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23 results for “partition function”
Biomass totals and root biomass (partitioned by percent of total leaf area) for species, tissue type, and functional group for the Arctic LTER experimental 1981 mesic acidic tussock tundra (MAT81) for the 2000 and 2015 harvests, Toolik Field Station, Alaska.
Whole plant biomass totals and root biomass (partitioned by percent of total leaf area) for species, tissue type, and functional group for the Arctic LTER experimental 1981 mesic acidic tussock tundra (MAT81) for the 2000 and 2015 harvests. Because most of the root biomass could not be identified to species in either 2000 or 2015, the calculation of root biomass and element content for roots not identified to species was estimated by the proportion of those species’ contributions to total leaf area. Specific Leaf Area (SLA = leaf area per gram leaf, centimeter squared per gram) values were available from several previous harvests of this experiment; in the present study, we used measurements from the 1995 harvest (Shaver et al. 2001).
Ideal gas thermodynamic functions for NO from the total partition sum and its moments
<p><span><span>to be published in the Journal of Physical and Chemical Reference Data</span></span></p> <p><span><span> </span>The total internal partition sum, <em>Q</em><sub>int</sub>(<em>T</em>), and the translational partition sum, <em>Q</em><sub>trans</sub>(<em>T</em>), were computed for six isotopologues of NO: <sup>14</sup>N<sup>16</sup>O,<sup> 15</sup>N<sup>16</sup>O, <sup>14</sup>N<sup>18</sup>O, <sup>14</sup>N<sup>17</sup>O,<sup> 15</sup>N<sup>18</sup>O, <sup>15</sup>N<sup>17</sup>O.<span> </span>These were used to determine the total partition sum, <em>Q</em> (<em>T</em>), and its first and second moments, Q'(T)</span><span></span><span>, and Q"(T) </span><span></span><span>.<span> </span>The total internal partition sum was computed using term values determined using the term values of Qu <em>et al.</em> [MNRAS, 504, 5768-5777, (2021)] for <sup>14</sup>N<sup>16</sup>O and Wong <em>et al</em>. [MNRAS, 470, 882-897, (2017)] for the other isotopologues.<span> </span>These term values are the best available and hence provide the most accurate total internal partition sums and its first and second moments.<span> </span>The uncertainties in <em>Q</em><sub>int</sub>(T), its moments, and the resulting thermodynamic functions were determined in terms of the uncertainty in the term values and the uncertainty due to the convergence of the partition sum and its moments.<span> </span>From these quantities the isobaric heat capacity, the Helmholtz energy, the entropy, the enthalpy, the Gibbs function, and the JANAF [Chase <em>et al</em>., J. Phys. Chem. Ref. Data, 14, 1-856, 1985] functions: <em>hef</em>, and <em>gef</em> and their uncertainties were computed on a 1 K grid from 1 to 9000 K.<span> </span>The data are compared with the literature values.<span> </span>The resulting thermodynamic quantities are the most accurate determined from direct summation of <em>Q</em>(<em>T</em>), </span><span>Q'(T)</span><span></span><span>, and Q"(T)</span>.</p>
Data Related to Osorio-Forero, Foustoukos, Cardis et al., "Noradrenergic locus coeruleus activity functionally partitions NREMS to gatekeep the NREM-REM cycle"
<p>This Zenodo Upload contains the Transparent Data Files for an updated version of the manuscript currently published in Nature Neuroscience</p> <p>and entitled </p> <p><em>'</em>Infraslow noradrenergic locus coeruleus activity fluctuations control are gatekeepers of the NREM–REM sleep cycle' </p> <p>published by the authors as indicated in the author list.</p>
Low-cost prediction of molecular and transition state partition functions via machine learning
<p>This dataset contains the vibrational, rotational, translational, and electronic partition functions for 35,883 organic chemistry molecular structures taken from the Grambow et. al dataset [1]. It was used to train ML deep neural networks to predict unknown transition state partition functions as well as partition functions for known molecular structures [2]</p> <p>The partition functions were computed at temperatures in the range T= [50, 2000] K with the rigid rotor, rigid body, harmonic oscillator approximations. Reactions involve no more than 7 C, N, or O atoms.</p> <p>Frequencies for the vibrational partition functions were taken from [1] where they were computed with DFT at the ωB97X-D3/def2-TZVP level of theory.</p> <p>For the rotational partition function, symmetry numbers were obtained by evaluating proper and improper invariant rotations of the structures. We note that structures involving two molecules were not separated: vibrational frequencies and symmetry numbers were computed for the aggregate structure.</p> <p>For each reaction, partition functions were calculated at 50 temperatures sampled uniformly from the inverse temperature range 1/T = [1/2000, 1/50] K<sup>-1</sup>. This corresponds to 11,961 reactions, 35,883 total structures, and 1,794,150 total partition function examples.