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17 results for “water clusters”
Dataset of "Molecular dynamics of evaporative cooling of water clusters"
<p>The cooling of water clusters through evaporation into a vacuum is studied using classical molecular dynamics with the SPC water model, and the results are compared with semimacroscopic theory. A model based on the Hertz–Knudsen equation underestimates the cooling rates. A modified approach, which accounts for the Kelvin equation, provides better results. While the rotational temperature of the clusters is in equilibrium with their internal temperature, the translational temperature of the clusters “as individual particles” remains unchanged.</p>
GFN2-xTB structures of iCOM adsorbed on a cluster model of water molecules derived from a periodic model of crystalline ice
<p>This dataset contains the atomic coordinates in the <a href="http://www.moldraw.unito.it/">.</a>xyz format of the GFN2-xTB optimized structures of 20 iCOMs adsorbed at the surface of a cluster of 84 water molecules mimicking the periodic model of crystalline water icy grain as described by Ferrero, S.; Zamirri, L., Ceccarelli, C.; Witzel, A.; Rimola, A.; Ugliengo, P. ApJ, (2020) 904:11. For all considered structures we also provided a specific file in the Gaussian format with the computed harmonic frequencies. Each file can be easily converted in input for the variety of quantum mechanical programs, like VASP, QE, Gaussian 16 etc.</p> <p> </p> <p> </p>
Dataset of the publication: Influence of Fe-clustering on the water oxidation performance of two-dimensional layered double hydroxides
<p>Dataset of the publication: Influence of Fe-clustering on the water oxidation performance of two-dimensional layered double hydroxides</p> <p>DOI: 10.1039/d1dt03737d</p> <p>Seijas-Da Silva, A; Oestreicher, V; Coronado, E; Abellán, G</p> <p>Dalton Trans., 2022,51, 4675-4684</p> <p> </p>
Synthesis of urea on the surface of interstellar water ice clusters.
<p>The Supporting Material contains the cartesian coordinates of B3LYP-D3(BJ)/ma-def2-TZVP optimized minima and transition state for the reaction studied in the paper, in .xyz format, computed using <a href="https://gaussian.com/">O</a><a href="https://orcaforum.kofo.mpg.de/">RCA</a> code. The folders are relative to:</p> <ul> <li>gas phase reactions;</li> <li>reactions modelled on the 18 water molecules cluster: <ul> <li>closed-shell + closed-shell;</li> <li>closed-shell + radical;</li> <li>radical + radical (2 outcomes);</li> <li>ion-pair formation (2 pathways);</li> </ul> </li> </ul>
Regional and fine-scale local adaptation in salinity tolerance in Daphnia inhabiting contrasting clusters of inland saline waters
<p>Freshwater salinisation is an important threat to biodiversity, ecosystem functioning, and the provision of ecosystem services. Therefore, understanding the capacity of species to adapt to salinity gradients is crucial. Clusters of naturally saline habitats represent ideal test cases to study the extent and scale of local adaptation to salinisation. We studied local genetic adaptation of the water flea Daphnia magna, a key component of pond food webs, to salinity in two contrasting landscapes - a dense cluster of sodic bomb crater ponds and a larger-scale cluster of soda pans. We show regional differentiation in salinity tolerance reflecting the higher salinity levels of soda pans versus bomb crater ponds. We found local adaptation to differences in salinity levels at the scale of tens of metres among bomb crater pond populations but not among geographically more distant soda pan populations. The population-level salinity tolerance range was reduced in more saline bomb crater ponds through an upward shift of the minimum salt tolerance observed across clones and a consequent gradual loss of less tolerant clones in a nested pattern. Our results show genetic adaptation to salinity gradients at different spatial scales and fine-tuned local adaptation in neighbouring habitat patches in a natural landscape.</p>
Data and geometries for "Understanding X-ray absorption in liquid water using triple excitations in multilevel coupled cluster theory"
<p>Geometries and raw and processed data for the paper "Understanding X-ray absorption in liquid water using<br>triple excitations in multilevel coupled cluster theory"</p> <p>This work has received funding from the European Research Council (ERC)<br>under the European Union’s Horizon 2020 Research and Innovation Program<br>(grant agreement no. 101020016 and 860553), the Research Council of Norway through FRINATEK (project no. 275506), the Swedish Research Council (grant agreement no. 2021-04521), the Independent Research Fund Denmark--Natural Sciences, DFF-RP2 (grant no. 7014-00258B)<br>Computing resources from UNINETT Sigma2—the National Infrastructure for High Performance Computing<br>and Data Storage in Norway (project no. NN2962k),<br>from DeIC—Danish Infrastructure Cooperation (grant no. DeiC-DTU-N3-2023027), and from the Swiss National Supercomputing Centre (project ID uzh1).</p>
Predicting Properties of Periodic Systems from Cluster Data: A Case Study of Liquid Water
