Transcriptome Assembly and Characterization of the Benthic Annelid Paramphinome jeffreysii

Species of the phylum Annelida have been essential as model organisms in the studies of biology, neurobiology, evolution, ecology, and phylogenomics. Prior work using genomics and transcriptomics has provided new insights into the evolution of Annelida, such as phylogenetic relationships, life history, and lifestyle adaptations. Little biological information is known about the amphinomid Paramphinome jeffreysii. Although transcriptome data have been available since 2014, complete annotations of gene content is not publically available. The objective of this research is to annotate the transcriptome of P. jeffreysii in order to contribute towards a more comprehensive understanding of the biological pathways, cellular components, and molecular functions of the species. Cellular and metabolic processes, as well as biological regulation were among the top biological processes discovered, while binding, catalytic activity, and transporter activity were among the top molecular functions found. The top-hit species included a brachiopod, Lingula anatina, as well as Capitella teleta (second top hit), and several mollusks, highlighting the lack of available comparable annotated data for Amphinomida, and Annelida in general within public databases. Therefore, the continued exploration of transcriptomics in non-model organisms, such as P. jeffreysii, allows for continuing comparative research

First Principles Simulations of Boron Diffusion in Graphite

Boron strongly modifies electronic and diffusion properties of graphite. We report the first ab initio study of boron interaction with the point defects in graphite, which includes structures, thermodynamics, and diffusion. A number of possible diffusion mechanisms of boron in graphite are suggested. We conclude that boron diffuses in graphite by a kick-out mechanism. This mechanism explains the common activation energy, but large magnitude difference, for the rate of boron diffusion parallel and perpendicular to the basal plane. © 2007 The American Physical Society

A symbolic network-based nonlinear theory for dynamical systems observability

EBM and MSB acknowledge the Engineering and Physical Sciences Research Council (EPSRC), grant Ref. EP/I032608/1. ISN acknowledges partial support from the Ministerio de Economía y Competitividad of Spain under project FIS2013-41057-P and from the Group of Research Excelence URJC-Banco de Santander.Peer reviewedPublisher PD

Priority Queue Formulation of Agent-Based Bathtub Model for Network Trip Flows in the Relative Space

Agent-based models have been extensively used to simulate the behavior of travelers in transportation systems because they allow for realistic and versatile modeling of interactions. However, traditional agent-based models suffer from high computational costs and rely on tracking physical locations, raising privacy concerns. This paper proposes an efficient formulation for the agent-based bathtub model (AB2M) in the relative space, where each agent's trajectory is represented by a time series of the remaining distance to its destination. The AB2M can be understood as a microscopic model that tracks individual trips' initiation, progression, and completion and is an exact numerical solution of the bathtub model for generic (time-dependent) trip distance distributions. The model can be solved for a deterministic set of trips with a given demand pattern (defined by the start time of each trip and its distance), or it can be used to run Monte Carlo simulations to capture the average behavior and variation stochastic demand patterns, described by probabilistic distributions of trip distances and departure times. To enhance the computational efficiency, we introduce a priority queue formulation, eliminating the need to update trip positions at each time step and allowing us to run large-scale scenarios with millions of individual trips in seconds. We systematically explore the scaling properties and discuss the introduction of biases and numerical errors. The systematic exploration of scaling properties of the modeling of individual agents in the relative space with the AB2M further enhances its applicability to large-scale transportation systems and opens up opportunities for studying travel time reliability, scheduling, and mode choices

La jurisprudencia del Comite de Libertad Sindical de la Organizacion Internacional del Trabajo ante el caso Chileno entre los anos 1970 y junio 2005.

86 p.La presente investigación tiene por objeto analizar la jurisprudencia del Comité de libertad sindical de la OIT con la finalidad de dar cuenta del estado del principio de libertad sindical en chile entre los años 1970 y junio de 2005. Para alcanzar este fin se acudió al método jurídico deductivo. Del análisis jurisprudencial se obtuvo conceptualizaciones variadas que reflejan la perspectiva del Comité referente a las distintas etapas en que se divide la investigación y además la precaria situación de la libertad sindical, especialmente durante el régimen militar. En fin, la investigación busca ser un aporte para esta disciplina Jurídica en la cual las organizaciones sindicales juegan un rol primordial