</p> <p>The file Partition_Functions.tar.gz contains directories entitled “rxnXXXXXX” where XXXXXX is a reaction number identifier. Each contain three files “rXXXXXX.csv”, “pXXXXXX.csv”, “tsXXXXXX.csv” corresponding to data from the reactant (“r”), product (“p”), and transition state (“ts”) for reaction XXXXXX. Note that the directory structure and the reaction identifiers are the same as used in the original structure dataset by Grambow et al. and the corresponding structures can easily be extracted from that dataset. Each comma separated value (csv) file contains 50 rows and the following columns:</p> <table> <tbody> <tr> <td> <p><strong> Column label</strong></p> </td> <td> <p><strong> Values</strong></p> </td> </tr> <tr> <td> <p> T [K]</p> </td> <td> <p> Temperature</p> </td> </tr> <tr> <td> <p> qpart_ele [unitless]</p> </td> <td> <p> Electronic partition function</p> </td> </tr> <tr> <td> <p> qpart_trans [unitless]</p> </td> <td> <p> Translational partition function</p> </td> </tr> <tr> <td> <p> qpart_vib [unitless]</p> </td> <td> <p> Vibrational partition function</p> </td> </tr> <tr> <td> <p> qpart_rot [unitless]</p> </td> <td> <p> Rotational partition function</p> </td> </tr> <tr> <td> <p> qpart [unitless]</p> </td> <td> <p> Partition function</p> </td> </tr> <tr> <td> <p> log_qpart_trans [unitless] </p> </td> <td> <p> Natural logarithm of translational partition function</p> </td> </tr> <tr> <td> <p> log_qpart_rot [unitless]</p> </td> <td> <p> Natural logarithm of rotational partition function</p> </td> </tr> <tr> <td> <p> log_qpart_vib [unitless]</p> </td> <td> <p> Natural logarithm of vibration partition function</p> </td> </tr> <tr> <td> <p> log_qpart [unitless]</p> </td> <td> <p> Natural logarithm of partition function</p> </td> </tr> </tbody> </table> <p> </p> <p>[1] C. A. Grambow, L. Pattanaik, and W. H. Green, “Reactants, products, and transition states of elementary chemical reactions based on quantum chemistry,” <em>Sci. Data</em>, <strong>7</strong>:1–8, 2020.</p> <p>[2] Komp, E. Valleau, S. “Low-cost prediction of molecular and transition state partition functions via machine learning”, arXiv:, 2022.</p> <p> </p>
Data for: Many-body thermodynamics on quantum computers via partition function zeros
<p>Partition functions are ubiquitous in physics: they are important in determining the thermodynamic properties of many-body systems, and in understanding their phase transitions. As shown by Lee and Yang, analytically continuing the partition function to the complex plane allows us to obtain its zeros and thus the entire function. Moreover, the scaling and nature of these zeros can elucidate phase transitions. Here we show how to find partition function zeros on noisy intermediate-scale trapped ion quantum computers in a scalable manner, using the XXZ spin chain model as a prototype, and observe their transition from XY-like behavior to Ising-like behavior as a function of the anisotropy. While quantum computers cannot yet scale to the thermodynamic limit, our work provides a pathway to do so as hardware improves, allowing the future calculation of critical phenomena for systems beyond classical computing limits.</p>
Data for: Many-body thermodynamics on quantum computers via partition function zeros
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Data from: Taxonomic divergence and functional convergence in Iberian spider forest communities: insights from beta diversity partitioning
Aim The main aims were to determine: i) the relative contribution of species replacement and richness difference components to overall taxonomic (TDβ) and functional (FDβ) beta diversity of spider communities; ii) the degree to which TDβ and FDβ components can be explained by the environmental or geographic predictors; iii) whether FDβ components were lower than expected given the underlying TDβ variation. Location This study was carried out in 22 oak forest sites across the Iberian Peninsula. The area comprises two biogeographic regions, Eurosiberian (North) and Mediterranean (Centre and South). Methods Spiders were sampled using a standardized protocol. A species x traits matrix was constructed. Total taxonomic (TDβtotal) and total functional (FDβtotal) beta diversity were calculated, by pairwise comparisons, and partitioned into their replacement (βrepl) and richness difference (βrich) components. Mantel tests were used to relate taxonomic and functional dissimilarity with environmental and geographic distances. A spatial eigenfunction model was constructed and the variation of TDβ and FDβ explained by environment and geographic predictors was quantified. Null models were used to test if FDβ was higher or lower than expected given TDβ. Results βrepl was the dominant component contributing to 84.2% and 72.8% for TDβtotal and FDβtotal, respectively. TDβtotal and FDβtotal (and their replacement components) were higher between- than within-biogeographic regions. TDβtotal and TDβrepl were positively correlated with environmental and geographic distances, even when controlling