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Subject: Physics Subject: Biology

1 to 10 of 22 Results

Library of optimal control pulse sequences for biomolecular NMR spectroscopy Aug 2, 2024 Joseph, David; Griesinger, Christian, 2024, "Library of optimal control pulse sequences for biomolecular NMR spectroscopy", https://doi.org/10.17617/3.CBOUXH, Edmond, V1 This data set is part of the publication Library of optimal control pulse sequences for biomolecular NMR spectroscopy (manuscript in preparation). by D. Joseph and C. Griesinger. All reported pulse sequence codes and the necessary parameter files and additional OC pulse shapes ar...
Pair distributions and membrane-mediated interactions of arc-shaped particles on spherical and tubular vesicles Jul 11, 2024 Bonazzi, Francesco; Weikl, Thomas, 2024, "Pair distributions and membrane-mediated interactions of arc-shaped particles on spherical and tubular vesicles", https://doi.org/10.17617/3.DIF595, Edmond, V1 This dataset contains data from Monte Carlo simulations of triangulated membrane vesicles with segmented, bound arc-shaped particles of two different sizes (in hdf5 format) and Mathematica notebooks to determine pair distributions, 2-dimensional free energy landscapes, and 1-dime...
Data for paper 'A cytokinetic ring-driven cell rotation achieves Hertwig's rule in early development' May 27, 2024 Middelkoop, Teije, 2024, "Data for paper 'A cytokinetic ring-driven cell rotation achieves Hertwig's rule in early development'", https://doi.org/10.17617/3.WPVJHQ, Edmond, V1 Raw microscopy data for 'A cytokinetic ring-driven cell rotation achieves Hertwig's rule in early development', accepted for publication in PNAS, 2024. The data is organized by figure/subfigure and for each figure there is a separate 'notes.txt' file with explanatory text.
Investigation of bSSFP frequency response changes during a functional experiment at 9.4 T Apr 19, 2024 Iyyappan Valsala, Praveen, 2024, "Investigation of bSSFP frequency response changes during a functional experiment at 9.4 T", https://doi.org/10.17617/3.ZRZUBE, Edmond, V1 All data was acquired using an accelerated 3D stack-of-spirals sequence at a Siemens Magnetom 9. 4 T human MRI scanner. A resting-state phase-cycling experiment to assess data quality and two functional phase-cycling experiments with temporally shifted paradigm (see Figure 4) to...
A data-driven estimation of the ribosome drop-off rate in S. cerevisiae reveals a correlation with the genes length. Mar 26, 2024 Awad, Sherine; Valleriani, Angelo; Chiarugi, Davide, 2024, "A data-driven estimation of the ribosome drop-off rate in S. cerevisiae reveals a correlation with the genes length.", https://doi.org/10.17617/3.H7OPIB, Edmond, V1 Ribofilio is a software package that estimates the drop-off rate of ribosomes. It is a python package that takes as a required input the reference genome and the footprint. If the mRNA reads are available, this can be used as an optional parameter for normalization. The tool uses...
Multiscale simulations of the CP43 photosynthetic antenna complex: QM/MM, TD-DFT and PMM data Mar 4, 2024 Pantazis, Dimitrios A.; Bhattacharjee, Sinjini; Daidone, Isabella; Arra, Srilatha, 2023, "Multiscale simulations of the CP43 photosynthetic antenna complex: QM/MM, TD-DFT and PMM data", https://doi.org/10.17617/3.S2DPUE, Edmond, V2 Primary computational data used in multiscale studies of the CP43 photosynthetic antenna.
Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus Feb 20, 2024 Girard, Martin; Olvera de la Cruz, Monica; Marko, John; Erbas, Aykut, 2024, "Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus", https://doi.org/10.17617/3.P08YSZ, Edmond, V1 Dataset for ring polymers under confinement as a model for chromatin in the cell nucleus
MD simulations and energy minimizations of cellulose crystals Dec 17, 2023 Kullmann, Richard; Weikl, Thomas, 2023, "MD simulations and energy minimizations of cellulose crystals", https://doi.org/10.17617/3.1FPW2C, Edmond, V1 Microsecond-long simulations trajectories and results from energy minimizations for cellulose Ibeta and II crystals composed of 52 chains of cellulose 6-mers, 8-mers, 10-mers, or 12-mers.
STM images and DFT structures of glycoconjugates Oct 7, 2023 Anggara, Kelvin, 2023, "STM images and DFT structures of glycoconjugates", https://doi.org/10.17617/3.3F5JPU, Edmond, V2 Raw STM images of glycans and glycoconjugates were given in the SXM format outputted directly from the Nanonis control software, which can be opened using WSXM or Gwyddion. Computed structures were given in XYZ format, which can be opened by common molecular modeling software suc...
MINSTED tracking of single biomolecules Sep 26, 2023 Scheiderer, Lukas; von der Emde, Henrik; Hesselink, Mira; Weber, Michael; Hell, Stefan, 2023, "MINSTED tracking of single biomolecules", https://doi.org/10.17617/3.YIQGGB, Edmond, V1 We show that MINSTED localization, a method whereby the position of a fluorophore is identified with precisely controlled beams of a STED microscope, tracks fluorophores and hence labeled biomolecules with nanometer/millisecond spatio-temporal precision. By updating the position...

