil. A partir da revisão de materiais de herbários e coletas a campo foi confirmada a ocorrência de 10 gêneros e 20 espécies, 17 nativas e duas subespontâneas: Andropogon L. (7 spp.), Bothriochloa Kuntze (2), Eriochrysis P. Beauv. (1), Hyparrhenia Andersson ex E. Fourn. (1), Imperata Cirillo (1), Ischaemum L. (1), Rhytachne Desv. (1), Saccharum L. (3), Schizachyrium Nees (2) e Sorghum Moench (1). Os gêneros Bothriochloa e Rhytachne são registrados pela primeira vez para a Ilha de Santa Catarina. São apresentadas chaves de identificação para gêneros e espécies, ilustrações, informações sobre distribuição geográfica, habitat, período de floração e comentários para cada táxon.<br>The present work is a survey of the taxa in the tribe Andropogoneae (Panicoideae - Poaceae) that occur on the Island of Santa Catarina, Florianópolis, Brazil. Based on a review of herbarium specimens and fieldwork, 20 species were recorded in the following 10 genera: Andropogon L. (7 spp.), Bothriochloa Kuntze (2), Eriochrysis P. Beauv. (1), Hyparrhenia Andersson ex E. Fourn. (1), Imperata Cirillo (1), Ischaemum L. (1), Rhytachne Desv. (1), Saccharum L. (3), Schizachyrium Nees (2) and Sorghum Moench (1). Seventeen of the species are native, and two species are subspontaneous. Bothriochloa and Rhytachne are recorded here, for the first time, for the Island of Santa Catarina. This work provides key to the genera and species, as well as illustrations, information about geographic distribution, habitat, phenology, and comments about each taxon presented in the study