Lumping Of Species Research Articles

Entropy production and lumping of species can effectively reduce complex cell signaling pathways

A complicated issue in many cell signaling pathways is mainly related to the number of state variables and parameters. This is computationally very expensive, it may sometimes difficult to predict their model dynamics. Such problems in cell signaling pathways can be simplified and analyzed easily based on model reduction approaches. In this work, we suggest a model reduction technique based on entropy production analysis and lumping of isolated species. The proposed approach provides an improvement in the field of cell signaling pathways. We apply this technique to minimize the number of reactions and elements for the elongation factors EF–Tu and EF–Ts pathways. Computational simulations are computed for the given initial values and parameters. The results provide accuracy and important agreement between the original and reduced models. More interestingly, the model approaches here may apply to a variety of complex cell signaling networks and may use for theoretical and practical purposes.

Novel splitting/lumping index reflects the history of species concepts applied to bumblebees (Insecta: Apidae)

AbstractSplitting or lumping of species is a concern because of its potential confounding effect on comparisons of biodiversity and on conservation assessments. By comparing global lists of species reported by previous authors to lists of the presently recognized species that were known to those authors, a simple ratio can be used to describe their relative splitting or lumping of species. One group of ‘model’ organisms claimed for the study of what species are and how to recognize them is bumblebees. A comparison of four bumblebee subgenera shows: (1) an early phase (up to and including 1931) showing splitting, in which taxonomy was dominated by a typological concept of invariant species with heavy reliance on colour-pattern characters; (2) a middle phase (1935–98) showing lumping, associated with a shift to a polytypic concept of species emphasizing morphological characters, often justified with an interbreeding concept of species, but only rarely associated directly with process-related characters; and (3) a recent phase (after 2000), using a concept of species as evolutionarily independent lineages, as evidenced by corroboration from integrative assessment, usually including evidence for coalescents of species in fast-evolving genes compared with morphology. Analysis of splitting or lumping should help to improve biodiversity comparisons and conservation.

Including analytically reduced chemistry (ARC) in CFD applications

Reacting numerical simulations today are often based on either fitted global reaction schemes, comprised of a few empirical reactions, or pre-tabulated laminar flame solutions computed with detailed chemistry. Although both methods can accurately predict global quantities such as laminar flame speed and burnt gas composition, they have significant limitations. In particular, neither are able to directly and adequately describe the complexity of pollutant chemistry. In the context of reducing harmful emissions of the next generation of aeronautical combustors, however, including these needed additional kinetic details in combustion simulations is becoming essential. Direct integration of detailed chemistry in accurate turbulent combustion models is not a viable option in the foreseeable future, because of excessive computational demands and numerical stiffness. In this context, Analytically Reduced Chemistry (ARC) represents an attractive compromise between accuracy and efficiency, and is already employed in relatively complex Direct Numerical Simulations (DNS) and Large Eddy Simulations (LES). ARCs are knowledge-based compact mechanisms retaining only the most relevant kinetic information as extracted directly, and without fitting, from detailed chemical models using specialized reduction techniques (important species identification through graph search, lumping of species with similar features, short-living species identification, etc.). In recent years, several multi-step efficient and automated reduction tools have been developed, enabling the easy generation of ARCs with minimum input and knowledge from the user. The main objective of this paper is to present a review of ARCs for fuels ranging from methane to aviation kerosene surrogates, recently derived with such a multi-step automated reduction tool: YARC. Information about the applicability and range of validity of each derived mechanism are given, along with further references. Each one was specifically derived to be convenient to use in CFD; in particular, the stiffness was regarded as a key factor and the final number of transported species never exceeds thirty. In a final section, the great potential of the methodology is illustrated in a multi-phase, reactive LES application where the fuel is a real multi-component transportation fuel. To that end, an ARC based on a Jet A described by the novel Hybrid Chemistry (HyChem) approach is coupled with the Dynamically Thickened Flame LES (DTFLES) model and directly integrated into the LES solver AVBP. A Lagrangian spray description is used. Results are compared to experimental data in terms of temperature and major species (CO2, H2O, CO, NO) mass fractions, leading to very satisfying results.

