Coalescence Model Research Articles

Comparison of bubbles interaction mechanisms of two-group Interfacial Area Transport Equation model

This work deals with 3D simulations of complex bubbly, cap-bubbly and churn regimes exhibiting bubbles of different shapes and with broad bubble size distribution. The first contribution of this work is to investigate and compare several bubble interaction mechanisms of coalescence and fragmentation for the 2-Group Interfacial Area Transport Equation (IATE) model. For two of these models, this is the first time their performances are assessed within a CFD code. The second contribution is to propose and assess a novel model of fragmentation and coalescence. Finally, a validation versus experimental data on three different configurations and three different regimes is performed. In particular, the interaction mechanisms are analyzed for one specific regime. The implementation of the two-group IATE model has been systematically performed in the 3D NEPTUNE CFD code.

Evolutionary dynamics of influenza A/H1N1 virus circulating in India from 2011 to 2021

Influenza A viruses (IAV) are fast-evolving pathogens with a very high mutation rate (2.0×10-6 to 2.0×10-4) compared to the influenza B (IBV) and influenza C (ICV) viruses. Generally, the tropical regions are considered as the reservoir for the IAV's genetic and antigenic evolutionary modification to be reintroduced into the temperate region. Therefore, in connection to the above facts, the present study emphasized on the evolutionary dynamic of the pandemic-2009 H1N1 (pdmH1N1) influenza virus in India. A total of Ninety-two whole genome sequences of pdmH1N1 viruses circulating in India during the 2009 post-pandemic era were analysed. The temporal signal of the study, indicating strict molecular clock evolutionary process and the overall substitution rate is 2.21×10-3/site/year. We are using the nonparametric Bayesian Skygrid coalescent model to estimates the effective past population dynamic or size over time. The study exhibits a strong relation between the genetic distances and collection dates of the Indian pdmH1N1 strain. The skygrid plot represents the highest exponential growth of IAV in rainy and winter seasons. All the genes of Indian pdmH1N1 were under purifying selective pressure. The Bayesian time-imprinted phylogenetic tree represents the following clade distributions in the country within the last 10years; I) clade 6, 6C, and 7 were co-circulating between the 2011 to 2012 flu season; II) the clade 6B was introduced into circulation in the late seasons of 2012; III) lastly, the clade 6B remain existing in the circulation and segregated into subclade 6B.1 with five different subgroup (6B.1A, 6B.1A.1, 6B.1A.5a, 6B.1A.5a.2, 6B.1A.7). The recent circulating strain of Indian H1N1 strain represent the insertion of basic-amino acid arginine (R) in the cleavage site (325/K-R) of HA protein and amino acid mutation (314/I-M) on the lateral head surface domain of NA protein. Moreover, the study indicates the sporadic presence of the oseltamivir-resistant (275/H-Y) H1N1 variant in circulation. The present study suggests the purifying selective pressure and stochastic ecological factors for the existence and adaptation of a certain clade 6B in the host populations and additional information on the emergence of mutated strains in the circulation.

PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the Inheritance of Gene Flow.

We consider the evolution of phylogenetic gene trees along phylogenetic species networks, according to the network multispecies coalescent process, and introduce a new network coalescent model with correlated inheritance of gene flow. This model generalizes two traditional versions of the network coalescent: with independent or common inheritance. At each reticulation, multiple lineages of a given locus are inherited from parental populations chosen at random, either independently across lineages or with positive correlation according to a Dirichlet process. This process may account for locus-specific probabilities of inheritance, for example. We implemented the simulation of gene trees under these network coalescent models in the Julia package PhyloCoalSimulations, which depends on PhyloNetworks and its powerful network manipulation tools. Input species phylogenies can be read in extended Newick format, either in numbers of generations or in coalescent units. Simulated gene trees can be written in Newick format, and in a way that preserves information about their embedding within the species network. This embedding can be used for downstream purposes, such as to simulate species-specific processes like rate variation across species, or for other scenarios as illustrated in this note. This package should be useful for simulation studies and simulation-based inference methods. The software is available open source with documentation and a tutorial at https://github.com/cecileane/PhyloCoalSimulations.jl.

