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Replication data of Buchmeiser group for: "Stereoselective Ring Expansion Metathesis Polymerization with Cationic Molybdenum Alkylidyne N-Heterocyclic Carbene Complexes"
No full textSynthetic proofs in form of 1H, 13C, 19 F NMR spectra, as well as GPC traces for polymers, the presented MALDI-TOF spectrum, Data files for the crystal structure as well as data for the theoretical calculations are reported. All primary data files of measurements and processed data of the journal article mentioned under related publications from Buchmeiser and Kästner group can be found here. The data is structured according to figures and schemes in the research article and contains the following data types: bruker NMR folder, .cif, .txt., .pdf
GALÆXI Application: NASA Rotor 37
No full text
This Dataset contains the setup data for the NASA Rotor 37 test case which corresponds to the application section in the GALÆXI Paper (Section 6).
Reference (Link):
L. Reid, R. D. Moore, Design and overall performance of four highly
loaded, high speed inlet stages for an advanced high-pressure-ratio core
compressor, Technical Report 1337, NASA Lewis Research Center,
Cleveland, OH, United States, 1978.
Executable of FLEXI/GALÆXI can be built using the
build.py script:
python3 build.py ./build-folder ./userblock.txt
Note: Please ensure that all necessary dependencies of GALÆXI/FLEXI are available (including CUDA) and a Python3 environment is installed on the system. Moreover, the NASA rotor test case is a large scale setup, such that a consumer GPU/CPU might not be able to run the case
Replication Data for: "Development and plausibility assessment of an active human body model in numerical cyclist to vehicle collision simulations based on real-life accident data"
No full textThis dataset contains all necessary files and descriptions to extend the finite element passive THUMSv4 pedestrian human body model into a muscle-driven active human body model. It also contains all the necessary tools to reposition the standard THUMSv4 pedestrian model into the pose of a cyclist as described in the publication "Development and plausibility assessment of an active human body model in numerical cyclist to vehicle collision simulations based on real-life accident data" by Trube et al. (2024
NGS data related to Rajaram et al.: Allele specific DNA demethylation ...
No full textMethod overview
To achieve targeted locus and allele-specific DNA demethylation, HEK293 cells were transfected with two plasmids. One plasmid contains, dCas9 fused to a SunTag with five repeats of the GCN4 peptide, separated by 22 aa long linkers, and scFv-fused TET1CD, as well as a GFP reporter protein. The other plasmid is a multiguide plasmid with 4 individual sgRNAs flanked by U6 promoter and gRNA scaffold, and a DsRed fluorophore. Control experiments were conducted with a scrambled sgRNA that does not have a binding site in the human genome. Initial studies showed that cells positive for two plasmids exhibited detectable fluorescence of the corresponding reporter proteins on day 3 post-transfection. Hence, FACS sorting was conducted at this time point. A part of the sorted cells was used immediately for downstream analysis, the other part was re-seeded to harvest at later time points.
For DNA methylation analysis, genomic DNA was isolated from the cell samples and subjected to bisulfite treatment. Library preparation was performed using the bisulfite-converted samples, followed by NGS and data analysis. All methylation experiments were conducted in three independent biological replicates.
For measurement of the genomic allele frequencies, genomic DNA of the untreated samples was used for the amplification of the region around the target SNP and an exonic region with additional SNP for each target, which was followed by library preparation, NGS and data analysis.
To monitor the variation in the expression of the target genes, RNA was isolated from the treated cells on Day 6. cDNA synthesized from the isolated RNA was used for the library preparation of the exonic region. The library was subjected to NGS followed by data analysis.
All experiments were conducted in three independent biological replicates.
Method details
The gDNA of transfected HEK293 cells sorted by FACS was extracted using QIAmp DNA Mini Kit (Qiagen). 500 ng of genomic DNA was subjected to overnight digestion with EcoRV which is not cutting in any of the target amplicons. Zymo EZ DNA Methylation-Lightning Kit (D5030-E) was used for bisulfite conversion. The library for NGS was prepared by two consecutive PCR reactions (Leitao et al, 2018). Firstly, bisulfite converted genomic DNA of each sample was amplified with target gene specific primers. The gene specific optimized amount of a product from the first PCR was used as a template for the second PCR to add the Illumina TruSeq sequencing adapters. Final products were quantified, pooled in equimolar amounts and purified using SPRIselect beads (Beckman Coulter). Ready-to-use pools of libraries were sequenced on NovaSeq 6000 using a PE250 flow cell (Novogene).