Effect of ambient temperature on species lumping for total organic gases in gasoline exhaust emissions

Volatile organic compound (VOCs) emissions from sources often need to be compressed or “lumped” into species classes for use in emissions inventories intended for air quality modeling. This needs to be done to ensure computational efficiency. The lumped profiles are usually reported for one value of ambient temperature. However, temperature-specific detailed profiles have been constructed in the recent past - the current study investigates how the lumping of species from those profiles into different atmospheric chemistry mechanisms is affected by temperature, considering three temperatures (−18 °C, −7 °C and 24 °C). The mechanisms considered differed on the assumptions used for lumping: CB05 (carbon bond type), SAPRC (ozone formation potential) and RACM2 (molecular surrogate and reactivity weighting). In this space, four sub-mechanisms for SAPRC were considered. Scaling factors were developed for each lumped model species and mechanism in terms of moles of lumped species per unit mass. Species which showed a direct one-to-one mapping (SAPRC/RACM2) reported scaling factors that were unchanged across mechanisms. However, CB05 showed different trends since one compound often is mapped onto multiple model species, out of which the paraffinic double bond (PAR) is predominant. Temperature-dependent parameterizations for emission factors pertaining to each lumped species class and mechanism were developed as part of the study. Here, the same kind of model species showed varying lumping parameters across the different mechanisms. These differences could be attributed to differing approaches in lumping. The scaling factors and temperature-dependent parameterizations could be used to update emissions inventories such as MOVES or SMOKE for use in chemical transport modeling.

Reduction of Multiphase Atmospheric Chemistry

The aim of this article is to investigate the dynamical behaviour ofmultiphase atmospheric chemical mechanisms. Reducing procedures areapplied to a multiphase chemical box model including gas-phasereactions, aqueous-phase reactions and interfacial mass transfer. The lumping of species is computed in an automatic wayusing an efficient algorithm (apla). The computed lumped species arerelated to the fast behaviour of chemical and microphysical processessuch as Chapman cycle, ionic dissociations within the cloud drops andinterfacial Henry's equilibria. Depending on some parameters (liquidwater content, droplet radius) mixed lumped species (including both phases) may also becomputed. We show the existence of hierarchical reduced models due to the existence ofmultiple timescales. We use a special algorithm (dan2) in order tosolve the reduced models. Such models are accurate and the relative errorremains under the threshold of 1%. The speed-up is up to a factor 5comparedwith a fully implicit method (Gear) for the same accuracy. The key pointis that it provides a good qualitative understanding for the behaviourof the kinetic scheme.

A Possible Method for the Rapid Assessment of Biodiversity

Inventories of vertebrate and flowering plants are frequently used as surrogates for estimates of total biodiversity. This is in part because the inclusion of invertebrates and nonflowering plants is perceived as being too time‐consuming, costly, and difficult because of the shortage of specialists. Estimates of the species richness of field samples of spiders, ants, polychaetes, and mosses made by a biodiversity technician and by specialist taxonomists were compared. The biodiversity technician received a few hours training in the taxonomy of each group and separated specimens into recognizable taxonomic units (RTUs). The specialists sorted to species. For the three animal groups the biodiversity technician recorded 165 taxa and the specialists 147, with the error for the ants and spiders being 13% or less. A small amount of splitting and lumping of species was detected. The concordance of estimates remained very similar when small subsamples were used. The procedure was repeated by 13 undergraduates using a subsample of spiders. Their average error was 14.4%. The greatest similarity in estimates was for the mosses, but with high levels of splitting and lumping this result was entirely fortuitous. The results suggest that RTU estimates made by biodiversity technicians may be sufficiently close to formal taxonomic estimates of species richness to be useful for the rapid assessment of biodiversity. They also show, however, that the procedures outlined here should be used on invertebrate and nonflowering plant groups before they can be confidently included in biodiversity surveys.