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285 results for “evolution models”
Data from: Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): developing a model system for the evolution of marine bioluminescence
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Data from: A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods
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Model-derived backbarrier marsh width from GEOMBEST+ simulations of barrier island-marsh coupled evolution for a range of environmental conditions.
Model-derived backbarrier marsh width from GEOMBEST+ simulations of barrier island-marsh coupled evolution for a range of environmental conditions. The input parameters were varied for a range of 10 different values for each of the flux of overwash (.2-2 m^3/yr), the rate of sea level rise (1-10mm/yr), and the flux of bay sediment (2-20 m^3/yr) Each simulation was for a one meter change in sea level, starting from one of three initial conditions, an empty backbarrier basin, starting with a narrow (400m wide) backbarrier marsh, and starting with a marsh-filled (2000m wide) backbarrier basin. With 10 variants of each parameter input and 3 initial conditions, this results in 3,000 total simulations run. Each row in the spreadsheet contains the input and output values for an individual simulation. The outputs reported are the final backbarrier marsh width, defined as the distance from the backside of the barrier island to the landward most marsh cell, the change in marsh width, and the rate of change in marsh width.
Properties of OB star−black hole systems derived from detailedbinary evolution models
<p>Input files to reproduce the MESA simulations used in <a href="https://arxiv.org/abs/1912.09826">Langer et al. (2020)</a></p> <p>MESA version 8845</p> <p>For instructions, refer to the README.md file included.</p>
Supplementary Data for Multiform: Multi-objective Evolution of Requirements Models Constrained by Formal Verification Results
<p>This data set provides supplementary material for the article "<em>Multiform: Multi-objective Evolution of Requirements Models Constrained by Formal Verification Results</em>" (to appear). It contains the following files:</p> <ul> <li><strong>experiment-input-models.zip</strong> which contains the SML input models for the EBEAS and production cell examples that were used to conduct the experiment</li> <li><strong>experiment-results.tar</strong> which contains the computed candidate SML models as well as H2 database files that contain measurements.</li> <li><strong>experiment-results.pdf</strong> which summarizes the conducted controlled experiment and results.</li> </ul> <p> </p> <p><strong>Input models</strong> (example for EBEAS)</p> <ul> <li><strong>ebeas.sml</strong> contains the actual SML input model to be evolved</li> <li><strong>ebeas.ecore</strong> contains the metamodel of the EBEAS example</li> <li><strong>ebeas.xmi</strong> contains the object system of the EBEAS example that is used for the SML realizability check</li> <li><strong>ebeas.runconfig</strong> contains the runtime configuration for ScenarioTools that binds the SML input model with the object system</li> <li><strong>ebeas.cspec</strong> contains the solution space model used by Multiform.</li> </ul> <p> </p> <p><strong>Measurements</strong> are stored in an <a href="http://h2database.com/html/main.html">H2 database</a> file. To open one of the database files for the EBEAS or production cell examples extract the appropriate zip file to a local folder, navigate to the folder in a terminal, and start H2 with the appropriate database file as follows:</p> <pre><code>java -jar h2-1.4.199.jar -url jdbc:h2:./Statistics</code></pre> <p>A web-based SQL client will open in your browser. H2 cann be obtained free of charge from their homepage.</p> <p> </p> <p>The <strong>database schema</strong> consists of three simple tables:</p> <p><strong>SMLCANDIDATESTATISTICS</strong> contains measurements for each evolved candidate SML model and consists of the following columns:<br> <strong>ALGORITHM </strong>- one of 'Random', 'NSGA2', 'tabu-75-intensify'<br> <strong>SEED </strong>- seed id for which the measurement was taken<br> <strong>ITERATION </strong>- iteration id during whch the measurement was taken<br> <strong>CANDIDATE </strong>- unique id of the evaludated candidate SML model<br> <strong>SYNTHESISTIME </strong>- synthesis time of the evaludated candidate SML model<br> <strong>O1_SCENARIOS </strong>- objective value for o1<br> <strong>O2_FRAGMENTSRATIO </strong>- objective value for o2<br> <strong>O3_ENVFRAGMENTSRATIO </strong>- objective value for o3<br> <strong>C1_REALIZABILITY </strong>- constraint value for c1<br> <strong>C2_REACHABILITY </strong>- constraint value for c1</p> <p><strong>SMLITERATIONSTATISTICS </strong>contains aggregated statistical data for each iteration and consists of the following columns:<br> <strong>ALGORITHM </strong>- one of 'Random', 'NSGA2', 'tabu-75-intensify'<br> <strong>SEED </strong>- seed id for which the data was aggregated<br> <strong>ITERATION </strong>- unique id of this aggregated iteration data<br> <strong>ITERATIONSUCCESSRATE </strong>- achieved success rate in this