"Correcting" Gene Trees to be More Like Species Trees Frequently Increases Topological Error.

The evolutionary histories of individual loci in a genome can be estimated independently, but this approach is error-prone due to the limited amount of sequence data available for each gene, which has led to the development of a diverse array of gene tree error correction methods which reduce the distance to the species tree. We investigate the performance of two representatives of these methods: TRACTION and TreeFix. We found that gene tree error correction frequently increases the level of error in gene tree topologies by "correcting" them to be closer to the species tree, even when the true gene and species trees are discordant. We confirm that full Bayesian inference of the gene trees under the multispecies coalescent model is more accurate than independent inference. Future gene tree correction approaches and methods should incorporate an adequately realistic model of evolution instead of relying on oversimplified heuristics.

Study on the Numerical Model of Gas–Liquid Dispersion Driven by a Coaxial Mixer

As the flow basis for gas–liquid mixing, turbulence plays an important role in the movement of bubbles in a stirred tank. Motivated by the fact that the current models in the framework of computational fluid dynamics-population balance model lack an adequate assessment of the turbulence effects, the coaxial mixer was chosen as the subject of study, and different turbulence models, drag models, and breakup and coalescence models were compared and optimized. The results showed that the RNG k-ε model better characterized the turbulent scale and achieved a higher exactness for the gas-phase concentration in the axial direction. The Luo–Luo model modified based on the eddy capture mechanism could effectively describe the coalescence and breakup processes of bubbles. Additionally, in the presence of strong turbulence, the Ishii & Zuber model and the Brucato model outperformed other models in predicting gas dispersion and flow structure but still failed to capture the peak gas holdup. By analyzing the available data, a new correlation was proposed to elucidate the increase in drag coefficient caused by turbulence, which significantly improved the prediction accuracy of gas holdup.

Two-Way PBM-Euler Model for Gas and Liquid Flow in the Ladle.

Ladle metallurgy is an important steelmaking technology in high-quality steel production. The blowing of argon at the ladle bottom has been applied in ladle metallurgy for several decades. Until now, the issue of breakage and coalescence among bubbles was still far from being solved. In order to have a deep insight into the complex process of fluid flow in the gas-stirred ladle, the Euler-Euler model and population balance model (PBM) are coupled to investigate the complex fluid flow in the gas-stirred ladle. Here, the Euler-Euler model is applied to predict the two-phase flow, and PBM is applied to predict the bubble and size distribution. The coalescence model, which considers turbulent eddy and bubble wake entrainment, is taken into account to determine the evolution of the bubble size. The numerical results show that if the mathematical model ignores the breakage of bubbles, the mathematical model gives the wrong bubble distribution. For bubble coalescence in the ladle, turbulent eddy coalescence is the main mode, and wake entrainment coalescence is the minor mode. Additionally, the number of the bubble-size group is a key parameter for describing the bubble behavior. The size group number 10 is recommended to predict the bubble-size distribution.

Beam Energy Dependence of Triton Production and Yield Ratio (N_{t}×N_{p}/N_{d}^{2}) in Au+Au Collisions at RHIC.

We report the triton (t) production in midrapidity (|y|<0.5) Au+Au collisions at sqrt[s_{NN}]=7.7-200 GeV measured by the STAR experiment from the first phase of the beam energy scan at the Relativistic Heavy Ion Collider. The nuclear compound yield ratio (N_{t}×N_{p}/N_{d}^{2}), which is predicted to be sensitive to the fluctuation of local neutron density, is observed to decrease monotonically with increasing charged-particle multiplicity (dN_{ch}/dη) and follows a scaling behavior. The dN_{ch}/dη dependence of the yield ratio is compared to calculations from coalescence and thermal models. Enhancements in the yield ratios relative to the coalescence baseline are observed in the 0%-10% most central collisions at 19.6 and 27GeV, with a significance of 2.3σ and 3.4σ, respectively, giving a combined significance of 4.1σ. The enhancements are not observed in peripheral collisions or model calculations without critical fluctuation, and decreases with a smaller p_{T} acceptance. The physics implications of these results on the QCD phase structure and the production mechanism of light nuclei in heavy-ion collisions are discussed.

