cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15276372
title: DIM_Phase_transition_CG

description: This work is based on the following repository : https://doi.org/10.5281/zenodo.15173051This repository contains all the data produced regarding phase transition of 4-membrane systems containing different concentrations of DIM lipid, at temperatures ranging from 280 to 350K. The folders contain the resulting xtc trajectories, gro files, and tpr files for reproduction of the calculations. Below, a short description of the methodology : 

All simulations were performed with GROMACS version 2020.2. We conducted CG simulations of stacked lipid membranes in close proximity using the MARTINI3 force field and home made parameters for the DIM molecule. We built a simulation system consisting of 4 stacked membranes. Each individual membrane contained 154 POPC molecules, 470 DOPE molecules (DOPE/POPC molar ratio 3.05:1) and either 6, 12 or 18 molecules PDIM (PGL/lipid molar ratio 1%, 2%, 3%). The membranes were solvated with Martini 3 CG water (W) particles, with 3.33 W particles per lipid molecule, corresponding to about 13 atomistic water molecules per lipid. To preserve the lamellar membrane phase, the systems were equilibrated at 280 K, using the v-rescale thermostat with a time constant tT = 1.0 ps, and the Berendsen barostat with semi-isotropic pressure coupling, a reference pressure of 1.0 bar, a time constant tp = 5 ps, and a compressibility of 3 × 10-4 bar-1. Then 8 different simulations were launched, with temperatures ranging from 280 K to 350 K in 10 K increments. We executed the production runs in triplicate at each temperature, using a time step of 20 fs, for a total duration of 3 µs. The temperature was controlled using the Berendsen thermostat with a time constant tT = 1.0 ps, while the pressure was set using the Berendsen barostat with fully anisotropic pressure coupling, at a reference pressure of 1.0 bar, a time constant tp = 0.5 ps, and a compressibility of 1.0 × 10-5 bar-1. Constraints were imposed using the LINCS algorithm.The DIM force field parameters,  the Python and TCl files necessary to the reproduction of  figures are available in the parent repository.
DOI: 10.6084/m9.figshare.28892783
title: Dataset for "<b>Data to Physics in Minutes: An Agentic Large Language Model Solves a Competitive Adsorption Puzzle</b>"

description: Scientific modeling often requires navigating a trade-off between physical interpretability and empirical accuracy—a task that can take weeks of iteration, especially in systems with partial observability, structural complexity, and experimental errors. Here, we show how a state-of-the-art agentic reasoning-and-coding large language model, OpenAI o3, autonomously solved a modeling challenge in surface chemistry that puzzled us for months: quantifying the competitive adsorption of carboxylic acids on metal–organic layers. With experimental data and a concise problem formulation, o3 rapidly formulated a physically grounded adsorption model, derived the mathematical equations, implemented the corresponding codes to fit the experimental data, revised its assumptions, and ultimately derived a competitive adsorption model with three parameters that matched experimental data across more than a dozen of tested molecules. The resulting model—simple, mechanistically transparent, and quantitatively robust—incorporates both classical Langmuir competition and structural constraints such as site accessibility. Beyond addressing this particular challenge, our findings highlight a transformative shift in scientific methodology: from manual trial-and-error approaches to AI-driven hypothesis generation and model refinement. This represents a new paradigm in research, wherein language models surpass the traditional roles of machine learning in data analysis and computational support, actively participating in scientific reasoning and hypothesis development. Here is the experimental dataset in this work.
DOI: 10.15468/dl.qgtr92
title: Occurrence Download

description: A dataset containing 5986 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Bufo americanus Holbrook, 1836)"
 ]
}

 The dataset includes 5986 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005335-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gbtz2u
title: Occurrence Download

description: A dataset containing 7852 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Rana aurora Baird & Girard, 1852)"
 ]
}

 The dataset includes 7852 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005332-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kwq7e2
title: Occurrence Download

description: A dataset containing 169 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Culex perfuscus Edwards, 1914"
 ]
}

 The dataset includes 169 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005334-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15276358
title: PGL-TUB_Phase_transition_CG

description: This work is based on the following repository : https://doi.org/10.5281/zenodo.15173051This repository contains all the data produced regarding phase transition of 4-membrane systems containing different concentrations of PGL_TUB lipid, at temperatures ranging from 280 to 350K. The folders contain the resulting xtc trajectories, gro files, and tpr files for reproduction of the calculations. Below, a short description of the methodology : 

