1056 research outputs found
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Dataset for "Optical activity in third-harmonic Rayleigh scattering: a new route for measuring chirality"
No full textThis dataset contains results of measurements of third-harmonic Rayleigh scattering in suspensions of silver nanohelices and supporting numerical simulations. The data support the publication "Optical activity in third-harmonic Rayleigh scattering: a new route for measuring chirality".The exact data collection method is described in the related publication
CCDC 2032029: Experimental Crystal Structure Determination
No full textExperimental Crystal Structure Determination (CSD) Entry UVUMOQ: bis{N²,N⁴-bis[2,6-bis(propan-2-yl)phenyl]pentane-2,4-diiminato}-bis(μ-propyl)-di-ytterbium(ii). Chemical formula: C₆₄ H₉₆ N₄ Yb₂. Space Group: P 2₁/c (14). Cell: a 18.5744(2)Å b 14.87030(10)Å c 22.9981(2)Å, α 90° β 105.0910(10)° γ 90°.The methodology can be found in the associated paper
Dataset for "Ab initio reconstruction of small angle scattering data for membrane proteins in copolymer nanodiscs"
No full textThe purpose behind this dataset is to investigate the use of form-factor based SANS fitting methods and compare them to dummy-models generated using the ab initio modelling tools. The paper focusses on two different membrane proteins, outer membrane protein F (OmpF) and gramicidin incorporated into polymer nanodiscs with styene maleic acid (SMA). These constructs were compared to other techniques (DLS and CD) to discuss the differences that arise from investigating these complex systems using various methods. These were also compared to known crystal structures.
This dataset holds the raw data files for the paper titled: "Ab initio reconstruction of small angle scattering data for membrane proteins in copolymer nanodiscs". Techniques include; size exclusion chromatography (SEC) for purification prior to other techniques; circular dichroism (CD); dynamic light scattering (DLS); small angle neutron scattering (SANS) and ab initio modelling constructs.Samples were generated as described in "Ab initio reconstruction of small angle scattering data for membrane proteins in copolymer nanodiscs". In summary;
Gramicidin sample preparation:
A stock of 20 mM DMPC with 320 µM gramicidin liposomes were prepared and solubilised using SMA. Final concentrations were 10 mM DMPC, 160 µM gramicidin and 2.5 % (w/v) SMA.
OmpF enrichment:
Endogenous OmpF enrichment was adapted from previous literature (Efremov and Sazanov, 2012). E.coli cells are homogenised and broken, and membranes are harvested. Membranes were incubated with 1% (w/v) Triton X-100 for 15 minutes before ultracentrifugation. The resulting pellet was resuspended and incubated with 2% (w/v) Triton X-100 for 10 minutes before ultracentrifugation. The resulting pellet was solubilised with 2.5 % (w/v) SMA for 1 hour prior to ultracentrifugation, and the supernatant containing soluble OmpF-nanodiscs was collected. Excess polymer and aggregates were removed by size exclusion chromatography (SEC). Purified samples underwent lipid-exchange and buffer exchange for SANS and CD experimentation.
Lipid exchange:
To obtain lipid contrasts for SANS datasets, samples underwent lipid-exchange with deuterated-DMPC (d-DMPC) nanodiscs (10 mM d-DMPC with 1.5 % (w/v) SMA). Samples were then purified using SEC to remove excess polymer, followed by concentration using centrifugal filters.
Circular Dichroism:
Circular dichroism (CD) spectra were measured between 260 – 185 nm at 20°C using a 1.00 mm quartz cuvette using a Chirascan CD spectrometer (Applied Photophysics, UK) with the protein sample at 0.2 mg/mL for CD analysis. DMPC-only nanodiscs were used as a control. To remove any ‘background’ interference from the CD spectrum, the signal from the DMPC-only nanodisc sample was subtracted from that from the OmpF samples. The data was analysed using Dichroweb to determine the nature of the protein structure within the nanodiscs.
