1056 research outputs found
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Dataset for "Assessing molecular simulation for the analysis of lipid monolayer reflectometry"
No full textReduced neutron reflectometry dataset associated with a contrast series of DSPC (distearoyl phosphatidylcholine) at the air-water interface. Molecular dynamics simulations at four different areas per molecule are included for three different force-fields. This dataset was used in the publication "Assessing molecular simulation for the analysis of lipid monolayer reflectometry".Within this dataset are neutron reflectometry profiles that were collected at the ISIS Neutron and Muon Source, specifically the SURF instrument.
Also within this dataset are the trajectories and input files for the molecular dynamics simulations of the lipid monolayers that were run using the GROMACS software.The neutron reflectometry data are presented as received following the experiment and the on-site data reduction process.For technical details for the neutron reflectometry experiment, please see Hollinshead et al., 2009 (DOI: 10.1021/la8028319). The .dat files are text files in space-separated value format.
The molecular dynamics simulations were all run on the SCARF cluster at the RAL site, over 16 to 32 nodes. The production runs, that consist of 50 ns (simulation time) data, sampled every 0.1 ns. The GROMACS software (http://www.gromacs.org/) is required read the .cpt, .edr, .pdb, .tpr and .trr files. The .log and .gro files may be opened in a text editor. Please refer to the GROMACS reference manual for details of these file formats
Data supporting "Structure and properties of ‘Type IV’ lanthanide nitrate hydrate:urea deep eutectic solvents"
No full textThis dataset contains reduced neutron and X-Ray scattering data. These data can be used to model and determine the nanostructure of novel 'Type IV' lanthanide nitrate hydrate:urea deep eutectic solvents (in this case Ln = Ce), using Empirical Potential Structure Refinement (EPSR) modelling.Neutron data were collected using the NIMROD diffraction instrument at TS2 of the STFC ISIS neutron and muon facility. Samples were measured into flat-plate TiZr cells of 1mm pathlength and measured for 2 hours. X-Ray data were collected with a Panalytical X'Pert PRO II instrument, with samples loaded into quartz glass X-Ray capillaries of 2 mm pathlength.Data were normalised, reduced and processed using standard procedures in GudrunN (neutron) and GudrunX (X-Rays). The provided files are corrected total scattering files, suitable for use in EPSR modelling of scattering data.This data can be modelled using EPSR, more details of which can be found here: https://www.isis.stfc.ac.uk/Pages/Empirical-Potential-Structure-Refinement.asp
Dataset Containing Online Communities Metadata
Get PDFSets of statistics derived from posts to two sets of online forums, each serving an ideological community. The posts were grouped into six-month time slices; four consecutive time slices were analysed for Community A, and one time slice for Community B. The quantities measured relate to the textual content of users' posts, their level of participation in threads, and the network of other users to whom they are connected by replies and quoting. The data were collected in 2011-2012 as part of an internal project.The data were collected by screen-scraping publicly visible online community forum posts. Further details are available in the README file.Last two years (Community A) and six months (Community B) taken from SQL database of full scrape. Content removed. Sub-forum names obfuscated. User IDs MD5 encoded.The data are encoded as comma-separated value files
Dataset for ''High Flux Thin-Film Nanocomposites with Embedded Boron Nitride Nanotubes for Nanofiltration''
No full textThis dataset relates to the nanocomposite membranes discussed in the paper "High Flux Thin-Film Nanocomposites with Embedded Boron Nitride Nanotubes for Nanofiltration". It contains the raw data for the membranes' surface zeta potential, salts rejection, permeance, chlorine resistance, contact angle, fouling tests, humic acid rejection, and methylene blue rejection, as well as X-ray photoelectron spectroscopy (XPS) data. In addition, this data contains transmission electron microscopy (TEM), field-emission scanning electron microscopy (FESEM) and optical microscopy data supporting and supplemental to those presented in the paper. Viewing of the paper is necessary for a full understanding of the dataset.The methodology used to gather this dataset is fully described in the "Materials and Methods" section of the related article.OriginLab was the software used to generate the graphs.