All simulations were performed with GROMACS version 2020.2. We conducted CG simulations of stacked lipid membranes in close proximity using the MARTINI3 force field and home made parameters for the PGL_TUB molecule. We built a simulation system consisting of 4 stacked membranes. Each individual membrane contained 154 POPC molecules, 470 DOPE molecules (DOPE/POPC molar ratio 3.05:1) and either 6, 12 or 18 molecules PGL_TUB (PGL/lipid molar ratio 1%, 2%, 3%). The membranes were solvated with Martini 3 CG water (W) particles, with 3.33 W particles per lipid molecule, corresponding to about 13 atomistic water molecules per lipid. To preserve the lamellar membrane phase, the systems were equilibrated at 280 K, using the v-rescale thermostat with a time constant tT = 1.0 ps, and the Berendsen barostat with semi-isotropic pressure coupling, a reference pressure of 1.0 bar, a time constant tp = 5 ps, and a compressibility of 3 × 10-4 bar-1. Then 8 different simulations were launched, with temperatures ranging from 280 K to 350 K in 10 K increments. We executed the production runs in triplicate at each temperature, using a time step of 20 fs, for a total duration of 3 µs. The temperature was controlled using the Berendsen thermostat with a time constant tT = 1.0 ps, while the pressure was set using the Berendsen barostat with fully anisotropic pressure coupling, at a reference pressure of 1.0 bar, a time constant tp = 0.5 ps, and a compressibility of 1.0 × 10-5 bar-1. Constraints were imposed using the LINCS algorithm.The PGL_TUB force field parameters,  the Python and TCl files necessary to the reproduction of  figures are available in the parent repository.
DOI: 10.5281/zenodo.15276359
title: PGL-TUB_Phase_transition_CG

description: This work is based on the following repository : https://doi.org/10.5281/zenodo.15173051This repository contains all the data produced regarding phase transition of 4-membrane systems containing different concentrations of PGL_TUB lipid, at temperatures ranging from 280 to 350K. The folders contain the resulting xtc trajectories, gro files, and tpr files for reproduction of the calculations. Below, a short description of the methodology : 

All simulations were performed with GROMACS version 2020.2. We conducted CG simulations of stacked lipid membranes in close proximity using the MARTINI3 force field and home made parameters for the PGL_TUB molecule. We built a simulation system consisting of 4 stacked membranes. Each individual membrane contained 154 POPC molecules, 470 DOPE molecules (DOPE/POPC molar ratio 3.05:1) and either 6, 12 or 18 molecules PGL_TUB (PGL/lipid molar ratio 1%, 2%, 3%). The membranes were solvated with Martini 3 CG water (W) particles, with 3.33 W particles per lipid molecule, corresponding to about 13 atomistic water molecules per lipid. To preserve the lamellar membrane phase, the systems were equilibrated at 280 K, using the v-rescale thermostat with a time constant tT = 1.0 ps, and the Berendsen barostat with semi-isotropic pressure coupling, a reference pressure of 1.0 bar, a time constant tp = 5 ps, and a compressibility of 3 × 10-4 bar-1. Then 8 different simulations were launched, with temperatures ranging from 280 K to 350 K in 10 K increments. We executed the production runs in triplicate at each temperature, using a time step of 20 fs, for a total duration of 3 µs. The temperature was controlled using the Berendsen thermostat with a time constant tT = 1.0 ps, while the pressure was set using the Berendsen barostat with fully anisotropic pressure coupling, at a reference pressure of 1.0 bar, a time constant tp = 0.5 ps, and a compressibility of 1.0 × 10-5 bar-1. Constraints were imposed using the LINCS algorithm.The PGL_TUB force field parameters,  the Python and TCl files necessary to the reproduction of  figures are available in the parent repository.
DOI: 10.15468/dl.tjv9d6
title: Occurrence Download

description: A dataset listing the 2723 species recorded in GBIF matching the query:
{
 "and" : [
 "GadmGid is VNM",
 "OccurrenceStatus is Present",
 "Year 2009-2009"
 ]
}

 The dataset's 2723 records were derived from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005316-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v5ys6f
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Culex neavei Theobald, 1906"
 ]
}

 The dataset includes 55 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005336-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ecwws5
title: Occurrence Download

description: A dataset containing 211685 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chelonia mydas (Linnaeus, 1758)"
 ]
}