iteration<br> <strong>ACCUMULATEDSUCCESSRATE </strong>- achieved aggregated success reate until this iteration<br> <strong>ACCUMULATEDHYPERVOLUMEINDICATOR </strong>- achieved hypervolume until this iteration<br> <strong>NUMITERATIONPARETOEQUIVALENTCANDIDATES </strong>- number of pareto-equivalent candidate SML models in this iteration<br> <strong>NUMACCUMULATEDPARETOEQUIVALENTCANDIDATES </strong>- number of pareto-equivalent candidate SML models until this iteration<br> <strong>NUMITERATIONPARETODOMINANTCANDIDATES </strong>- number of pareto-dominant candidate SML models in this iteration<br> <strong>NUMACCUMULATEDPARETODOMINANTCANDIDATES </strong>- number of pareto-dominant candidate SML models until this iteration<br> <strong>ITERATIONSYNTHESISTIME </strong>- total synthesis time of this iteration<br> <strong>ACCUMULATEDSYNTHESISTIME </strong>- accumulated total synthesis time until this iteration</p> <p><strong>SMLSEEDSTATISTICS</strong> contains aggregated statistical data for each seed and consists of the following columns:<br> <strong>ALGORITHM </strong>- one of 'Random', 'NSGA2', 'tabu-75-intensify'<br> <strong>SEED </strong>- unique id of this aggregated seed data<br> <strong>SUCCESSRATE</strong>- achieved success rate in this seed<br> <strong>HYPERVOLUMEINDICATOR </strong>- achieved hypervolume in this seed<br> <strong>NUMPARETOEQUIVALENTCANDIDATES </strong>- number of pareto-equivalent candidate SML models in this seed<br> <strong>NUMPARETODOMINANTCANDIDATES </strong>- number of pareto-dominant candidate SML models in this seed<br> <strong>TOTALSYNTHESISTIME </strong>- total synthesis time of this seed</p> <p> </p> <p><strong>Please note</strong>: the database files contain data for algorithms 'tabu-50-intensify' and 'tabu-25-intensify' representing evaluation runs with different Tabu search configurations. However, these still need to be analyzed and <strong>experiment-results.pdf</strong> refers to '<strong>tabu-75-intensify</strong>' only.</p>
Model output data for "Negative density-dependent dispersal emerges from the joint evolution of density- and body condition-dependent dispersal strategies"
<p>Empirical studies have documented both positive and negative density-dependent dispersal, yet most theoretical models predict positive density dependence as a mechanism to avoid competition. Several hypotheses have been proposed to explain the occurrence of negative density-dependent dispersal, but few of these have been formally modeled. Here, we developed an individual based model of the evolution of density-dependent dispersal. This model is novel in that it considers the effects of density on dispersal directly, and indirectly through effects on individual condition. Body condition is determined mechanistically, by having juveniles compete for resources in their natal patch. We found that the evolved dispersal strategy was a steep, increasing function of both density and condition. Interestingly, although populations evolved a positive density-dependent dispersal strategy, the simulated metapopulations exhibited negative density-dependent dispersal. This occurred because of the negative relationship between density and body condition: high density sites produced low condition individuals that lacked the resources required for dispersal. Our model therefore generates the novel hypothesis that observed negative density-dependent dispersal can occur when high density limits the ability of organisms to disperse. We suggest that future studies consider how phenotype is linked to the environment when investigating the evolution of dispersal.</p>
Data from: Testing gradual and speciational models of evolution in extant taxa: the example of ratites
Ever since Eldredge and Gould proposed their model of punctuated equilibria, evolutionary biologists have debated how often this model is the best description of nature and how important it is compared to the more gradual models of evolution expected from natural selection and the neo-Darwinian paradigm. Recently, Cubo proposed a method to test whether morphological data in extant ratites are more compatible with a gradual or with a speciational model (close to the punctuated equilibrium model). As shown by our simulations, a new method to test the mode of evolution of characters (involving regression of standardized contrasts on their expected standard deviation) is easier to implement and more powerful than the previously proposed method, but the Mesquite module CoMET (aimed at investigating evolutionary models using comparative data) performs better still. Uncertainties in branch length estimates are probably the largest source of potential error. Cubo hypothesized that heterochronic mechanisms may underlie morphological changes in bone shape during the evolution of ratites. He predicted that the outcome of these changes may be consistent with a speciational model of character evolution because heterochronic changes can be instantaneous in terms of geological time. Analysis of a more extensive dataset confirms his prediction despite branch length uncertainties: evolution in ratites has been mostly speciational for shape-related characters. However, it has been mostly gradual for size-related ones.