SANS:
Measurements were made on the SANS2d instrument at ISIS Neutron and Muon source (Harwell, UK) using 1mm thick quartz Hellma cells and placed in a temperature-controlled sample holding rack at 25C. Three contrasts were used for gramicidin; d-DMPC with hydrogenated-PBS (h-PBS), d-DMPC with 32% deuterated-PBS (d-PBS) and hydrogenated-DMPC with d-PBS; OmpF contrasts were partially deuterated bacterial lipids (d-bact) with h-PBS, d-bact with 32% d-PBS and d-bact with d-PBS.
Dynamic light scattering:
All DLS measurements were performed using a Malvern Panalytical Zetasizer Nano ZS. Size distribution was measured and is shown on a log scale, plotted using Igor Pro 6 (Wavemetrics) software.CD:
Background was subtracted from CD data using lipid-only nanodiscs to remove any polymer inference. The data were analysed using Dichroweb and compared using predicted CD spectra for OmpF crystal structure (PDB ID: 2OMF), determined by PDBMD2CD.
SANS:
Data were corrected, solvent subtracted and reduced to 1-D curves using Mantid software.
Gramicidin nanodisc SANS data ab initio modelling:
To create an overall shape of the gramicidin nanodisc, DAMMIF was used before further refinement using; DAMSEL, DAMSUP, DAMAVER, DAMFILT, and DAMSTART. Lastly, the models were passed through DAMMIN, to compare against the original data file.
OmpF nanodisc SANS data ab initio modelling:
A multi-phase construct was generated using MONSA for the OmpF-nanodiscs. Further refinement was conducted for each phase separately using; DAMSEL, DAMSUP, DAMAVER, DAMSTART and DAMFILT. The two refines phases were then superimposed using SUPCOMB to correct their orientation to one another.CD:
CD spectra obtained by a Chirascan CD spectrometer (Applied Photophysics, UK). Data was analysed using DICROWEB web interface and compared to predicted CD spectra from crystal structures (PDB ID: 2OMF) using PDBMD2CD web interface. Data was visualised using Igor Pro 6 (Wavemetrics) software.
DLS:
DLS measurements were performed using a Malvern Panalytical Zetasizer Nano ZS and visualised using Igor Pro 6 (Wavemetrics) software.
SANS:
SANS data obtained by SANS2d instrument at ISIS Neutron and Muon source (Harwell, UK) and reduced to 1-D curves using Mantid software. Resulting datasets can be visualised using Igor Pro 6 (Wavemetrics) and fitted using cylindrical nanodisc models (part of the SANS analysis software developed at NIST, modified to incorporate the water content in the shell).
Ab initio model constructs:
Initial models are generated using Data analysis software (ATSAS). For gramicidin nanodiscs, DAMMIF, DAMSEL, DAMSUP, DAMAVER, DAMFILT, DAMSTART and DAMMIN, were used to refine and generate the final model construct against the original data file. These create a .pdb file which can be visualised using Visual Molecular Dynamics (VMD) software. For OmpF nanodiscs, MONSA, DAMSEL, DAMSUP, DAMAVER, DAMSTART, DAMFILT and SUPCOMB were used to refine, generate the final model construct against the original data file and to correct the multiple phase orientations to one another. These create a .pdb file which can be visualised using Visual Molecular Dynamics (VMD) software.Details of the data and labelling is available in the README.txt file
Dataset for "Micro-lensed negative-curvature fibre probe for Raman spectroscopy"
No full textThis dataset contains data supporting the results presented in the paper "Micro-lensed negative-curvature fibre probe for Raman spectroscopy". It includes the data used to plot each figure (in .txt format).
