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Data and Code for "Comparing the Effects of Euclidean Distance Matching and Dynamic Time Warping in the Clustering of COVID-19 Evolution"

This repository contains the datasets and data sources, analysis code, and workflow associated with the manuscript "Comparing the Effects of Euclidean Distance Matching and Dynamic Time Warping in the Clustering of COVID-19 Evolution". The following resources are provided: <ul> <li> Data Files: <ul> <li><code>time_series_data.csv</code>: A curated time series dataset with dates as rows and NUTS 2 regions as columns. Each column is labeled using a 4-letter abbreviation format "CC.RR", where "CC" represents the country code and "RR" represents the region code. This same abbreviation is also included in the accompanying GeoJSON file.</li> <li><code>geometry_data.geojson</code>: A GeoJSON file representing the spatial boundaries of the NUTS 2 regions, with the same 4-letter abbreviations used in the CSV file. EPSG:4326.</li> <li><code>COVID19_data_sources.xlsx</code>: This Excel file contains important metadata regarding the sources of COVID-19 data used in this study. It includes: <ul> <li>Source of the data for each country</li> <li>Official website(s)</li> <li>The agency responsible for the data</li> <li>Description of the processing steps used to curate the data into the final time series.</li> </ul> </li> </ul> </li> <li> Code: <ul> <li><code>analysis.py</code>: A Python script used to process and analyze the data. This code can be run using Python 3.x. The libraries required to run this script are listed in the first lines of the code. The code is organized in different numbered sections (1), (2), ... and sub-sections (1a), (1b) ... Make sure to run the script one (sub-)section at a time, so that everything stays overviewable and you don't get all the output at once.</li> </ul> </li> <li> Workflow: <ul> <li><code>workflow.png</code> : A detailed workflow according to the Knowledge Discovery in Databases (KDD) process, outlining the steps involved in processing and analyzing the data, including the methods used. This workflow provides a comprehensive guide to reproducing the analysis presented in the paper.</li> </ul> </li> </ul>

Model results and data associated with "Antecedent effect models as an exploratory tool to link climate drivers to herbaceous perennial population dynamics data"

Model results and data (including Bayesian posteriors) associated with "Antecedent effect models as an exploratory tool to link climate drivers to 3 herbaceous perennial population dynamics data". This is a repository created to store the posteriors of the models fit within this project. Because these occupy so much space, it makes sense to store them in a separate repository. There are two directories: <ul> <li>model_results/ contains all of the posteriors (files with character pattern main_posterior_#.csv). The three types of files contained in this directory are described in metadata_model_results.xlsx. The number # corresponds to column "index" in file raw_data/design_insample.csv.</li> <li>raw_data/ is mostly not essential: it contains the raw data to fit models, and it replicates folder data/ in repository https://dx.doi.org/10.5281/zenodo.13909628.</li> </ul>

opencc-by-4.0Jul 2023View details →

Dataset for ""A dynamic isotope effect in the nucleophilic substitution reaction F- + CD3I"

Dataset for ""A dynamic isotope effect in the nucleophilic substitution reaction F- + CD3I"

Photophysical and Spectroscopic dataset for Carrier Dynamics and Recombination in Ag-In-Zn-S Quantum Dots

(1) HR-TEM images of alloyed AgIn1.5Zn1.9S3.6 (A1) and AgIn1.5Zn4.4S6.8 (A2) nanocrystals. (2) Energy-dispersive spectra of alloyed AgIn1.5Zn1.9S3.6 (A1) and AgIn1.5Zn4.4S6.8 (A2) nanocrystals. (3) UV-vis-NIR spectra of A1 nanocrystals and A1-MV, where the nanocrystals are conjugated with methyl viologen (MV2+) molecules. (4) (a) Normalized PL decays of A1 nanocrystals measured at various detection wavelengths, (b and c) PL decays measured at room temperature for A1 and A2 nanocrystals, (d and e) PL decays measured at various temperatures for A1 and A2 nanocrystals. (5) Transient absorption (TA) spectra for A1 nanocrystals for various pump-probe delays.   This work was supported by National Science Centre Poland Grant No. 2019/35/B/ST3/04235. P.K., P.B., and A.P. acknowledge the financial support from the National Science Centre of Poland, Grant No. 2022/45/B/ST5/02120.