Data from: Serial homology and correlated characters in morphological phylogenetics: modeling the evolution of dental crests in placentals
Accurate modeling of the complexity of morphological evolution is crucial for morphological phylogenetics and for performing tests on a wide variety of evolutionary scenarios. In this context, morphological integration and the problem of correlated categorical characters represent a major challenge. In particular, the magnitude and implications of correlations among serially homologous structures such as teeth have been much debated but were never tested statistically within a broad phylogenetic context. Here, we present a large-scale empirical study analyzing the serial variation of cingular crests on successive molars (M1, M2 and M3) of 274 placental species in a phylogenetic context. Both likelihood analyses and analysis of phylogenetic co-distributions demonstrated highly correlated evolution in the entire sample and thus the non-independence of these serial features at a macroevolutionary scale. Likelihood analyses show that their serial variation should be better scored within a single composite character model with constrained paths for transitions enabling simultaneous changes on all three molars, which suggests a strong developmental or genetic integration. These results are congruent with current molecular and developmental knowledge related to dental morphological variation and call into question the frequent use of separate characters scored on serially homologous structures of the dentition in phylogenetic analyses. Overall, they provide long-overdue and clear empirical evidence that in-depth studies of patterns of integration constitute an essential step towards more realistic character construction and modeling. This approach is critical for more accurate morphological phylogenetics and, more generally, for testing macroevolutionary scenarios on groups of correlated characters.
Data from: Predation's role in life-history evolution of a livebearing fish and a test of the Trexler-DeAngelis model of maternal provisioning
Populations experiencing consistent differences in predation risk and resource availability are expected to follow divergent evolutionary trajectories. For example, live-history theory makes specific predictions for how predation should drive life-history evolution, and according to the Trexler-DeAngelis model for the evolution of matrotrophy, post-fertilization maternal provisioning is most likely to evolve in environments with consistent, high levels of resource availability. Using the model system of Bahamas mosquitofish (Gambusia hubbsi) inhabiting blue holes with and without the piscivorous bigmouth sleeper (Gobiomorus dormitor), we provide some of the strongest tests of these predictions to date, as resource availability does not co-vary with predation regime in this system, and we examine numerous (14) isolated natural populations. We found clear evidence for the expected life-history divergence between predation regimes, and empirical support of the Trexler-DeAngelis model. Moreover, based on molecular and lab-rearing data, our study offers strong evidence for convergent evolution of similar life histories in similar predation regimes, largely matching previous phenotypic patterns observed in other poeciliid lineages (Brachyrhaphis spp., Poecilia reticulata), and further supports the notion that matrotrophy is most likely to evolve in stable high-resource environments.
