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This is a set of 4000 copper (Cu) nanoparticle FINAL CONFIGURATIONS, for use in data-driven studies. These structures have been optimized (fully relaxed) using molecular dynamics with an embedded atom... more (EAM) interatomic potential, at various temperatures and growth rates.
All files are in XYZ format, and the naming convention is defined in the accompanying csv file that lists all of the structural features and energetic properties (see Supporting Attachments).
Sizes range from 133 atoms to 19591 atoms, with both crystalline and non-crystalline configurations and regions. Each nanoparticle has been characterised using a variety of topological features, including size, lattice structure, surface curvature and a number of order parameters. The final two columns in the accompanying csv file are target labels, providing the total energy and the excess formation energy. Other features can also be used as labels as desired.less
Machine Learning Group Operating Cost - Nanostructure Data Bank - Published 29 Jan 2020
Outdoor freshwater mesocosms spiked with varying concentrations of copper were sampled in order to profile microbial communities. Samples collected include water, sediment and cellulose baits. DNA was... more extracted from all sample types. In addition to this, RNA was extracted from sediment samples and reverse transcribed to get cDNA. The v4 region of the 16S ribosomal RNA gene was amplified using Earth Microbiome primers 515F and 806R.
The 16S rRNA gene amplicons were sequenced on the Illumina MiSeq platform with 250 base pair-end reads. Forward and reverse read alignments, quality filtering, chimera checking and OTU clustering were performed using USEARCH v9.
OTU sequences were submitted to GenBank, however, 130 were found to be too novel for submission and thus are made available here.less
Legacy data - Microbial community survey - Published 10 Oct 2017
eDNA metabarcoding was performed to assess the effects of copper on the establishment of the benthic eukaryote community within a series of environmentally relevant copper contaminated fresh... morewater mesocosms. The data is obtained from a recolonization experiment contained five treatments : control (C) and four sediment copper concentrations (very low (VL), low (L), high (H) and very high (VH)), each with four replicates. The data represents samples obtained on seven occasions subsequent to the experiment being established: 15, 31, 135, 161, 365, 407 and 497 days.
Details on the experimental design are available in:
Gardham, S., G. C. Hose, S. L. Simpson, C. Jarolimek, and A. A. Chariton. 2014. Long-term copper partitioning of metal-spiked sediments used in outdoor mesocosms. Environmental Science and Pollution Research 21:7130-7139.
1177.2 Estuarine Health Assessment - Experiment - Published 29 Sep 2014