Light nuclei production in Au+Au collisions at 3 GeV from coalescence model* *Supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB34000000) and the National Natural Science Foundation of China (12205342)

The nucleon coalescence model is one of the most popular theoretical models for light nuclei production in high-energy heavy-ion collisions. The production of light nuclei d, t, He, and He is studied using the transport model JAM with a simplified afterburner coalescence at GeV Au+Au collisions. We scan the cut-off of phenomenological coalescence parameters, i.e., the relative spatial distance and momentum difference , for the formation of light nuclei by nucleon coalescence to reproduce the light nuclei spectra measured by the STAR experiment. The results indicate a potential connection between the coalescence parameters and the binding energy as well as the diameter of these light nuclei.

Carbon Condensation via [4 + 2] Cycloaddition of Highly Unsaturated Carbon Chains.

We present computational studies of reaction pathways for alkyne/polyyne dimerization that represent plausible early steps in mechanisms for carbon condensation. A previous computational study of the ring coalescence and annealing model of C60 formation revealed that a 1,4-didehydrobenzocyclobutadiene intermediate (p-benzyne derivative) has little to no barrier to undergoing an unproductive retro-Bergman cyclization, which brings into question the relevance of that reaction pathway. The current study investigates an alternative model, which proceeds through an initial [4 + 2] cycloaddition instead of a [2 + 2] cycloaddition. In this pathway, the problematic intermediate is avoided, with the reaction proceeding via a (potentially) more kinetically stable tetradehydronaphthalene derivative. The computational studies of the [2 + 2] and [4 + 2] model systems, with increasing alkyne substitutions, reveal that the para-benzyne diradical of the [4 + 2] pathway has a significantly greater barrier to ring opening than the analogous intermediates of the [2 + 2] pathway and that alkyne substitution has little effect on this important barrier. These studies employ spin-flip, time-dependent density functional theory (SF-TDDFT) to provide suitable treatment of open-shell diradical intermediates.

A taxonomic revision of the ecologically important Ochna holstii (Ochnaceae) complex using molecular and morphological data

Background and aims – Ochna holstii and its allies represent an ecologically important group in a variety of lowland to montane habitats in tropical eastern and southern Africa. Identifying and delimiting species within this group has proved challenging due to a lack of variation in morphological characters. We combine genomic-scale data of multiple accessions per species with morphological data to generate a taxonomic revision for the Ochna holstii complex using a multi-evidence approach. Material and methods – A total of 50 samples representing eight species were analysed using target enrichment and a custom bait kit. Phylogenetic analysis was conducted using the multi-species coalescent model and a concatenation maximum likelihood method, and gene tree discordance was investigated. Herbarium specimens of the O. holstii complex were studied in detail for informative morphological characters, supplemented where possible from field collections, and a full taxonomic revision is provided. Key results – Within Ochna sect. Schizanthera Clade I, our study confirms that all species are monophyletic and supported by morphological data with the exception of O. holstii, which is paraphyletic. A new species, O. mchanga, previously confused with O. polyneura, is described, and the placement of another recently described species, O. maguirei, is confirmed for the first time using molecular data. Conclusion – The widespread montane tree Ochna holstii is non-monophyletic in its current circumscription and likely gave rise to the more range-restricted O. oxyphylla and O. stolzii. We suggest that an integrated taxonomy approach, using both molecular and morphological data, is essential for deciphering difficult species relationships in Ochna.

Hypernuclei production with a modified coalescence model in BUU transport calculations

In this paper, the usual momentum- and coordinate-space distance criteria for creating nuclear clusters in transport simulations are readdressed by using a dynamical, covariant description in an off-shell Boltzmann-Uehling-Uhlenbeck transport approach. The free parameter of this clustering scheme is the cluster formation time, which is fitted through the FOPI data of low energy charged cluster multiplicities in Au+Au collisions at 150 A MeV, and 400 A MeV incident energies. The coalescence model is used to estimate the yields of the ^3H_Lambda , ^5H_{Lambda Lambda }, ^6He_{Lambda Lambda } single and double strange hypernuclei in central Au+Au collisions between 2, and 20 A GeV incident energies, giving comparable results to estimations from other methods.

