DaRUS (University of Stuttgart)
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Data for: Mechanistic Modeling of In Vivo Translation in Escherichia coli Reliably Identifies Well-Adapted and Optimized RNA Sequences
No full textThe DaRUS repository entails and supplements the simulation data, MATLAB model and graphics for the publication: "Mechanistic Modeling of In Vivo Translation in Escherichia coli Reliably Identifies Well-Adapted and Optimized RNA Sequences
Replication data of B3 group for: "Tethering chiral Rh diene complexes inside mesoporous solids: experimental and theoretical study of substituent, pore and linker effects on asymmetric catalysis"
No full textIn this dataset HPLC (high performance liquid chromatography) chromatograms of the products of the rhodium-catalyzed 1,2-addition and NMR (nuclear magnetic resonance) spectra of all prepared ligands, catalysts and catalysis products (NMR) are included. Furthermore, the excel sheets for kinetics as well as ICP-OES (inductively coupled plasma optical emission spectroscopy) data for Rh on OMS (ordered mesoporous silica) are included
Visual Analysis System to Explore the Visual Quality of Multidimensional Time Series Projections
No full textSource code of our visual analysis system for the exploration of the visual quality of multidimensional time series projections.
This project contains source code for preprocessing data and the visual analysis system. Additionally, we added precomputed data for immediate use in the visual analysis system.
Our project contains the following directories/files of interest:
datasets: Data sets for the use with our visual analysis system. The data can also be generated with the data preparation scripts.
static, templates, and dimRed: Java script / Python code of our visualization approach.
run_windows: Scripts to run our system on windows.
run_linux: Scripts to run our system on linux.
datasets.txt: List of directories used in preprocessing and for the visualization.
Please have a look at the README file for more details
Supplementary material for "The Effects of Surfaces and Confinement on Formic Acid Dehydrogenation Catalyzed by an Immobilized Ru-H Complex: Insights from Molecular Simulation and Neutron Scattering"
No full textThis dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter-files (directory mdp) are provided for bulk simulations of pure dioxane and formic acid as well as mixture of both in pore and bulk simulation. The pore simulation is divided into three steps, an energy-minimization, an NVT equilibration, and an NVT production simulation run. While the bulk simulations introduce an NpT step after the first equilibration step and an NpT production run instead of a NVT production. Provided structure files are of an already equilibrated system. Object files are supplied which can be used to load the generated pores into PoreMS for later alteration and analysis. Results of density of pore systems are provided in hdf5 format to be processed with the PoreAna python package. Jupyter notebooks to load and display with PoreAna the data are provided. Also yaml files which contain the density of the pure and mixture bulk simulations are added to the data set. Here an accompanying jupyter notebook to read the yaml files is supplied with.
In addition, the data set contains data from IR and NMR experiments.
We recommend viewing the data by choosing the option "Tree"
Dumux code for Stokes-Darcy mortar method
No full textThis dataset contains the source code for the examples shown in
Boon, W.M., Gläser, D., Helmig, R. and Yotov, I.
A mortar method for the coupled Stokes-Darcy problem using the MAC scheme for Stokes and mixed finite elements for Darcy.
Comput Geosci (2024). https://doi.org/10.1007/s10596-023-10267-6
with the open-source simulator Dumux. The first one investigates the orders of convergence with respect to the mesh size for different element types, as well as the efficiency of the interface preconditioner. The second example simulates flow through a channel around a porous obstacle. The third one presents a porous medium with a highly heterogeneous permeability field based on the Society of Petroleum Engineers SPE10 benchmark, over which a free-flow field is simulated. The code can be used, for instance, to reproduce the results published at DaRUS
POREMAPS 1.0.0: Code, Benchmarks, Applications
No full textInitial release 1.0.0 for POREMAPS, PORous Media Anisotropic Permeability Solver for Stokes flow including benchmarks and applications according to Krach et al. (2024). POREMAPS is a Finite Difference Method (FDM) -based parallized Stokes flow solver using MPI, specifically designed to process large binarized 3D image datasets of porous media such as X-Ray Computed Tomography (XRCT) images.
This repository contains three blocks, namely code, input data, and results for flow simulations in porous materials with respect to evolving anisotropies, all related to the publication Krach et al. (2024):
POREMAPS_code.tar.gz
Release 1.0.0 for POREMAPS, a FDM-based PORous Media Anisotropic Permeability Solver for Stokes flow. POREMAPS is a free and open-source simulator for computing permeability tensors of porous materials from binary image data. The compressed file contains the source code, a concise manual, and tools for post-processing. The code is also available via the git repository.
POREMAPS_benchmarks.tar.gz
The benchmarks file includes input geometries and input files for the solver for Poiseuille flow, channel flow, flow through regular sphere packings, in flat, pseudo-3D domains, and around ellipsoids. Also included are the resulting velocity and pressure fields as well as information on neighborhood and domain decomposition. Input files are text files and have .inp file extension. Voxel-based computer-generated input geometries and results are provided as RAW image files.