Library of optimal control pulse sequences for biomolecular NMR spectroscopy

Aug 2, 2024

Joseph, David; Griesinger, Christian, 2024, "Library of optimal control pulse sequences for biomolecular NMR spectroscopy", https://doi.org/10.17617/3.CBOUXH, Edmond, V1

This data set is part of the publication Library of optimal control pulse sequences for biomolecular NMR spectroscopy (manuscript in preparation). by D. Joseph and C. Griesinger. All reported pulse sequence codes and the necessary parameter files and additional OC pulse shapes ar...

Pair distributions and membrane-mediated interactions of arc-shaped particles on spherical and tubular vesicles

Jul 11, 2024

Bonazzi, Francesco; Weikl, Thomas, 2024, "Pair distributions and membrane-mediated interactions of arc-shaped particles on spherical and tubular vesicles", https://doi.org/10.17617/3.DIF595, Edmond, V1

This dataset contains data from Monte Carlo simulations of triangulated membrane vesicles with segmented, bound arc-shaped particles of two different sizes (in hdf5 format) and Mathematica notebooks to determine pair distributions, 2-dimensional free energy landscapes, and 1-dime...

Data for paper 'A cytokinetic ring-driven cell rotation achieves Hertwig's rule in early development'

May 27, 2024

Middelkoop, Teije, 2024, "Data for paper 'A cytokinetic ring-driven cell rotation achieves Hertwig's rule in early development'", https://doi.org/10.17617/3.WPVJHQ, Edmond, V1

Raw microscopy data for 'A cytokinetic ring-driven cell rotation achieves Hertwig's rule in early development', accepted for publication in PNAS, 2024. The data is organized by figure/subfigure and for each figure there is a separate 'notes.txt' file with explanatory text.

Investigation of bSSFP frequency response changes during a functional experiment at 9.4 T

Apr 19, 2024

Iyyappan Valsala, Praveen, 2024, "Investigation of bSSFP frequency response changes during a functional experiment at 9.4 T", https://doi.org/10.17617/3.ZRZUBE, Edmond, V1

All data was acquired using an accelerated 3D stack-of-spirals sequence at a Siemens Magnetom 9. 4 T human MRI scanner. A resting-state phase-cycling experiment to assess data quality and two functional phase-cycling experiments with temporally shifted paradigm (see Figure 4) to...

A data-driven estimation of the ribosome drop-off rate in S. cerevisiae reveals a correlation with the genes length.

Mar 26, 2024

Awad, Sherine; Valleriani, Angelo; Chiarugi, Davide, 2024, "A data-driven estimation of the ribosome drop-off rate in S. cerevisiae reveals a correlation with the genes length.", https://doi.org/10.17617/3.H7OPIB, Edmond, V1

Ribofilio is a software package that estimates the drop-off rate of ribosomes. It is a python package that takes as a required input the reference genome and the footprint. If the mRNA reads are available, this can be used as an optional parameter for normalization. The tool uses...

Multiscale simulations of the CP43 photosynthetic antenna complex: QM/MM, TD-DFT and PMM data

Mar 4, 2024

Pantazis, Dimitrios A.; Bhattacharjee, Sinjini; Daidone, Isabella; Arra, Srilatha, 2023, "Multiscale simulations of the CP43 photosynthetic antenna complex: QM/MM, TD-DFT and PMM data", https://doi.org/10.17617/3.S2DPUE, Edmond, V2

Primary computational data used in multiscale studies of the CP43 photosynthetic antenna.

Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus

Feb 20, 2024

Girard, Martin; Olvera de la Cruz, Monica; Marko, John; Erbas, Aykut, 2024, "Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus", https://doi.org/10.17617/3.P08YSZ, Edmond, V1

Dataset for ring polymers under confinement as a model for chromatin in the cell nucleus

MD simulations and energy minimizations of cellulose crystals

Dec 17, 2023

Kullmann, Richard; Weikl, Thomas, 2023, "MD simulations and energy minimizations of cellulose crystals", https://doi.org/10.17617/3.1FPW2C, Edmond, V1

Microsecond-long simulations trajectories and results from energy minimizations for cellulose Ibeta and II crystals composed of 52 chains of cellulose 6-mers, 8-mers, 10-mers, or 12-mers.

STM images and DFT structures of glycoconjugates

Oct 7, 2023

Anggara, Kelvin, 2023, "STM images and DFT structures of glycoconjugates", https://doi.org/10.17617/3.3F5JPU, Edmond, V2

Raw STM images of glycans and glycoconjugates were given in the SXM format outputted directly from the Nanonis control software, which can be opened using WSXM or Gwyddion. Computed structures were given in XYZ format, which can be opened by common molecular modeling software suc...

MINSTED tracking of single biomolecules

Sep 26, 2023

Scheiderer, Lukas; von der Emde, Henrik; Hesselink, Mira; Weber, Michael; Hell, Stefan, 2023, "MINSTED tracking of single biomolecules", https://doi.org/10.17617/3.YIQGGB, Edmond, V1

We show that MINSTED localization, a method whereby the position of a fluorophore is identified with precisely controlled beams of a STED microscope, tracks fluorophores and hence labeled biomolecules with nanometer/millisecond spatio-temporal precision. By updating the position...

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