For expression analysis, RNA was isolated from the sorted cells using Qiagen RNeasy extraction kit (Cat. No. 74034). By an additional treatment with TURBO DNA-free™ Kit (Ambion #AM1907) the residual genomic DNA from the samples were removed. 500 ng of the DNase-free RNA was used for cDNA synthesis with Applied Biosystems- High-Capacity cDNA Reverse Transcription Kit (Cat No 4368814). NRT was used as a negative control for cDNA synthesis, where the reaction was conducted without addition of the reverse transcriptase enzyme. In addition, NTC (no template control) reactions were included. The transcripts were subjected to library preparation in a two-step PCR process as mentioned above. For amplification of the genomic regions, 10 ng of the isolated genomic DNA was used. Two-step library preparation was carried out for NGS of genomic regions.
All NGS data were obtained in the form of FASTQ files.
Data analysis
NGS data in a FASTQ format was analyzed as described (Rajaram et al., 2023) on the Galaxy platform (https://usegalaxy.org/) (The Galaxy platform for accessible, reproducible and collaborative biomedical analyses, 2022), where all the following tools are available. First, Illumina adapter sequences were removed using Trim Galore!. Afterwards, two paired-end reads were merged using Pear and reads with low quality were removed with Filter FASTQ. All NGS data files were subjected to this processing.
For quantitative analysis of the methylation at individual CpG sites, the following steps were carried out. De-multiplexing of individual samples tagged with combinations of barcodes and Illumina indices was done by converting the FASTQ files using FASTQ to Tabular, followed by selection of lines with the tool Select and re-conversion of the files to a FASTQ format with Tabular to FASTQ. For the alignment of reads to a reference sequence, bwameth was used and the DNA methylation at each CpG site was analyzed by applying the tool MethylDackel. The output files were processed using Microsoft Excel.
For the analysis of the allelic ratios of the transcript and genomic region, de-multiplexing of individual samples tagged with combinations of barcodes and Illumina indices was done by converting the FASTQ files using FASTQ to Tabular, followed by selection of lines with the tool Select. Input for the selection of lines was provided in accordance to the SNP of interest. Output of the tool Select provides the number of reads corresponding to each allele.
References
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic acids research 2022, 50, W345-W351, doi: 10.1093/nar/gkac247
Rajaram, N.; Kouroukli, A.G.; Bens, S.; Bashtrykov, P.; Jeltsch, A. Development of super-specific epigenome editing by targeted allele-specific DNA methylation. Epigenetics Chromatin 2023, 16, 41, doi: 10.1186/s13072-023-00515-5</a
Material Testing Data for Coreless Filament Winding Using Small-Scale, Star-Type Specimens
No full textTo understand the fabrication influence on mechanical properties and to compare different material combinations, 5 star-type composite specimens were tested. Each specimen was fabricated using coreless filament winding (CFW) and exhibits a bundle cross-section of 20mm. The star specimen replicates a typical CFW system with fiber interaction at different locations and similar uncertainties as actual building components derived from the fabrication process and/or material inconsistencies.
The specimens were tested in compression, each data point consists of the standard force, deformation amount, and testing time. Five specimens were used: Specimen 1 consists of carbon fibers with petrochemical resin as a point of reference, Specimen 2,3, and 4 are based on a combination of flax fiber and petrochemical resin and specimen 5 combines flax fibers with bio-based resin.
The data serves as a base for the evaluation of the fabrication process and equipment, the structural performance and to compare the environmental impact of different material combinations using Life Cycle Analysis (LCA) indices
biphasic-kinematic-growth
No full textThis dataset contains the code and produced result files for the investigations presented in Suditsch et al. (DOI-LINK). In this work a biphasic model in the framework of the Theory of Porous Media (doi:10.1007/978-3-662-04999-0) is combined with a kinematic description according to Rodriguez et al. (doi:10.1016/0021-9290(94)90021-3).
The script comparision_Growth_Formulations.py produces all used
data and with create_plots.ipynb all plots can be created. In TPM_2Phase_MAo_LMo_MAs_Growth.py and Rodriguez1994.py calculation routines for the respective
theories are written. For convenience, general functions are outsourced into the helper.py file. In README, a rough summary of the basic equations of the coupled kinematic-multiphasic growth model are shown. It is followed by an installation guide. Additionally to the github (https://github.com/masud-src/biphasic-kinematic-growth) repository, the generated result files can be found in the output folder
Data for: Semi-Continuous Biomanufacturing for Maximizing the Production of Complex Chemicals and Fuels: A Case Study on Amorpha-4,11-diene
No full textThe DaRUS repository contains the raw data corresponding to the figures of the manuscript "Semi-Continuous Biomanufacturing for Maximizing the Production of Complex Chemicals and Fuels: A Case Study on Amorpha-4,11-diene".