POREMAPS_applications.tar.gz
The applications contain binarized data for the applications discussed in Krach et al. (2024). These include 18 data sets on uniaxially compressed foams and 139 data sets on clogging porous structures. The former is generated by micro-XRCT and comprises 6 snapshots for different uniaxial compression states. The second data set contains image-based geometries of calcite precipitation in micromodels. The original data set is published in Weinhardt et al. (2022).
All data sets are prepared in such a way that they are in accordance with the boundary conditions specified in the input files. This applies in particular to the applications that have been mirrored to meet periodic boundary conditions. Voxel size, convergence criterion, etc. can be found in the corresponding input files. Preprocessing also includes the removal of non-interconnected pores so that the specified porosity corresponds to the effective porosity.
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NGS data related to Albrecht et al.: Locus specific and stable DNA demethylation at the H19/IGF2 ICR1 by epigenome editing using a dCas9-SunTag system and the catalytic domain of TET1
No full textMethod overview
For targeted DNA demethylation of the H19/IGF2 ICR1, HEK293 cells were transfected with two plasmids, one containing 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 second plasmid encodes five sgRNAs targeting the ICR1 and a DsRed fluorophore. On day 3 post-transfection, GFP- and DsRed-positive cells were sorted by FACS. A part of the sorted cells was used immediately for downstream analysis, the other part was re-seeded to harvest at later time points. Genomic DNA was isolated from the cells and bisulfite or oxidative bisulfite conversion was conducted. For amplicon-based DNA methylation analysis, libraries were prepared from bisulfite-converted DNA using two consecutive PCRs in which barcodes, indices and sequencing adapters are added. Samples were sequenced by NGS and data was analyzed.
Method details
The gDNA of transfected HEK293 cells sorted by FACS was isolated using the QIAmp DNA Mini Kit (Qiagen) according to the manufacturer's instructions. 500 ng gDNA was fragmented enzymatically by overnight digestion using 40 U EcoRV-HF (a non-cutter in the genomic regions desired for amplification) (New England BioLabs, Inc.) in CutSmart buffer in a total volume of 20 µl. The next day, bisulfite conversion was conducted using the EZ DNA Methylation-Lightning™ Kit (ZYMO RESEARCH) according to the manufacturer's protocol. Oxidative bisulfite conversion was performed using the TrueMethyl® oxBS Module (Part No. 0414, Tecan Genomics, Inc.) according to the manufacturer's instructions. Amplicons of interest were amplified in a first PCR1 with locus-specific primers, which also contained barcodes and adapters complementary to PCR2 primers. The PCR1 product was used as template for PCR2, in which Illumina TruSeq sequencing indices are added to the amplicons. Sample concentrations were measured using the NanoDrop 1000 (Thermo Fisher Scientific) and equimolar amounts of samples were pooled. Paired-end Illumina sequencing with 250 bp read length was performed by Novogene (UK) Company Limited.
Data analysis
NGS data in a FASTQ format was analyzed basically 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. In brief, 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. 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.
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
Supplementary videos for PhD thesis: Laminar-to-turbulent transition in airfoil boundary layer flows at oscillating inflow conditions
No full textVideos from direct numerical simulations (DNS) of the laminar-to-turbulent transition under unsteady inflow conditions.
The flow visualizations correspond to the results of section 3.4 of the PhD thesis "Laminar-to-turbulent transition in airfoil boundary layer flows at oscillating inflow conditions", see Related Publication below
Replication Data for: "Light-driven molecular motors embedded in covalent organic frameworks"
No full textThe incorporation of molecular machines into the backbone of porous framework structures will facilitate nano actuation, enhanced molecular transport, and other out-of-equilibrium host–guest phenomena in well-defined 3D solid materials. In this work, we detail the synthesis of a diamine-based light-driven molecular motor and its incorporation into a series of imine-based polymers and covalent organic frameworks (COF). We study structural and dynamic properties of the molecular building blocks and derived self-assembled solids with a series of spectroscopic, diffraction, and theoretical methods. Using an acid-catalyzed synthesis approach, we are able to obtain the first crystalline 2D COF with stacked hexagonal layers that contains 20 mol% molecular motors. The COF features a specific pore volume and surface area of up to 0.45 cm3 g-1 and 604 m2 g-1, respectively. Given the molecular structure and bulkiness of the diamine motor, we study the supramolecular assembly of the COF layers and detail stacking disorders between adjacent layers. We finally probe the motor dynamics with in situ spectroscopic techniques revealing current limitations in the analysis of these new materials and derive important analysis and design criteria as well as synthetic access to new generations of motorized porous framework materials.
Open *.cif and *.xyz files with a visualization software (see http://ww1.iucr.org/iucr-top/cif/), *.raw files with WinXPOW, *.sp files with PerkinElmer Spectrum software, *.mnova files with MestReNova, *.fq/.gr/iq/sq files with a text editor, *.cdr files with CorelDraw 2020, *.docx *.xlsx with Microsoft Office, *.opju with Origin, and *.pro files with TOPAS. Spectral data (independent of origin) may also be opened and processed with Spectragryph
Your visualisations are going places: Performance data for scientific visualisation on gaming consoles
No full textThe data set contains performance data (mainly frame times) for rendering spherical glyphs and scalar fields on Xbox Series consoles, mobile game consoles and a reference PC with different GPUs