The instrument-supplied metadata for the TEM image is as follows:
CM_VERSION: 1.0;
CM_TIME: 09:11:40;
CM_INSTRUMENT: JEM-2100 Plus;
CM_FRAME_SIZE: 3296 2472;
CM_EFECT_BIT: 8;
CM_MAG: 20000;
$SM_MICRON_MARKER: 500.0nm
Monte Carlo code, input files, and simulation outputs for contact-based collective move simulations of MOF formations (cobalt succinate)
No full textA C++ implementation of a molecular Monte Carlo simulation with a contact-based collective move algorithm (CCMC: Contact Cluster Monte Carlo). This simulation features periodic boundary conditions. Interaction energies are defined by two-body distance/energy potentials of mean force, suitable for implicit-solvent simulations.
Input files are provided for simulations of assembly in the cobalt succinate system.
Inputs and outputs of production runs are provided, as these are the full datasets underlying our paper reporting the CCMC method and initial results.The code was written in standard C++ on a Linux system. The data were produced by running the code with inputs provided on a Linux system. The outputs are provided as plain-text simulation output files: molecular structures in CIF format, and statistical reports of the number and size of molecular clusters.The simulation outputs were processed in plain text in order to extract data for input to spreadsheets.All work was conducted on a multiprocessor Linux desktop workstation
Single molecule experimental data for unphosphorylated Aurora-A measurements in Gilburt et al, Chemical Science 2019
No full textRaw and partially processed data for the dwell time histogram in the following publication: James A H Gilburt, Paul Girvan, Julian Blagg, Liming Ying, Charlotte A Dodson (2019) Ligand discrimination between active and inactive activation loop conformations of Aurora-A kinase is unmodified by phosphorylation. Chemical Science
Dataset for "Salt bridge impact on global rigidity and thermostability in thermophilic citrate synthase"
No full textA packaged software for use in salt bridge analysis in protein stability and rigidity. Reads in a hydrogenated and uniquely atomically numbered pdb file and provides constraint files "cov.in" "hbonds.in" and "hphobes.in" - for use with the FIRST softwares rigidity analysis suite - that correctly handle salt bridges and strong polar interactions within the structure.
Also included are the hydrogenated and formatted pdb files of a variety of thermophilic citrate synthase structures as used in the work for the publication "Salt bridge impact on global rigidity and thermostability in thermophilic citrate synthase" by this dataset's authors.The .pdb files were taken from the RCSB PDB. The code files were written entirely in house unless otherwise commented and referenced within the code.The .pdb files were hydrogenated with the web service Molprobity and renumbered by opening in a visualisation software such as Pymol or Avogadro and saving new unique atomic numbering, as Molprobity provides all new hydrogens with a serial number of 0
Testing learning models of rule-based judgment
No full textThe dataset reports participants judgments, the features of the judgment objects, and the correct criterion for every subject in every learning trial. After 200 trials, the task structure changes.
Detailed explanations and coding methods can be found in the ReadMe-files under the Data.zip folder
Data sets for the Journal of Statistical Mechanics: Theory and Experiment article entitled "Ordering on different length scales in liquid and amorphous materials"
No full textData sets used to prepare Figures 1-10 & 12 in the Journal of Statistical Mechanics: Theory and Experiment article entitled "Ordering on different length scales in liquid and amorphous materials".
Figure 1 shows representative structure factors S(k) for several amorphous materials plotted as a function of kd where d is the nearest-neighbour distance.
Figure 2 shows the number-number partial structure factor S_{NN}(k) measured for amorphous silicon (solid curve), amorphous germanium (broken [red] curve) and the network-forming glasses SiO_2, GeO_2, ZnCl_2 and GeSe_2, plotted as a function of kd where d is the Si-Si or Ge-Ge bond distance for amorphous silicon and germanium, respectively, or the A-X bond distance for the network glasses.
Figure 3 shows the measured concentration-concentration partial structure factor S_{CC}(k) for glassy SiO_2, GeO_2, ZnCl_2 and GeSe_2, plotted as a function of kd where d = r_{AX} is the A-X bond distance.