Effect of microstructure on the thermal conductivity of disordered carbon

Computational methods are used to control the degree of structural order in a variety of carbonmaterials containing primarily sp2 bonding. Room-temperature thermal conductivities arecomputed using non-equilibrium molecular dynamics. Our results reproduce experimental data foramorphous and glassy carbons and confirm previously proposed structural models for vitreouscarbons. An atomistic model is developed for highly oriented thin films seen experimentally, with amaximum computed thermal conductivity of 35 W m1 K1. This value is much higher than thatof the amorphous and glassy structures, demonstrating that the microstructure influences thethermal conductivity more strongly than the density

A diagnosis of low-order dynamics in the atmosphere of Mars

Introduction: There is considerable evidence that shows that the Martian atmosphere behaves in a more regular fashion than its terrestrial counterpart [1, 2, 3, 4]. This evidence leads to the hypothesis of theMartian climate attractor being of a relatively low dimension, which, in turn, would imply the possibility of describing the state of the atmosphere by means of a relatively few degrees of freedom. We explore this hypothesis by assuming that the atmospheric total energy (TE), i.e. the sum of kinetic energy and total potential energy (gravitational potential energy plus internal energy), is confined in a few coherent structures which dynamically interact nonlinearly with each other

Transient teleconnection event at the onset of a planet-encircling dust storm on Mars

We use proper orthogonal decomposition (POD) to study a transient teleconnection event at the onset of the 2001 planet-encircling dust storm on Mars, in terms of empirical orthogonal functions (EOFs). There are several differences between this and previous studies of atmospheric events using EOFs. First, instead of using a single variable such as surface pressure or geopotential height on a given pressure surface, we use a dataset describing the evolution in time of global and fully three-dimensional atmospheric fields such as horizontal velocity and temperature. These fields are produced by assimilating Thermal Emission Spectrometer observations from NASA's Mars Global Surveyor spacecraft into a Mars general circulation model. We use total atmospheric energy (TE) as a physically meaningful quantity which weights the state variables. Second, instead of adopting the EOFs to define teleconnection patterns as planetary-scale correlations that explain a large portion of long time-scale variability, we use EOFs to understand transient processes due to localised heating perturbations that have implications for the atmospheric circulation over distant regions. The localised perturbation is given by anomalous heating due to the enhanced presence of dust around the northern edge of the Hellas Planitia basin on Mars. We show that the localised disturbance is seemingly restricted to a small number (a few tens) of EOFs. These can be classified as low-order, transitional, or high-order EOFs according to the TE amount they explain throughout the event. Despite the global character of the EOFs, they show the capability of accounting for the localised effects of the perturbation via the presence of specific centres of action. We finally discuss possible applications for the study of terrestrial phenomena with similar characteristics

A comparative study of density functional and density functional tight binding calculations of defects in graphene

The density functional tight binding approach (DFTB) is well adapted for the study of point and line defects in graphene based systems. After briefly reviewing the use of DFTB in this area, we present a comparative study of defect structures, energies and dynamics between DFTB results obtained using the dftb+ code, and density functional results using the localised Gaussian orbital code, AIMPRO. DFTB accurately reproduces structures and energies for a range of point defect structures such as vacancies and Stone-Wales defects in graphene, as well as various unfunctionalised and hydroxylated graphene sheet edges. Migration barriers for the vacancy and Stone-Wales defect formation barriers are accurately reproduced using a nudged elastic band approach. Finally we explore the potential for dynamic defect simulations using DFTB, taking as an example electron irradiation damage in graphene

Graphene edge structures: Folding, scrolling, tubing, rippling and twisting

Conventional three-dimensional crystal lattices are terminated by surfaces, which can demonstrate complex rebonding and rehybridisation, localised strain and dislocation formation. Two dimensional crystal lattices, of which graphene is the archetype, are terminated by lines. The additional available dimension at such interfaces opens up a range of new topological interface possibilities. We show that graphene sheet edges can adopt a range of topological distortions depending on their nature. Rehybridisation, local bond reordering, chemical functionalisation with bulky, charged, or multi-functional groups can lead to edge buckling to relieve strain, folding, rolling and even tube formation. We discuss the topological possibilities at a 2D graphene edge, and under what circumstances we expect different edge topologies to occur. Density functional calculations are used to explore in more depth different graphene edge types.Comment: Additional figure in published versio