We have developed a novel miniature micro-lensed fibre probe for Raman spectroscopy. The fibre probe consists of a single negative-curvature fibre (NCF) and a spliced, cleaved, micro-lensed fibre cap. Using a single NCF, we have minimized the generated Raman background from the silica and maintained the diameter of the probe to be less than 0.5 mm. In addition, the cap provided fibre closure by blocking the sample from entering the hollow parts of the fibre, enabling the use of the probe in in-vivo applications. Moreover, the micro-lensed cap poses an improved collection efficiency (1.5 times increase) compared to a cleaved end cap. The sensing capabilities of the micro-lensed probe are demonstrated by measuring different concentrations of glucose in aqueous solutions.The different data collection methods used for the collection of the data are described in the paper "Micro-lensed negative-curvature fibre probe for Raman spectroscopy"
Dataset for "A classical molecular dynamics study into the effect of Si/Al ratio and silanol nest defects on water diffusion in zeolite HY"
No full textThis dataset relates to 2 ns molecular dynamics simulations of water in zeolite HY at loadings of 5–33 wt%, in systems with Si/Al ratios ranging from 5 to fully siliceous. Included are the input and output files of the simulations, carried out using DLPLOY 4, needed to reproduce all data and analysis in the publication "A classical molecular dynamics study into the effect of Si/Al ratio and silanol nest defects on water diffusion in zeolite HY".Molecular dynamics simulations were carried out using the DLPOLY 4 code to generate atomic positions of water over a 2 ns simulation. Further methodological details may be found in the Computational Methods section of the associated manuscript.DLPOLY 4 code was used to generate the data (https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx). Inputs needed to do so are included
Dataset for "Parameter Reduction and Optimisation for Point Cloud and Occupancy Mapping Algorithms"
No full textIn the applications of occupancy mapping, the scene to be explored is normally large and objects are of irregular shapes. In this case, it is difficult to evaluate the performance of a mapping approach since the ground truth can hardly be obtained. This dataset aims to provide small measured scenes with ground truths for evaluation purposes.
Videos are recorded in .svo files. These files can be opened with the tools provided in ZED SDK which can be downloaded at Stereo Labs website (https://www.stereolabs.com). Images in the videos can be extracted using the API in ZED SDK and the camera parameters can also be accessed by ZED API.
Ground truth files are in .ot format. These files can be viewed by octovis package. To install octovis, run 'sudo apt-get install octovis' in Ubuntu.
Camera trajectories produced by ORB-SLAM and keyframe poses produced by ORB-SLAM are in .txt files. Most text editors can open files of this type.This dataset contains 20 video files used for occupancy mapping. The dataset was recorded with a ZED stereo camera (Stereo Labs, USA) in two environments at University of Bath, in front of buildings and in a parking lot. Targets in the dataset are two boxes whose external surfaces are either with a plain brown cardboard texture or are covered with randomly generated Voronoi diagrams. The average size of the polygons in each diagram is about 3 cm x 3 cm. The colour of each polygon is randomly generated. The Voronoi diagrams are printed in 300 DPI on the posters of A0 size and cropped to cover the surfaces of boxes. Two boxes are arranged in a layout as one of five free tetrominoes, i.e., I, O, T, L and S, in the Tetris game. The camera obits the boxes twice in a anti-clock direction to capture videos. Ground truths are also included in this dataset package.The device for data collection is a ZED camera from Stereo Labs, USA. Software is ZED SDK which is available at https://www.stereolabs.com
Dataset for "Asymmetric Backward Peaking Radiation Pattern from a Relativistic Particle Accelerated by Lightning Leader Tip Electric Field"