for a biogeographic effect, but their functional counterparts were only correlated with environmental distance. Variation partitioning showed that pure environmental and spatially structured environmental effects had a small contribution to beta diversity, except for TDβrich. The observed slopes of the regressions of FDβtotal and FDβrepl in relation to environmental distance were slower than the null model expectations. Main conclusions Spider' assemblages variation was mainly determined by the replacement, and not the net loss, of species and traits. TDβ was influenced by niche filtering and dispersal limitation, whereas FDβ was mainly generated by niche filtering. A high level of functional convergence among spider communities, despite the high taxonomic divergence, revealed the signal of replacement of species performing similar functions across sites.
Rovibrational partition functions of fulminic acid (HCNO), cyanic acid (HOCN), and isofulminic acid (HONC)
<p>Rovibrational partition functions of fulminic acid (HCNO), cyanic acid (HOCN), and isofulminic acid (HONC)</p>
Partition Function Estimation: A Quantitative Study
<p>Dataset, results, executables, and scripts relevant to the paper 'Partition Function Estimation: A Quantitative Study' published in IJCAI'21.</p>
Data from: Partitioning the effects of plant diversity on ecosystem functions at different trophic levels
<p class="MsoNormal"><span>Biodiversity effects on ecosystem functioning can be partitioned into complementarity effects, driven by many species, and selection effects, driven by few. Selection effects occur through interspecific abundance shifts (dominance) and intraspecific shifts in functioning. Complementarity and selection effects are often calculated for biomass, but very rarely for secondary productivity, i.e. energy transfer to higher trophic levels. We calculated diversity effects for three functions: aboveground biomass, insect herbivory and pathogen infection, the latter two as proxies for energy transfer to higher trophic levels, in a grassland experiment (PaNDiv) manipulating species richness, functional composition, nitrogen enrichment and fungicide treatment. Complementarity effects were on average positive and selection effects negative for biomass production and pathogen infection and multiple species contributed to diversity effects in mixtures. Diversity effects were on average less pronounced for herbivory. Diversity effects for the three functions were not correlated, because different species drove the different diversity effects. Benefits (and costs) from growing in diverse communities, be it reduced herbivore or pathogen damage or increased productivity either due to abundance increases or increased productivity per area were distributed across different plant species, leading to highly variable contributions of single species to diversity effects on different functions. These results show that different underlying ecological mechanisms can result in similar overall diversity effects across functions.</span></p>
Data from: Taxonomic divergence and functional convergence in Iberian spider forest communities: insights from beta diversity partitioning
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Data from: The ‘heritability’ of domestication and its functional partitioning in the pig
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Data from: Partitioning the effects of plant diversity on ecosystem functions at different trophic levels
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Data from: Functional niche partitioning in Therizinosauria provides new insights into the evolution of theropod herbivory
Dietary specialization is generally considered to be a crucial factor in driving morphological evolution across extant and extinct vertebrates. The ability to adapt to a specific diet and to exploit ecological niches is thereby influenced by functional morphology and biomechanical properties. Differences in functional behaviour and efficiency can therefore allow dietary diversification and the coexistence of similarly adapted taxa. Therizinosauria, a group of secondarily herbivorous theropod dinosaurs, is characterized by a suite of morphological traits thought to be indicative of adaptations to an herbivorous diet. Digital reconstruction, theoretical modelling and computer simulations of the mandibles of therizinosaur dinosaurs provides evidence for functional niche partitioning in adaptation to herbivory. Different mandibular morphologies present in therizinosaurians were found to correspond to different dietary strategies permitting coexistence of taxa. Morphological traits indicative of an herbivorous diet, such as a downturned tip of the lower jaw and an expanded postdentary region, were identified as having stress mitigating effects. The more widely distributed occurrence of these purported herbivorous traits across different dinosaur clades suggests that these features also could have played an important role in the evolution and acquisition of herbivory in other groups.