Data from: A phenotype-genotype codon model for detecting adaptive evolution
A central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods make inferences mainly from either phenotypic data or genetic data alone. A small number of models have been developed to infer correlations between the rate of molecular evolution and changes in a discrete or continuous life history trait. But such correlations are not necessarily evidence of adaptation. Here we present a novel approach called the phenotype-genotype branch-site model (PG-BSM) designed to detect evidence of adaptive codon evolution associated with discrete-state phenotype evolution. An episode of adaptation is inferred under standard codon substitution models when there is evidence of positive selection in the form of an elevation in the nonsynonymous-to-synonymous rate ratio ω to a value ω > 1. As it is becoming increasingly clear that ω > 1 can occur without adaptation, the PG-BSM was formulated to infer an instance of adaptive evolution without appealing to evidence of positive selection. The null model makes use of a covarion-like component to account for general heterotachy (i.e., random changes in the evolutionary rate at a site over time). The alternative model employs samples of the phenotypic evolutionary history to test for phenomenological patterns of heterotachy consistent with specific mechanisms of molecular adaptation. These include (i) a persistent increase/decrease in ω at a site following a change in phenotype (the pattern) consistent with an increase/decrease in the functional importance of the site (the mechanism); and (ii) a transient increase in ω at a site along a branch over which the phenotype changed (the pattern) consistent with a change in the site's optimal amino acid (the mechanism). Rejection of the null is followed by post hoc analyses to identify sites with strongest evidence for adaptation in association with changes in the phenotype as well as the most likely evolutionary history of the phenotype. Simulation studies based on a novel method for generating mechanistically realistic signatures of molecular adaptation show that the PG-BSM has good statistical properties. Analyses of three real alignments show that site patterns identified post hoc are consistent with the specific mechanisms of adaptation included in the alternate model. Further simulation studies show that the covarion-like component of the PG-BSM plays a crucial role in mitigating recently discovered statistical pathologies associated with confounding by accounting for heterotachy-by-any-means.
Data from: A two-state model of tree evolution and its applications to alu retrotransposition
Models of tree evolution have mostly focused on capturing the cladogenesis processes behind speciation. Processes that derive the evolution of genomic elements, such as repeats, are not necessarily captured by these existing models. In this paper, we design a model of tree evolution that we call the dual-birth model, and we show how it can be useful in studying the evolution of short Alu repeats found in the human genome in abundance. The dual-birth model extends the traditional birth-only model to have two rates of propagation, one for active nodes that propagate often, and another for inactive nodes, that with a lower rate, activate and start propagating. Adjusting the ratio of the rates controls the expected tree balance. We present several theoretical results under the dual-birth model, introduce parameter estimation techniques, and study the properties of the model in simulations. We then use the dual-birth model to estimate the number of active Alu elements and their rates of propagation and activation in the human genome based on a large phylogenetic tree that we build from close to one million Alu sequences.
Data from: Modeling effects of environmental change on wolf population dynamics, trait evolution, and life history
Environmental change has been observed to generate simultaneous responses in population dynamics, life history, gene frequencies, and morphology in a number of species. But how common are such eco-evolutionary responses to environmental change likely to be? Are they inevitable, or do they require a specific type of change? Can we accurately predict eco-evolutionary responses? We address these questions using theory and data from the study of Yellowstone wolves. We show that environmental change is expected to generate eco-evolutionary change, that changes in the average environment will affect wolves to a greater extent than changes in how variable it is, and that accurate prediction of the consequences of environmental change will probably prove elusive.
Data from: Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system
The evolution of migration in birds has fascinated biologists for centuries. In this study, we performed phylogenetic-based analyses of Catharus thrushes, a model genus in the study of avian migration, and their close relatives. For these analyses, we used both mitochondrial and nuclear genes, and the resulting phylogenies were used to trace migratory traits and biogeographic patterns. Our results provide the first robust assessment of relationships within Catharus and relatives and indicate that both mitochondrial and autosomal genes contribute to overall support of the phylogeny. Measures of phylogenetic informativeness indicated that mitochondrial genes provided more signal within Catharus than did nuclear genes, whereas nuclear loci provided more signal for relationships between Catharus and close relatives than did mitochondrial genes. Insertion and deletion events also contributed important support across the phylogeny. Across all taxa included in the study, and for Catharus, possession of long-distance migration is reconstructed as the ancestral condition, and a North American (north of Mexico) ancestral area is inferred. Within Catharus, sedentary behaviour evolved after the first speciation event in the genus and is geographically and temporally correlated with Central American distributions and the final closure of the Central American Seaway. Migratory behaviour subsequently evolved twice in Catharus and is geographically and temporally correlated with a recolonization of North America in the late Pleistocene. By temporally linking speciation events with changes in migratory condition and events in Earth history, we are able to show support for several competing hypotheses relating to the geographic origin of migration.