Investigating the cluster production mechanism with isospin triggering: Thermal models versus coalescence models

Isospin triggering allows to distinguish coalescence from thermal production of light clusters in heavy ion collisions. Triggering on $Y({\ensuremath{\pi}}^{\ensuremath{-}})\ensuremath{-}Y({\ensuremath{\pi}}^{+})$ allows to select very neutron or proton rich final states. The deuteron (cluster) production with coalescence ($d\ensuremath{\propto}n\ifmmode\cdot\else\textperiodcentered\fi{}p$) leads then to an inverse parabolic dependence of the deuteron yield on $\mathrm{\ensuremath{\Delta}}{Y}_{\ensuremath{\pi}}$. In contrast, in a thermal model, cluster production is independent on $\mathrm{\ensuremath{\Delta}}{Y}_{\ensuremath{\pi}}$. The observation of a maximum deuteron (cluster) yield as function of $\mathrm{\ensuremath{\Delta}}{Y}_{\ensuremath{\pi}}$ provides confirmation of the coalescence mechanism.

Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade).

In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction site-associated DNA sequencing and cytochrome b) to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. We complemented these analyses with posterior predictive simulations to assess the fit of the genomic data to the multispecies coalescent model. We also employed a novel approach to time-calibrate a phylogenetic network. Our results show several instances of mito-nuclear discordance and consistent support for a reticulated history, supporting the view that the complex evolutionary history of the kingii clade is characterized by extensive gene flow and rapid diversification events. We discuss our findings in the contexts of the "gray zone" of speciation, phylogeographic patterns in the Patagonian region, and taxonomic outcomes. [Model adequacy; multispecies coalescent; multispecies network coalescent; phylogenomics; species delimitation.].

Genome-wide data reveal cryptic diversity and hybridization in a group of tree ferns

Discovery of cryptic diversity is essential to understanding both the process of speciation and the conservation of species. Determining species boundaries in fern lineages represents a major challenge due to lack of morphologically diagnostic characters and frequent hybridization. Genomic data has substantially enhanced our understanding of the speciation process, increased the resolution of species delimitation studies, and led to the discovery of cryptic diversity. Here, we employed restriction-site-associated DNA sequencing (RAD-seq) and integrated phylogenomic and population genomic analyses to investigate phylogenetic relationships and evolutionary history of 16 tree ferns with marginate scales (Cyatheaceae) from China and Vietnam. We conducted multiple species delimitation analyses using the multispecies coalescent (MSC) model and novel approaches based on genealogical divergence index (gdi) and isolation by distance (IBD). In addition, we inferred species trees using concatenation and several coalescent-based methods, and assessed hybridization patterns and rate of gene flow across the phylogeny. We obtained highly supported and generally congruent phylogenies inferred from concatenated and summary-coalescent methods, and the monophyly of all currently recognized species were strongly supported. Our results revealed substantial evidence of cryptic diversity in three widely distributed Gymnosphaera species, each of which was composite of two highly structure lineages that may correspond to cryptic species. We found that hybridization was fairly common between not only closely related species, but also distantly related species. Collectively, it appears that scaly tree ferns may contain cryptic diversity and hybridization has played an important role throughout the evolutionary history of this group.