 The dataset includes 211685 records from 405 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005319-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/dc3-2r3-skk
title: Calepina irregularis (Asso) Thell.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/dnv-7cd-jc3
title: Campanula ramosissima Sm.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/qe7-lql-z7x
title: Bromus rubens L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/z1g-dt7-p1b
title: Calepina irregularis (Asso) Thell.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/8l7-jeq-a3m
title: Calepina irregularis (Asso) Thell.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/p63-lm1-exh
title: Campanula ramosissima Sm.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/brb-jrk-8sb
title: Bromus sterilis L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/eqf-whk-n58
title: Campanula ramosissima Sm.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/9n7-9es-gym
title: Bromus sterilis L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/4s2-tr4-rhw
title: Carex sylvatica Huds.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/lq1-epl-lnc
title: Campanula ramosissima Sm.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/7pg-ec2-f7v
title: Carex pendula Huds.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/bzv-8c8-geq
title: Bromus sterilis L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/2ja-cwv-krn
title: Bromus sterilis L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/152-g46-r9f
title: Bromus sterilis L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/nph-y1r-znn
title: Bromus sterilis L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/5wv-bzx-nyt
title: Carex ovalis Gooden.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/gcf-cmw-cx4
title: Carex muricata L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/ajh-0t4-pxm
title: Beta maritima L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/c62-jnj-w7x
title: Bupleurum glumaceum Sm.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/jat-g4y-z92
title: Bupleurum lancifolium Hornem.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/azc-v5q-yqb
title: Bupleurum glumaceum Sm.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/svh-sl2-6cc
title: Bupleurum glumaceum Sm.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/y5c-jp6-mfb
title: Carex leersii F.W.Schultz

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/kgk-1a1-6zc
title: Carex leersii F.W.Schultz

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/rl5-dws-4xl
title: Avena sterilis subsp. ludoviciana (Durieu) Nyman

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.15468/dl.uzuu42
title: Occurrence Download

description: A dataset containing 9425 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cynorkis Thouars"
 ]
}

 The dataset includes 9425 records from 123 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0113044-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/m4g-me9-bdn
title: Avena sterilis subsp. ludoviciana (Durieu) Nyman

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.15468/dl.q4fpzp
title: Occurrence Download

description: A dataset containing 1087 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amanses scopas (Cuvier, 1829)"
 ]
}

 The dataset includes 1087 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0113045-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/wqj-61t-pge
title: Avena sterilis subsp. ludoviciana (Durieu) Nyman

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/ykr-rr5-et3
title: Avena sterilis subsp. ludoviciana (Durieu) Nyman

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/pw9-53d-134
title: Bupleurum trichopodum Boiss. & Spruner

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/q23-n0j-b3b
title: Avena barbata Pott ex Link

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/2h9-189-lla
title: Bupleurum trichopodum Boiss. & Spruner

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/7yb-hw6-ysq
title: Bupleurum trichopodum Boiss. & Spruner

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/des-fr4-cj1
title: Bupleurum trichopodum Boiss. & Spruner

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/ahp-m1f-f6k
title: Capsella bursa-pastoris (L.) Medik.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/wdy-zfs-6pd
title: Bupleurum trichopodum Boiss. & Spruner

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/rf3-7wr-sxw
title: Bupleurum trichopodum Boiss. & Spruner

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/mct-c7h-p9z
title: Capsella bursa-pastoris (L.) Medik.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/zxj-mrd-1xp
title: Bupleurum trichopodum Boiss. & Spruner

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/qle-sve-jaf
title: Capsella bursa-pastoris (L.) Medik.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.15468/dl.viqkq7
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000960-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q8y7h9
title: Occurrence Download

description: A dataset containing 823521 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ghana",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 823521 records from 835 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067388-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3vzjfz
title: Occurrence Download

description: A dataset containing 1129 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Artibeus fraterculus Anthony, 1924"
 ]
}

 The dataset includes 1129 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019812-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mdqp4c
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025090-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.oggtvm
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015659-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z7z7mf
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025084-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.osiepu
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000089-160526112335914/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.frrktd
title: Occurrence Download

description: A dataset containing 109551332 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Insecta"
 ]
}

 The dataset includes 109551332 records from 9447 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042407-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17306634
title: Data for the article "Classical and quantum chaotic synchronization in coupled dissipative time crystals" (arXiv:2509.20922)