Data from: Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages
Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modelled accurately using the Γ distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or under-parameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10,000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42,337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these 3 sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modelled by a combination of 8 edge-specific rate matrices (4 for V1 and 4 for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the 7 species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species.
Data from: Contemporary ecological interactions improve models of past trait evolution
Despite the fact that natural selection underlies both traits and interactions, evolutionary models often neglect that ecological interactions may, and in many cases do, influence the evolution of traits. Here, we explore the interdependence of ecological interactions and functional traits in the pollination associations of hawkmoths and flowering plants. Specifically, we develop an adaptation of the Ornstein-Uhlenbeck model of trait evolution that allows us to study the influence of plant corolla depth and observed hawkmoth-plant interactions on the evolution of hawkmoth proboscis length. Across diverse modelling scenarios, we find that the inclusion of contemporary interactions can provide a better description of trait evolution than the null expectation. Moreover, we show that the pollination interactions provide more-likely models of hawkmoth trait evolution when interactions are considered at increasingly fine-scale groups of hawkmoths. Finally, we demonstrate how the results of best-fit modelling approaches can implicitly support the association between interactions and trait evolution that our method explicitly examines. In showing that contemporary interactions can provide insight into the historical evolution of hawkmoth proboscis length, we demonstrate the clear utility of incorporating additional ecological information to models designed to study past trait evolution.
Data from: A test of the "flexible stem" model of evolution: ancestral plasticity, genetic accommodation, and morphological divergence in the threespine stickleback radiation
If an ancestral stem group repeatedly colonizes similar environments, developmental plasticity specific to that group should consistently give rise to similar phenotypes. Parallel selection on those similar phenotypes could lead to the repeated evolution of characteristic ecotypes, a property common to many adaptive radiations. A key prediction of this "flexible stem" model of adaptive radiation is that patterns of phenotypic divergence in derived groups should mirror patterns of developmental plasticity in their common ancestor. The threespine stickleback radiation provides an excellent opportunity to test this prediction because the marine form is representative of the ancestral stem group, which has repeatedly given rise to several characteristic ecotypes. We examined plasticity of several aspects of shape and trophic morphology in response to diets characteristic of either the derived benthic or limnetic ecotypes. When marine fish were reared on alternative diets, plasticity of head and mouth shape paralleled phenotypic divergence between the derived ecotypes, supporting the flexible stem model. Benthic and limnetic fish exhibited patterns of plasticity similar to the marine population; however, some differences in population means were present, as well as subtle differences in shape plasticity in the benthic population, indicating a role for genetic accommodation in this system.
Data from: Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach
Chromosome number is a key feature of the higher-order organization of the genome, and changes in chromosome number play a fundamental role in evolution. Dysploid gains and losses in chromosome number, as well as polyploidization events, may drive reproductive isolation and lineage diversification. The recent development of probabilistic models of chromosome number evolution in the groundbreaking work by Mayrose et al. (2010, ChromEvol) have enabled the inference of ancestral chromosome numbers over molecular phylogenies and generated new interest in studying the role of chromosome changes in evolution. However, the ChromEvol approach assumes all changes occur anagenetically (along branches), and does not model events that are specifically cladogenetic. Cladogenetic changes may be expected if chromosome changes result in reproductive isolation. Here we present a new class of models of chromosome number evolution (called ChromoSSE) that incorporate both anagenetic and cladogenetic change. The ChromoSSE models allow us to determine the mode of chromosome number evolution; is chromosome evolution occurring primarily within lineages, primarily at lineage splitting, or in clade-specific combinations of both? Furthermore, we can estimate the location and timing of possible chromosome speciation events over the phylogeny. We implemented ChromoSSE in a Bayesian statistical framework, specifically in the software RevBayes, to accommodate uncertainty in parameter estimates while leveraging the full power of likelihood based methods. We tested ChromoSSE's accuracy with simulations and re-examined chromosomal evolution in Aristolochia, Carex section Spirostachyae, Helianthus, Mimulus sensu lato (s.l.), and Primula section Aleuritia, finding evidence for clade-specific combinations of anagenetic and cladogenetic dysploid and polyploid modes of chromosome evolution.