Simulation of collective flow of protons and deuterons in Au+Au collisions at Ebeam=1.23A GeV with the isospin-dependent quantum molecular dynamics model

Collective flows of protons and deuterons for $\text{Au}+\text{Au}$ collisions at beam energy ${E}_{\text{beam}}=1.23A \mathrm{GeV}$ were simulated by an isospin-dependent quantum molecular dynamics model. Two coalescence models, namely, naive coalescence and dynamical coalescence models, are compared for the formation of deuterons. After a reasonable agreement of the proton and deuteron rapidity spectra with the high acceptance dielectron spectrometer data is obtained, we apply an event-plane method to calculate the first four order collective flow coefficients and the ratios of $\ensuremath{\langle}{v}_{4}\ensuremath{\rangle}/{\ensuremath{\langle}{v}_{2}\ensuremath{\rangle}}^{2}$ and $\ensuremath{\langle}{v}_{3}\ensuremath{\rangle}/(\ensuremath{\langle}{v}_{1}\ensuremath{\rangle}\ensuremath{\langle}{v}_{2}\ensuremath{\rangle})$ and observe the scaling of the number of constituent nucleons between protons and deuterons. In addition, the dependence of ${\ensuremath{\varepsilon}}_{n}$ versus $\ensuremath{\langle}{v}_{n}\ensuremath{\rangle}$ and the ratio $\ensuremath{\langle}{v}_{n}\ensuremath{\rangle}/{\ensuremath{\varepsilon}}_{n}$ on the centrality is obtained. Finally, the Pearson coefficients $\text{corr}({v}_{n},{v}_{m})$ between the first four harmonic flows for protons and deuterons are studied as a function of rapidity and centrality.

Discrete element simulation of compression failure mechanism of SiC ceramic considering collinear flaws

A particle-based numerical simulation model was established for SiC ceramics, and a method of deleting the particles along the specified direction was chosen to produce a pair of pre-existing collinear flaws. A serial of simulations were carried out to investigate the effects of inclination angle and ligament length on the failure mechanism under uniaxial compression. The laws of crack initiation and propagation as well as the distribution laws of the stress field and displacement field around the pre-existing flaws were analyzed. The results showed that the influence of inclination angle θ on micro-crack initiation, propagation and coalescence was more significant than that of ligament length L for pre-existing collinear flaws. Meanwhile, three coalescence models can be found with the increase of the inclination angle. By analyzing the evolution process of the displacement and stress fields during the loading process, it was clearly that the first crack was induced by the tensile stress concentration, and the secondary crack was initiated and propagated with tensile and shear stress. Moreover, the propagation mechanism of the micro-crack was closely related to the evolution behaviours of the stress and displacement fields.

Phylogenomic evolutionary insights in the fern family Gleicheniaceae

The pantropical fern family Gleicheniaceae comprises approximately 157 species. Seven genera are currently recognized in the family, although their monophyly is still uncertain due to low sampling in phylogenetic studies. We examined the monophyly of the genera through extended sampling, using the first phylogenomic inference of the family including data from both nuclear and plastid genomes. Seventy-six samples were sequenced (70 Gleicheniaceae species and six outgroups) using high throughput sequencing, including all seven currently recognized genera. Plastid and nuclear data were recovered and assembled; the nuclear data was phased to reduce paralogy as well as hybrid noise in the final recovered topology. Maximum likelihood trees were built for each locus, and a concatenated dataset was built for both datasets. A species tree based on a multispecies coalescent model was generated, and divergence time analyses performed. We here present the first genomic phylogenetic inferences concerning Gleicheniaceae, confirming the monophyly of most genera except Sticherus, which we recovered as paraphyletic. Although most of the extant genera of Gleicheniaceae originated during the Mesozoic, several genera show Neogene and even Quaternary diversifications, and our results suggest that reticulation and polyploidy may have played significant roles during this diversification. However, some genera, such as Rouxopteris and Stromatopteris, appear to represent evolutionary relicts.

Demographic and spatially-explicit landscape genomic analyses in a tropical oak reveal the impacts of late Quaternary climate change on Andean montane forests.