<ul> <li> Description</li> </ul> <p>The 1520 water clusters were extracted from Ref. 1. The respective energies and atomic forces were recomputed at the revPBE-D3/def2-TZVP [2-6], B3LYP-D3/def2-TZVP [4-6, 7, 8], and BLYP-D3/def2-TZVP [4-6, 7, 9] level.</p> <ul> <li> Format</li> </ul> <p>The data is stored in python compressed array format (.npz) with the atomization energy in kcal/mol and atomic forces in kcal/mol/Ang. The data set contains five np.ndarray</p> <pre><code>import numpy as np data = np.load('revpbe.npz') data['R'] # Cartesian coordinates of nuclei in Ang. data['E'] # Total energy in kcal/mol data['F'] # Atomic forces in kcal/mol/Ang. data['N'] # Number of atoms in each structure data['Z'] # Nuclear charges</code></pre> <p>References</p> <ul> </ul> <p>[1] Molpeceres G., Zaverkin V., and Kästner J., “Neural-network assisted study of nitrogen atom dynamics on amorphous solid water – I. adsorption and desorption,” Mon. Not. R. Astron. Soc. 499, 1373 (2020).</p> <p>[2] P. E. Blöchl, “Projector augmented-wave method,” Phys. Rev. B 50, 17953 (1994).</p> <p>[3] Y. Zhang and W. Yang, “Comment on “generalized gradient approximation made simple”,” Phys. Rev. Lett. 80, 890 (1998).</p> <p>[4] S. Grimme, J. Antony, S. Ehrlich, and H. Krieg, “A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu,” J. Chem. Phys. 132, 154104 (2010).</p> <p>[5] F. Weigend and R. Ahlrichs, “Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy,” Phys. Chem. Chem. Phys. 7, 3297 (2005).</p> <p>[6] F. Weigend, “Accurate Coulomb-fitting basis sets for H to Rn,” Phys. Chem. Chem. Phys. 8, 1057 (2006).</p> <p>[7] A. D. Becke, “Density-functional thermochemistry. iii. the role of exact exchange,” J. Chem. Phys. 98, 5648 (1993).</p> <p>[8] P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch, “Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields,” J. Phys. Chem. 98, 11623 (1994).</p> <p>[9] C. Lee, W. Yang, and R. G. Parr, “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Phys. Rev. B 37, 785 (1988).</p>
Data Set "Accurate quantum-chemical fragmentation calculations for ion–water clusters with the density-based many-body expansion"
<p>This data set accompanies the publication "Accurate quantum-chemical fragmentation calculations for ion–water clusters with the density-based many-body expansion"</p> <p>It contains:</p> <p>- xyz files of all considered molecular structures.</p> <p>- PyADF input scripts for running the eb-MBE and db-MBE calculations.</p> <p>- raw results data from the eb-MBE and db-MBE calculations</p> <p>- Jupyter notebooks for generating the plots and tables</p>
Efficient parameterization of transferable Atomic Cluster Expansion for water
<p>This collection contains files associated with Journal of Chemical Theory and Computation. "Efficient parameterization of transferable Atomic Cluster Expansion for water" (2024) paper:</p> <p>- ACE potentials for water.</p> <p>-Active set inverted (ASI) for the ACE potential</p> <p>- Training dataset that was used for fitting Atomic Cluster Expansion potential.</p>
Regional and fine-scale local adaptation in salinity tolerance in Daphnia inhabiting contrasting clusters of inland saline waters
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Water Cluster Electron Density Database
<p>This database contains electron densities represented in the def2-universal-JFIT atom centered basis for select members of the Database of Water Cluster Minima from Rakshit and co-workers. All densities are projected from the one particle reduced density matrix with the total number of electrons constrained to the correct number. </p> <p> </p> <p>See attached description for details.</p>
Collision-induced dissociation of protonated uracil water clusters probed by molecular dynamics simulations
<p>This dataset contains the input and output files associated to the work of "Collision-induced dissociation of protonated uracil water clusters probed by molecular dynamics simulations"</p> <p> </p> <p> </p>
Dataset: Water-flume model geometries of a tall-building cluster in Beijing
<p>This dataset contains CAD drawings (.stl files) of five geometry variations of a cluster of tall buildings in Beijing. The dimensions are in model scale (S1 = 1:2400; S2 = 1:4800) and have units of mm. The models were used in water-flume experiments at the University of Southampton in collaboration with the University of Reading (flow and concentration measurements).</p> <p>This repository contains:</p> <ol> <li>wf_geometry_readme.pdf : Meta information and description of data in 'wf_geometry.zip'</li> <li>wf_geometry.zip : model drawings (.stl files)</li> </ol>
Exploration of the electron density and bare nuclear potential along the selected normal modes of the selected water clusters - W6 - changedHexamers
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Exploration of the electron density and bare nuclear potential along the selected normal modes of the selected water clusters - W6
Open the record for dataset details and reuse information.
A cluster-randomized trial of water, sanitation, handwashing and nutritional interventions on stress and epigenetic programming
GEO Series GSE261098. Homo sapiens. 745 samples. Type: Other.
A Method of Water Resources Accounting Based on Deep Clustering and Attention Mechanism under the Background of Integration of Public Health Data and Environmental Economy
<p>A dataset and code for paper</p>
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