Data from: Biophysical modeling of the temporal niche: from first principles to the evolution of activity patterns
Most mammals can be characterized as nocturnal or diurnal. However infrequently, species may overcome evolutionary constraints and alter their activity patterns. We modeled the fundamental temporal niche of a diurnal desert rodent, the golden spiny mouse, Acomys russatus. This species can shift into nocturnal activity in the absence of its congener, the common spiny mouse, A. cahirinus, suggesting that it was competitively driven into diurnality, and that this shift in a small desert rodent may involve physiological costs. Therefore, we compared metabolic costs of diurnal vs. nocturnal activity using a biophysical model to evaluate the preferred temporal niche of this species. The model predicted that energy expenditure during foraging is almost always lower during the day except during mid-day in summer at the less sheltered microhabitat. We also found that a shift in summer to foraging in less sheltered microhabitats in response to predation pressure and food availability involves a significant physiological cost moderated by midday reduction in activity. Thus adaptation to diurnality may reflect the 'ghost of competition past'; Climate-driven diurnality is an alternative but less likely hypothesis. While climate is considered to play a major role in the physiology and evolution of mammals, this is the first study to model its effect on the evolution of activity patterns of mammals.
Data file for the paper "General Models for the Electrochemical Hydrogen Oxidation and Hydrogen Evolution Reactions – Theoretical Derivation and Experimental Results Under Near Mass-Transport Free Conditions", J. Phys Chem. C., 2016, DOI:10.1021/acs.jpcc.6b00011
<p>The data in this folder is supplementary information for the paper:<br /> Anthony Kucernak and Christopher Zalitis, "General Models for the Electrochemical Hydrogen Oxidation and Hydrogen Evolution Reactions – Theoretical Derivation and Experimental Results Under Near Mass-Transport Free Conditions", J. Phys Chem. C., 2016, DOI:10.1021/acs.jpcc.6b00011</p> <p>The information is © Anthony Kucernak</p> <p>A description of the models used in these files is provided in that paper. Below is a description of the files</p> <p>Experimental Data.xlsx - This file contains the experimental data used to produce figures 6 and 7 in the aforementioned paper<br /> Model.xlsx - This file contains verified versions of the Heyrovsky-Volmer, Tafel-Volmer and Heyrovsky-Tafel-Volmer mechanisms developed in the paper mentioned above. These excel spreadsheets may be used to fit experimental data user the Solver function in Excel.</p> <p>Heyrovsky-Tafel.cdf, Heyrovsky-Tafel-Volmer.cdf, Tafel-Volmer.cdf, Heyrovsky-Volmer.cdf - These are "computable document format" files produced using Wolfram Mathematica. They allow easy and quick modification of model parameters to allow real-time exploration of the effect of the parameters on current density (as linear and Tafel plots), hydrogen coverage, Effective Tafel slope, and derived parameters. The CDF viewer is availble to download from the Wolfram site - www.wolfram.com</p>
Laurentide Ice Sheet evolution towards the Last Glacial Maximum using AWIESM model with interactive ice sheets
<p>This archive contains model data and figures associated with the study titiled "Rapid Laurentide Ice Sheet growth preceding the Last Glacial Maximum due to summer snowfall" (Niu et al., 2024). The comprehensive Earth system model AWI-ESM with interactive ice sheets is used for the model simulations. The notation of the individual files in the archive corresponds to the respective figure numbers in the paper. The respective file content is described by the corresponding figure caption in the paper.</p> <p>Niu, L., Knorr, G., Krebs-Kanzow, U. et al. Rapid Laurentide Ice Sheet growth preceding the Last Glacial Maximum due to summer snowfall. Nat. Geosci. (2024). https://doi.org/10.1038/s41561-024-01419-z</p> <p> </p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.