Figure 4 shows the measured number-concentration partial structure factor S_{NC}(k) for glassy SiO_2, GeO_2, ZnCl_2 and GeSe_2, plotted as a function of kd where d = r_{AX} is the A-X bond distance.
Figure 5 shows (a) the measured fragility index m as a function of the bond angle θ_{AXA}^{CS} for several AX_2 glass-forming systems; (b) the dependence of the height ratio of the peaks in S_{NN}(k) at k_1 and k_2 on the bond angle θ_{AXA}^{CS}; and (c) the A-X-A bond angle distribution n(θ_{AXA}) calculated using a polarisable ion model.
Figure 6 shows the pressure dependence of the measured total structure factor S(k) for glassy (a) ^{73}GeO_2 and (b) GeSe_2 plotted as a function of kd, where d = r_AX is the A-X bond distance. In (a) the neutron S(k) function is given for glassy ^{73}GeO_2, and in (b) the neutron S(k) function is compared to the X-ray S(k) function for glassy GeSe_2. In all cases, S(k) ≃ S_{NN}(k).
Figure 7 shows the decay of the total and number-number pair-distribution functions for liquid Au_{0.81}Si_{0.19} and glassy ZnCl_2.
Figure 8 shows the measured partial structure factor S_{AA}(k) for glassy SiO_2, GeO_2, ZnCl_2 and GeSe_2, plotted as a function of kd where d = r_{AA}^{CS} is the nearest-neighbour distance for corner-sharing tetrahedra. Also shown is S(k) versus kd for amorphous silicon and germanium where d = r_{SiSi} or d = r_{GeGe}, and S_{OO}(k) versus kd for LDA ice where d = r_{OO}.
Figure 9 shows the measured partial structure factor S_{XX}(k) for glassy SiO_2, GeO_2, ZnCl_2 and GeSe_2, plotted as a function of kd where d = r_{XX} is the position of the first major peak in the corresponding partial pair-distribution function g_{XX}(r).
Figure 10 shows the measured partial structure factor S_{AX}(k) for glassy SiO_2, GeO_2, ZnCl_2 and GeSe_2, plotted as a function of kd where d = r_{AX} is the A-X bond distance obtained from the first peak in the corresponding partial pair-distribution function g_{AX}(r).
Figure 12 shows a comparison between the Cl-Cl-Cl bond angle distribution for glassy ZnCl_2 generated by the reverse Monte Carlo (RMC) method, the bond angle distribution obtained from a hard sphere Monte Carlo (HSMC) simulation of the glass, and the bond angle distribution obtained from the large 7934 sphere random close packing model of Bernal and co-workers.The data sets were collected using the methods described in the published paper.The data sets were analysed using the methods described in the published paper.Figures 1 - 10 & 12 were prepared using QtGrace (https://sourceforge.net/projects/qtgrace/). The data set corresponding to a plotted curve within an QtGrace file can be identified by clicking on that curve.The files are labelled according to the corresponding figure numbers. The units for each axis are identified on the plots
Dataset for "Evaluating the suitability of standard thermal comfort approaches for hospital patients in air-conditioned environments in hot climates"
No full textThis research aims to examine the suitability of classical thermal comfort approaches for hospital patients. For that purpose, the data was gathered in three phases in May, June, and July 2017 at the International Medical Centre (IMC) in Jeddah, Saudi Arabia, which was selected as an example of a best-practice hospital. Environmental monitoring for a week of each month in the summer season was undertaken to assess thermal environmental parameters. This was supported by simultaneous comfort surveys of the sample patients.The used methodology is objective measurements and patients' surveys simultaneously.
Objective measurements: Indoor air temperature (Ta), mean radiant temperature (Tr), air velocity (V), and relative humidity (Rh), along with estimations of patients’ metabolic rates (met) and notes about clothing insulation (clo), were recorded.
Surveys: The survey consists of several questions; thermal sensation votes, health scale, parts of day, and demographics.Swema equipment was used to measure the indoor environment parameters. Data was stored in Excel and R was used to analyse the data
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