Biomanufacturing is emerging as a key technology for the sustainable production of chemicals, materials, and food ingredients using engineered microbes. However, despite billions of dollars of investment, few processes have been successfully commercialized due to a lack of attention on industrial-scale bioprocess design and innovation. This study addresses this challenge through the development of a novel semi-continuous bioprocess for the production of the terpene amorpha-4,11-diene (AMD4,11) using engineered Escherichia coli. Using a hydrophilic membrane for product and biomass retention, we successfully a) decoupled production at low growth rates (~0.01 1/h) and b) improved productivity 3-fold compared to traditional fed-batch fermentations. When cell recycling was implemented, we showed sustained production at the highest conversion yield and production rate for up to three cycles, demonstrating the robustness of both the strain and the process and highlighting the potential for new bioprocess strategies to improve the economic viability of industrial biomanufacturing
Coupled thermo-mechanical simulation results of a finite element discbrake
No full textSimulation Results of a Finite Element Discbrake
This dataset contains simulation results from a finite element (FE) model of a heated disc brake, represented in two configurations:
Simple Discbrake
A lower-resolution FE model featuring a single heated area.
1 layer, 60 elements, 146 nodes
7 degrees of freedom (DOFs) per node, 998 DOFs in total
Discbrake with Hole and Three Heated Areas
A higher-resolution FE model featuring a central hole and heating applied at three locations on both sides.
2 layers, 1390 elements, 2250 nodes
7 DOFs per node, 15750 DOFs in total
Both models are implemented in the commercial simulation software Abaqus.
Simulation Setup
Heat is applied through designated heat input areas with a constant heat flux of 5×106 ± 4.99×106 W/m².
Material properties are varied:
Heat conductivity
Density
Each simulation covers the time interval [0, 3] seconds for the simple discbrake and [0,10] seconds for the discbrake with a whole.
Initial conditions are set to zero.
Parameter vectors are sampled quasi-randomly using Halton sequences.
Output Data
Each simulation exports displacements and temperatures at all nodes. Velocities are computed using a second-order central difference scheme to extend the mechanical state.
Contents
Model Files
discbrake.inp/discbrake_with_hole.inp: Abaqus input files describing the FE models
runAbqSim_onlyHeat_1Point_smallHalton.m: Script to run simulations
write_odb_to_txt.m: Script to export Abaqus .odb files as .txt
utils/: Utility scripts for running and exporting simulations
disc_brake_with_hole_ref_coords.npy: reference configuration of the discbrake
disc_brake_with_hole_faces.npy: Faces of the discbrake for 3D visualization
Dataset (discbrake.npz/discbrake_with_hole.npz)
X: System states (temperatures and displacements) — shape [n_sim × n_timesteps × n_nodes × n_dofs]
t: Time vector — shape [n_timesteps × 1]
U: Input (heat flux) — shape [n_sim × n_timesteps × 1]
Mu: Simulation parameters (material properties) — shape [n_sim × 2]
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Replication Data for: Grassmann Extrapolation for Accelerating Geometry Optimization
No full textData for reproducibility of the numerical simulations of the research paper: Grassmann Extrapolation for Accelerating Geometry Optimizatio
TRChallenge - experimental results 2022
No full textThis dataset contains experimental data acquired from the benchmark system of the Tribomechadynamics Research Challenge [1]. The tests were part of Project 3 of the Tribomechadynamics Research Camp 2022 in Stuttgart [2]. CAD models, technical drawings and design documentation are available in [4].
Data obtained by linear modal testing is available, along with data obtained by three types of nonlinear tests, Phase Resonance Testing (PRT), Response Controlled Testing (RCT), and Excitation Controlled Testing (ECT). The test methods are described in [3].
Velocity data was acquired using a multi-point vibrometer (MPV). The 17 sensor locations are indicated in Figure 3 in [3]. Single-point/differential vibrometers (SPVs) were used for feedback control during the nonlinear tests. The SPV data is redundant with the MPV data, and is thus not contained in this dataset.
The naming and the content of each data file type is described in the file “README”.
REFERENCES
[1] http://tmd.rice.edu/ tribomechadynamics-research-challenge-2021/
[2] http://tmd.rice.edu/tribomechadynamics-research-camp/2022-graduate-projects/
[3] https://arxiv.org/abs/2403.07438
[4] https://doi.org/10.18419/darus-3147
ACKNOWLEDGEMENTS
M. Krack is grateful for the funding received by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) [Project 450056469, 495957501].
This work presents results of the Tribomechadynamics Research Camp (TRC). The authors thank MTU Aero Engines AG for sponsoring the TRC 2022.
The support from NSF grant No: 1847130 is appreciated by A. Bhattu.
S. Hermann is grateful for the funding received by the EIPHI Graduate School, ANR-17-EURE-0002.
N. Jamia gratefully acknowledges the support of the Engineering and Physical Sciences Research Council through the award of the Programme Grant “Digital Twins for Improved Dynamic Design”, grant number EP/R006768/1