Data - Host-guest dynamic behavior of melatonin encapsulated in beta-cyclodextrin nanosponges

Amber topologies, input coordinates and MD trajectories for the simulations of: <ul> <li>free melatonin in solution (gaff2+TIP3P)</li> <li>free beta-cyclodextrin in solution (GLYCAM-06j+TIP3P, GLYCAM-06j+OPC, GLYCAM-06j+OPC3)</li> <li>melatonin:beta-cyclodextrin monomeric inclusion complex in solution from three starting geometries (linear, folded1, and folded2) in solution (GLYCAM-06j+TIP3P+gaff2).</li> <li>nanopsonge models with acyclic (ns3, ns4, and ns5) and cyclic (ns5c and ns7c) topologies resulting from beta-cyclodextrin crosslinking with citric acid, in solution (GLYCAM-06j+TIP3P+gaff2).</li> <li>the same nanosponge models (3MT-ns3, 4MT-ns4, 5MT-ns5, 5MT-ns5c, and 7MT-ns7c) loaded with melatonin with 1:1 melatonin:beta-cyclodextrin ratio, in solution (GLYCAM-06j+TIP3P+gaff2).</li> </ul> All MD trajectories are saved with an even stride of 10 ns.

opencc-by-4.0Sep 2024View details →

A new parameterisation for homogeneous ice nucleation driven by highly variable dynamical forcings

This archive contains the data associated with the preprint of the article "A New Parameterization for Homogeneous Ice Nucleation Driven by Highly Variable Dynamical Forcings." The collection includes datasets used to construct the initial conditions for forcing an air parcel model with ice physics, outputs produced by the parcel model, and data necessary for generating the plots presented in the paper. A README file is provided, offering a detailed explanation of the contents and structure of the archive,

opencc-by-4.0Sep 2024View details →

Data for: A computational pipeline to observe the flexibility and dynamics of (plant) cytochrome P450 binding sites

Binding site flexibility and dynamics strongly affect the ability of proteins to accommodate substrates and inhibitors. The significance of these properties is particularly pronounced for proteins that are inherently flexible, such as cytochrome P450 enzymes (CYPs). While the research on human CYPs provides detailed knowledge on both structural and functional level, such analyses are still lacking for their plant counterparts. This study aims to bridge this gap. Firstly, we use molecular dynamics (MD) simulations to capture the full conformational ensemble for a certain plant CYP. Subsequently, we developed and applied a comprehensive methodology to analyse a number of binding site properties - size, flexibility, shape, hydrophobicity, and accessibility - using the fpocket and mdpocket packages on MD-generated trajectories. This led to a first categorization of 15 chosen plant CYPs based on their binding site's (dis)similarities. The workflow was tested and verified on human CYPs 1A2, 2A6, and 3A4 as their binding site characteristics are well known. In addition to confirming known binding site properties, we identified and named previously unseen binding site channels for CYPs 1A2 and 2A6. This study gives initial insights into the largely uncharted fields plant CYP substrate specificity and facilitates a more precise understanding of their largely unknown specific biological functions. It offers new insights into the structural and functional dynamics of plant CYPs, which may facilitate a more accurate understanding of the fate of agrochemicals or the biotechnological design and exploitation of enzymes with specific functions. Additionally, it serves as a reference for future structural-functional analyses of CYP enzymes across various biological kingdoms.

The dataset of "Evaluation of Digital Supply Chain Technology's Impact on Sustainability Under the Moderate Effect of Supply Chain Dynamism: An Empirical Research in the Chinese Energy Supply Chain"

This dataset involves the data from the questionnaire, which come from the project "Evaluation of Digital Supply Chain Technology’s Impact on Sustainability Under the Moderate Effect of Supply Chain Dynamism: An Empirical Research in the Chinese Energy Supply Chain". It comprises three dimensions questions, technology, sustainability and supply chain dynamism. The datas come from two Chinese energy firms, China Resources Power Zhejiang Company and Hunan HuaDian Changsha Electric Co., Ltd.

Reproducibility pack for article: Quantum turbulence, superfluidity, non-Markovian dynamics, and wave function thermalization

The supplementary material contains a reproducibility pack for results presented in the paper: Quantum turbulence, superfluidity, non-Markovian dynamics, and wave function thermalization Aurel Bulgac, Matthew Kafker, Ibrahim Abdurrahman, and Gabriel Wlazłowski <a href="https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.6.L042003">Phys. Rev. Research 6, L042003 (2024)</a> The packs contain full information needed to restore the numerical simulation of dynamics of 12 quantum vortices. To be able to restore the results of calculations, you need to use the <a href="https://wslda.fizyka.pw.edu.pl/">W-SLDA Toolkit</a>. See the documentation of the <a href="https://wslda.fizyka.pw.edu.pl/">W-SLDA Toolkit</a> to learn how to use the code and the reproducibility packs.

opencc-by-4.0Apr 2024View details →

Supplementary Material: Investigating Interaction Dynamics of an Enantioselective Peptide Catalyzed Acylation Reaction

Supplementary material to the publication "Investigating Interaction Dynamics of an Enantioselective Peptide Catalyzed Acylation Reaction". The files contain the raw nuclear magnetic resonance (NMR) spectra and computed structures. A README-file with detailed information is provided.

