cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25606/surf.578c6039-71fcc1a9
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-034)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 034 of the 2048³ resolution collection.
DOI: 10.25606/surf.578c6039-e47583a1
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-047)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 047 of the 2048³ resolution collection.
DOI: 10.25606/surf.578c6039-4a7c57da
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-037)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 037 of the 2048³ resolution collection.
DOI: 10.25606/surf.578c6039-8c881367
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-039)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 039 of the 2048³ resolution collection.
DOI: 10.25606/surf.578c6039-412fa087
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-046)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 046 of the 2048³ resolution collection.
DOI: 10.5281/zenodo.2578980
title: Zebrafish Phenotype Ontology

description: Current release of Zebrafish Phenotype Ontology
DOI: 10.5281/zenodo.2578981
title: Zebrafish Phenotype Ontology

description: Current release of Zebrafish Phenotype Ontology
DOI: 10.5281/zenodo.2577920
title: Sensitivity Datasets - Leveraging Implicit Knowledge in Neural Networks for Functional Dissection and Engineering of Proteins

description: <strong>Leveraging Implicit Knowledge in Neural Networks for Functional Dissection and Engineering of Proteins</strong>

The Sensitivity datasets cover more than 800 proteins and are structured as follows. The sensitivity values are the mean of four DeeProtein replicates.

It is uploaded as tar.gz. and contains one directory.

File names contain the PDB<sup>1</sup> identifier and the respective chain identifier. 

The sequences and secondary structure information were downloaded from the RCSB Protein Databank and are available here: https://cdn.rcsb.org/etl/kabschSander/ss_dis.txt.gz This URL can be found with some explanation at http://www.rcsb.org/pdb/static.do?p=download/http/index.html

The secondary structure annotation relies on the DSSP Algorithm by Kabsch and Sander<sup>2</sup>.

 

<strong>The files are tab-separated and contain the following columns:</strong>


	<strong>Pos</strong> Position in the sequence, starting from zero
	<strong>AA</strong> Amino acid in that position
	<strong>sec</strong> Secondary structure as annotated in the RCSB Protein Databank
	<strong>dis</strong> if a region has not been experimentally observed (sometimes explains mismatches with crystal structures)
	<strong>GO:_______</strong> Sensitivity for the GO term


<strong>References</strong>


	The Protein Data Bank H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) Nucleic Acids Research, 28: 235-242. doi:10.1093/nar/28.1.235
	Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637, doi:10.1002/bip.360221211 (1983).
description: Authorship Statement
The following are members of the iGEM (international genetically engineered machines) Team Heidelberg 2017: Lukas Adam, Thore Bürgel, Roland Eils, Catharina Gandor, Daniel Heid, Mareike Daniela Hoffmann, Stefan Holderbach, Michael Jendrusch, Marita Klein, Irina Lehmann, Jan Mathony, Dominik Niopek, Pauline Pfuderer, Lukas Platz, Moritz Przybilla, Carolin Schmelas, Max Schwendemann, Julius Upmeier zu Belzen, Max Waldhauer (all from Germany).

Acknowledgements
This work was funded by the Klaus-Tschira foundation, the German Research Council (DFG) and the Federal Ministry of Education and Research (BMBF). We thank Jürgen Quittek and Matthias Niepert (both NEC, Heidelberg), Thomas Wollmann (IPMB, BioQuant and German Cancer Research Center (DKFZ), Heidelberg) for helpful discussions and Marc Hemberger (BioQuant, Heidelberg) for support with IT and GPU cluster use.
description: {"references": ["The Protein Data Bank H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) Nucleic Acids Research, 28: 235-242. doi:10.1093/nar/28.1.235", "Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637, doi:10.1002/bip.360221211 (1983)."]}
DOI: 10.17632/5b58jx5cvy.1
title: Data for: Test of the Validity of Bragg´s Rule for Mean Excitation Energies

description: We are investigated the effect of chemical binding on the validity of Bragg’s rule for the calculation of stopping cross sections and mean excitation energies. As test cases we use a series of small molecules and molecular ions, primarily carbon and nitrogen halides. We find that neglect of chemical binding nearly always reduces the mean excitation energies and that the fully atomic decomposition of any molecule but a diatomic molecule never gives the best fulfilment of Bragg’s rule. The best fulfilment of Bragg’s rule is obtained when as few bonds as possible are broken and when the choice of fragments is guided by chemical knowledge. By investigating several alternative fragmentation patterns for a molecule, guidelines for choice of optimal fragmentation are suggested.
DOI: 10.18739/a2n29p63k
title: Microstructure measurements from the Arcticmix cruise, Beaufort Sea, September 2015
DOI: 10.25606/surf.578c6039-0caeacae
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-109)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 109 of the 2048³ resolution collection.
DOI: 10.25606/surf.578c6039-176d2ac2
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-111)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 111 of the 2048³ resolution collection.
DOI: 10.25606/surf.578c6039-3a952e5b
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-112)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 112 of the 2048³ resolution collection.
DOI: 10.25606/surf.578c6039-8781eba6
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (1024-025)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 025 of the 1024³ resolution collection.
DOI: 10.18739/a2v40jz6c
title: Firn air content and firn area delineation on the Greenland ice sheet, 1953-2017
DOI: 10.25606/surf.578c6039-0bf84511
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-103)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 103 of the 2048³ resolution collection.
DOI: 10.25606/surf.578c6039-361efdc7
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-164)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 164 of the 2048³ resolution collection.
DOI: 10.25606/surf.578c6039-67c70a4f
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-162)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 162 of the 2048³ resolution collection.
DOI: 10.25606/surf.578c6039-ba8f0242
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-105)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 105 of the 2048³ resolution collection.