No full textThe purpose of the data is to mathematically model radiation intensity and patterns around a single charged relativistic/non-relativistic particle (electron) specifically for the bremsstrahlung process where the particle is assumed to be rotating in anti-clockwise direction. The dataset consists of four separate Maple worksheets. The first one models the bremsstrahlung particle trajectory. The second one models particle velocity from the leader tip electric field that accelerates particles to relativistic speeds. The third and fourth are worksheets that model the radiation patterns of the bremsstrahlung process around a charged relativistic/non-relativistic particle and it incorporates all the information used in first and second Maple worksheets about particle trajectory and the leader tip electric field, and hence the particle velocity arising from the electric field.The .mw files are Maple worksheets, written using Maple software version 2018.2. At the time of simulation, this operated on both Windows 64-bit and macOS X Catalina.The mathematical Maple code is just the mathematical code version of the actual, original theory created from scratch on paper. Maple code is just used to simulate the constructed theory. In order to run the code, start from the very beginning of the code where it says `restart;`. In addition, `restart;` is just there to clear the memory of the Maple software every time when simulating new results with new parameters or with different equations. This enables Maple to get rid of any unrequired numbers, definitions or assumptions that could cause confusions in the results of the new simulation
Data for the publication "Simulation of Earth-Ionosphere Cavity Resonances with Lightning Flashes Reported by OTD/LIS"
No full textThis data is to illustrate the theory, data analysis, and exemplary results of the data described in the corresponding publication entitled 'Simulation of Earth-Ionosphere Cavity Resonances with Lightning Flashes Reported by OTD/LIS'.This data lives in the context of the corresponding publication entitled 'Simulation of Earth-Ionosphere Cavity Resonances with Lightning Flashes Reported by OTD/LIS'. Any use of the data outside this specific context is considered to be unethical.
The data is described in three different forms that build on each other in a logical and hierarchical order.
(1) High level description: All the data is described in textual form in the corresponding publication in extensive detail.
(2) Middle level description: The actual values of the data and their units which are used in the publication are embedded in the corresponding standard Matlab .m files, one for each Figure. The Matlab programming language is explained on the website https://uk.mathworks.com/help/matlab/getting-started-with-matlab.html?s_cid=learn_doc
(3) Low level description: The binary data used by the Matlab .m files are embedded in the corresponding Matlab .mat files, one for each Figure. These .mat files are independent of the computing platform used.The work contributes to the United Nations Sustainable Development Goal on Climate Action (SDG13) to build knowledge and capacity to meet climate change (target 2.3 13.3)
Dataset for "A parametric optimisation study of urban geometry design to assess outdoor thermal comfort."
No full textThis dataset supports the study on the effect of urban geometry parameters, namely, building heights (H), street widths (W), aspect ratio (H/W) and orientation on the outdoor thermal comfort conditions in Cairo, Egypt. The study uses Grasshopper for Rhino3D and its environmental plugins, Ladybug-tools, to analyse thermal comfort represented by the Universal Thermal Climate Index (UTCI) of multiple geometry configurations. The data files include the input parameters (prefixed "in:"), processed data and the output UTCI (prefixed "out:") in each phase of the study.TT-Toolbox Colibri Iterator was used to iterate the simulation of each geometrical configuration consecutively. Upon each run, EnergyPlus calculates the outside surface temperatures, which are used as part of the Mean Radiant Temperature (MRT) calculation. Ladybug-tools plugins were used to agglomerate the data streamed from EnergyPlus and the Urban Weather Generator to estimate the UTCI. Upon each iteration, the Colibri plugin exported the results to a CSV file.Rhinoceros V.6 Service Release 29
Grasshopper Build 1.0.0007
Ladybug V.0.0.69 Honeybee V.0.0.6
CCDC 2034334: Experimental Crystal Structure Determination
No full textExperimental Crystal Structure Determination (CSD) Entry UVUNAD: tetrakis(μ-propenyl)-tetrakis(μ-N²,N⁴-bis[2,6-bis(propan-2-yl)phenyl]pentane-2,4-diiminato)-tetra-ytterbium(ii). Chemical formula: C₁₂₈ H₁₈₄ N₈ Yb₄,C₆ H₆. Space Group: P 2₁/n (14). Cell: a 18.4011(6)Å b 16.5304(5)Å c 21.0634(6)Å, α 90° β 104.094(3)° γ 90°.The methodology can be found in the associated paper
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