Data from: Below-ground resource partitioning alone cannot explain the biodiversity–ecosystem function relationship: a field test using multiple tracers
1. Belowground resource partitioning is among the most prominent hypotheses for driving the positive biodiversity-ecosystem function relationship. However, experimental tests of this hypothesis in biodiversity experiments are scarce, and the available evidence is not consistent. 2. We tested the hypothesis that resource partitioning in space, in time, or in both space and time combined drives the positive effect of diversity on both plant productivity and community resource uptake. At the community level, we predicted that total community resource uptake and biomass production above- and belowground will increase with increased species richness or functional group richness. We predicted that at the species level resource partition breadth will become narrower, and that overlap between the resource partitions of different species will become smaller with increasing species richness or functional group richness. 3. We applied multiple resource tracers (Li and Rb as potassium analogues, the water isotopologues - H218O and 2H2O, and 15N) in three seasons at two depths across a species and functional group richness gradient at a grassland biodiversity experiment. We used this multidimensional resource tracer study to test if plant species partition resources with increasing plant diversity across space, time, or both simultaneously. 4. At the community level, community resource uptake of nitrogen and potassium and above- and belowground biomass increased significantly with increasing species richness but not with increasing functional group richness. However, we found no evidence that resource partition breadth or resource partition overlap decreased with increasing species richness for any resource in space, time, or both space and time combined. Synthesis: These findings indicate that belowground resource partitioning may not drive the enhanced resource uptake or biomass production found here. Instead, other mechanisms such as facilitation, species-specific biotic feedback, or aboveground resource partitioning are likely necessary for enhanced overall ecosystem function.
Data from: Below-ground resource partitioning alone cannot explain the biodiversity–ecosystem function relationship: a field test using multiple tracers
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Data from: Functional niche partitioning in Therizinosauria provides new insights into the evolution of theropod herbivory
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Distinct structural and functional heterochromatin partitioning of lamin B1 and lamin B2 revealed using genome-wide Nicking Enzyme Epitope targeted DNA sequencing.
GEO Series GSE261834. Homo sapiens. 51 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Estimating Reciprocal Partition Functions to Enable Design Space Sampling
<p>Paper abstract:</p> <p>Reaction rates are a complicated function of molecular interactions, which can be selected from vast chemical design spaces. Seeking the design that optimizes a rate is a particularly challenging problem since the rate calculation for any one design is itself a difficult computation. Toward this end, we demonstrate a strategy based on transition path sampling to generate an ensemble of designs and reactive trajectories with a preference for fast reaction rates. Each step of the Monte Carlo procedure requires a measure of how a design constrains molecular configurations, expressed via the reciprocal of the partition function for the design. Though the reciprocal of the partition function would be prohibitively expensive to compute, we apply Booth’s method for generating unbiased estimates of a reciprocal of an integral to sample designs without bias. A generalization with multiple trajectories introduces a stronger preference for fast rates, pushing the sampled designs closer to the optimal design. We illustrate the methodology on two toy models of increasing complexity: escape of a single particle from a Lennard-Jones potential well of tunable depth and escape from a metastable tetrahedral cluster with tunable pair potentials.</p> <p>Notes:</p> <p>This .zip contains the source code, analysis scripts, and figure generation scripts for all the results in the paper.</p> <p>Paper link:</p> <p>https://arxiv.org/abs/1911.08535</p>
Gain-of-function RNA Polymerase II partitioning is a shared feature of diverse oncogenic fusions
GEO Series GSE267717. Homo sapiens. 14 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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