Data from: Hyperspectral imaging reveals differential carotenoid and chlorophyll temporal dynamics and spatial patterns in Scots pine under water stress

Data and codes associated with the manuscript 'Hyperspectral imaging reveals differential carotenoid and chlorophyll temporal dynamics and spatial patterns in Scots pine under water stress'.

ReaxANA: Analysis of Reactive Dynamics Trajectories for Reaction Network Generation

ReaxFF simulations, QM calculation input/output files, and Jupyter notebooks for data analysis and visualization.

Experimental data for Dynamic cover effects in lateral bedrock channel bank abrasion: Experiment and model comparison

Experimental data for bank erosion.xlsx contains the data used for the figures in the paper, and the distribution of bedrock bank erosion in the longitudinal direction in Run 1 - Run 18.

Molecular dynamics simulations of RNA Pol I closed complex in WT and with modifications to DNA base pairs -27 and -28

The starting structure for the modelling was cryo-EM based structure of S. cerevisiae pre-initiation complex, showing Pol I, RRN3 and CF bound on a rDNA promoter at 2.90 Å resolution. This structure (‘RNA Polymerase I closed conformation 2’; accession code: 6RQL) was downloaded from the PDB database and prepared using the Protein Preparation Workflow of Maestro with default settings. This included filling in missing sidechains, optimizing hydrogen bonds and protonation using PROPKA at pH 7.4, deleting water molecules >5Å from the heteroatoms and a short energy minimization using OPLS4 force field. The initial structures for the complexes with DNA mutations were constructed from this pre-processed structure by manually mutating the base pairs at position -28 or -27 of the rDNA promoter from C·G to A·T (tDNA·ntDNA) and from A·T to C·G, respectively. MD simulations (3*80 ns/system) were conducted with Desmond using default parameters from Schrödinger Suite version 2024-1 on the CSC (IT Center for Science, Finland) supercomputer Puhti.

Dataset of "Mapping of Internal Ionic/Electronic Transient Dynamics in Current-Voltage Operation of Perovskite Solar Cells"

This dataset supports the article: "Mapping of Internal Ionic/Electronic Transient Dynamics in Current-Voltage Operation of Perovskite Solar Cells"   Raw data for the article "Mapping of Internal Ionic/Electronic Transient Dynamics in Current-Voltage Operation of Perovskite Solar Cells". For further details see the readme.txt file.

Experimental and simulated data for the article "Reassessing the role and lifetime of Qx in the energy transfer dynamics of Chlorophyll a"

The .zip file contains: <ul> <li>Linear absorption spectra of Chl a in EtOH, acetone, and benzonitrile (BN)</li> <li>Low-temperature emission and excitation anisotropy datasets of Chl a in isopropanol</li> <li>Transient absorption (TA) datasets of Chl a in EtOH, acetone, and BN after B- and Q-band excitation (including pump spectra)</li> <li>Transient absorption anisotropy (TAA) datasets of Chl a in acetone after B-band excitation (including a pump spectrum)</li> <li>Optimized geometries for the Q-band ESA calculations</li> <li>Geometries for normal modes used for PES construction</li> </ul>

Trajectories of Microsecond Molecular Dynamics Simulations of the Orexin Receptor 2 System with Lemborexant

This data set contains psf files and trajectories (.dcd files) of the performed simulations for the orexin receptor 2 system: 1) the orexin type 2 receptor (OX2R) in complex with lemborexant, three replicas

Trajectories of Microsecond Molecular Dynamics Simulations of the Orexin Receptor 2 System with Compound 1

Succession of bacteria and archaea within the soil micro-food web shifts soil respiration dynamics

Supplementary Table 5. Overview over abundance changes, taxonomic affiliation, and response type of dominant ASVs under the different treatment combinations. M: maize litter , A: A. buetschlii, + and – signs indicate presence and absence, respectively.

Repository for "Light-induced cortical excitability reveals programmable shape dynamics in starfish oocytes"

Data and code repository for paper "Light-induced cortical excitability reveals programmable shape dynamics in starfish oocytes". DOI tbd.