Tropical Andes are one of the most important biodiversity hotspots on earth, yet our understanding on how their biotas have responded to Quaternary climatic oscillations is extraordinarily limited and the alternative models proposed to explain their demographic dynamics have been seldom formally evaluated. Here, we test the hypothesis that the interplay between the spatial configuration of geographical barriers to dispersal and elevational displacements driven by Quaternary cooling-warming cycles have shaped the demographic trajectories of montane oak forests (Quercus humboldtii) from the Colombian Andes. Specifically, we integrate genomic data and environmental niche modelling at fine temporal resolution to test competing spatially-explicit demographic and coalescent models, including scenarios considering (i) isotropic gene flow through the landscape, (ii) the hypothetical impact of contemporary barriers to dispersal (i.e., inter-Andean valleys), and (ii) distributional shifts of montane oak forests from the Last Glacial Maximum to present. Although our data revealed a marked genetic fragmentation of montane oak forests, statistical support for isolation-with-migration models indicate that geographically separated populations from the different Andean Cordilleras regularly exchange gene flow. Accordingly, spatiotemporally-explicit demographic analyses supported a model of flickering connectivity, with scenarios considering isotropic gene flow or currently unsuitable habitats as persistent barriers to dispersal providing a comparatively worse fit to empirical genomic data. Overall, these results emphasize the role of landscape heterogeneity on shaping spatial patterns of genomic variation in montane oak forests, rejecting the hypothesis of genetic continuity and supporting a significant impact of Quaternary climatic oscillations on their demographic trajectories.

Heterogeneity in the isolation of patches may be essential for the action of metacommunity mechanisms

The spatial isolation gradient of communities and the gradient in the species dispersal ability are recognized as determinants of biodiversity in metacommunities. In spite of this, mean field models, spatially explicit models, and experiments were mainly focused on idealized spatial arrangements of communities leaving aside the combining role of dispersal and isolation gradients in metacommunity processes. Consequently, we have an incipient understanding of the role of the real spatial arrangement of communities on biodiversity patterns. We focus on six metacommunities for which confident information about the spatial arrangement of water bodies is available. Using coalescent metacommunity models and null models that randomize the location of water bodies, we estimated the potential effect of the landscape on biodiversity and its dependence on species dispersal ability. At extremely low or high dispersal abilities, the location of ponds does not influence diversity because different communities are equally affected by the low or high incoming dispersal. At intermediate dispersal abilities, peripheral communities present a much lower richness and higher beta diversity than central communities. Moreover, metacommunities from real landscapes host more biodiversity than randomized landscapes, a result that is determined by the heterogeneity in the geographic isolation of communities. In a dispersal gradient, mass effects systematically increase the local richness and decrease beta diversity. However, the spatial arrangement of patches only has a large importance in metacommunity processes at intermediate dispersal abilities, which ensures access to central locations but limits dispersal in isolated communities. The ongoing reduction in spatial extent and simplification of the landscape may consequently undermine the metacommunity processes that support biodiversity, something that should be explicitly considered in preserving and restoring strategies.

Modeling and Simulation of Coalescence in the Context of Oil Mist Filtration

Today, aerosols are generated in many industrial processes like machining or in pneumatic compressors. The harmfulness of these droplets often lies in the liquid itself, as it can be toxic or cancerous while exhaled natural aerosols can carry pathogens. For health protection, the filtration of these aerosols is an important task. The wetting properties of the fibers have a large influence on the filtration efficiency and coalescence of droplets on the fibers. Oleophilic fibers are better in capturing the oil particles, while drainage increases using oleophobic fibers. For improved efficiency and drainage properties, a mixed-wet fiber system could therefore be advantageous. Describing droplet capture and coalescence in filter-scale simulations is computationally extremely demanding. We present a new approach for simulating oil mist deposition and droplet coalescence, specifically accounting for the wettability of the fibers, especially for mixed-wet filter media. The aim is to gain a more realistic pressure loss of a fibrous filter structure which takes the presence of the filtered phase into account as well as the coalescence of the liquid phase on the fibers depending on the wettability and the fluid parameters. Our approach is to model the shape of deposited droplets via weighted distance maps, according to the contact angles. Starting from a sphere, the shape is fitted on the solid surface such that the contact angle is met. For validation purposes, volume-of-fluid-based simulations were set up using the same droplet-fiber system as a reference to compare the droplet shape and pressure loss in the presence of oil droplets on the fiber surface.