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opencc-by-4.0Jan 2021View details →

Terahertz Spin-to-Charge Conversion by Interfacial Skew Scattering in Metallic Bilayers

Data of the publication "Terahertz Spin-to-Charge Conversion by Interfacial Skew Scattering in Metallic Bilayers" published in Advanced Materials, 33, 2006281 (2021). THz waveforms for a subset and RMS data - corrected for pump incoupling and THz outcoupling - for various F and N metallic bilayers and interface modifications as well as the calculated spin Hall angles for different interfacial impurities are provided.

opencc-by-4.0Oct 2023View details →

Dataset for "Reconfigurable Magnonic Crystals Based on Imprinted Magnetization Textures in Hard and Soft Dipolar-Coupled Bilayers"

The dataset consist of the data of the numerical simulations used to prepare the figures for the manuscript: Krzysztof Szulc, Silvia Tacchi, Aurelio Hierro-Rodríguez, Javier Díaz, Paweł Gruszecki, Piotr Graczyk, Carlos Quirós, Daniel Markó, José Ignacio Martín, María Vélez, David S. Schmool, Giovanni Carlotti, Maciej Krawczyk, and Luis Manuel Álvarez-Prado. Reconfigurable Magnonic Crystals Based on Imprinted Magnetization Textures in Hard and Soft Dipolar-Coupled Bilayers. ACS Nano 2022 16 (9), 14168-14177.Please read README.txt file to see the description of the data in the files.

opencc-by-4.0Jun 2020View details →

Biogenic supported lipid bilayers as a tool to investigate nano-bio interfaces

Colorimentric Nanoplasmonic Assay (CONAN) assay of EVs from TRAMP cells. UV/VIS spectrophotometer analysis of samples of EVs from TRAMP cell line incubated with gold nanoparticles, following the protocol described in Montis et al. <a href="https://doi.org/10.1016/j.jcis.2020.03.014">https://doi.org/10.1016/j.jcis.2020.03.014</a>

Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% DOPS with Na+ counterions using ff99 Ions

System: Symmetric bilayer of anionic DOPS (1,2-Dioleoyl-sn-glycero-3-phosphoserine 100 mol-%) lipids with sodium (Na+) counter ions. Number of DOPS: 128. Number of Na+-ions: 128. Number of waters: 4480. Lipid model: Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)]. Ion models:  Amber ff99 [J Åqvist J. Phys. Chem. 94 8021 (1990)]. Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Simulation engine: Amber16 [DA Case et al. AMBER 2017 UCSF (2017)]. Number of independent repeats per setup: 2. Trajectory lengths per repeat: 400 ns + 100 ns. Previously equilibrated for: 100 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Langevin' at T = 303 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984); J. Chem. Phys. 103 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Theory Comput. 9 3878 (2013)]. Van der Waals: Turned off between 1.0 nm and 1.5 nm. Constraints: Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [J. Comput. Phys. 23 327 (1977)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).

Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% POPS with Na+ counterions using Joung-Cheatham Ions

System: Symmetric bilayer of anionic POPS (palmitoyl-oleoyl-phosphatidylserine 100 mol-%) lipids with sodium (Na+) counter ions. Number of POPS: 128. Number of Na+-ions: 128. Number of waters: 4480. Lipid model: Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)]. Ion model: Joung–Cheatham [IS Joung, TE Cheatham III J. Phys. Chem. B 112 9020 (2008)]. Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Simulation engine: Amber16 [DA Case et al. AMBER 2017 UCSF (2017)]. Number of independent repeats per setup: 2. Trajectory lengths per repeat: 400 ns + 100 ns. Previously equilibrated for: 100 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Langevin' at T = 298 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984); J. Chem. Phys. 103 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Theory Comput. 9 3878 (2013)]. Van der Waals: Turned off between 1.0 nm and 1.5 nm. Constraints: Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [J. Comput. Phys. 23 327 (1977)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).

Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% POPS with Na+ counterions using ff99 ions

System: Symmetric bilayer of anionic POPS (palmitoyl-oleoyl-phosphatidylserine 100 mol-%) lipids with sodium (Na+) counter ions. Number of POPS: 128. Number of Na+-ions: 128. Number of waters: 4480. Lipid model: Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)]. Ion model: Amber ff99 [J Åqvist J. Phys. Chem. 94 8021 (1990)]. Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Simulation engine: Amber16 [DA Case et al. AMBER 2017 UCSF (2017)]. Number of independent repeats per setup: 2. Trajectory lengths per repeat: 400 ns + 100 ns. Previously equilibrated for: 100 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Langevin' at T = 298 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984); J. Chem. Phys. 103 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Theory Comput. 9 3878 (2013)]. Van der Waals: Turned off between 1.0 nm and 1.5 nm. Constraints: Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [J. Comput. Phys. 23 327 (1977)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).

Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% DOPS with Na+ counterions using Joung-Cheetham Ions

System: Symmetric bilayer of anionic DOPS (1,2-Dioleoyl-sn-glycero-3-phosphoserine 100 mol-%) lipids with sodium (Na+) counter ions. Number of DOPS: 128. Number of Na+-ions: 128. Number of waters: 4480. Lipid model: Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)]. Ion models: Joung–Cheatham [IS Joung, TE Cheatham III J. Phys. Chem. B 112 9020 (2008)]. Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Simulation engine: Amber16 [DA Case et al. AMBER 2017 UCSF (2017)]. Number of independent repeats per setup: 2. Trajectory lengths per repeat: 400 ns + 100 ns. Previously equilibrated for: 100 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Langevin' at T = 303 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984); J. Chem. Phys. 103 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Theory Comput. 9 3878 (2013)]. Van der Waals: Turned off between 1.0 nm and 1.5 nm. Constraints: Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [J. Comput. Phys. 23 327 (1977)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).

opencc-by-4.0Aug 2021View details →

Supporting data for "Dispersive sensing of charge states in a bilayer graphene quantum dot"

Supporting data and analysis scripts for all figures in the article "Dispersive sensing of charge states in a bilayer graphene quantum dot", Appl. Phys. Lett. 118, 093104 (2021); <a href="https://doi.org/10.1063/5.0040234">https://doi.org/10.1063/5.0040234</a> The files are sorted according to the figures/panels in the publication with a "0-README.txt" file including further information.  The following versions of Pyhton and the packages have been used: python: 3.6.10 numpy: 1.18.1 matplotlib: 3.1.3 scipy: 1.4.1

opencc-by-4.0May 2023View details →

Non-identical moire twins in bilayer graphene revealed by valley Hall effect measurements

The superlattice obtained by aligning a monolayer graphene and boron nitride (BN) inherits from the hexagonal lattice a sixty degrees periodicity with the layer alignment. It implies that, in principle, the properties of the heterostructure must be identical for 0$^{\circ}$ and 60$^{\circ}$ of layer alignment. Here, we demonstrate, using dynamically rotatable van der Waals heterostructures, that the moir\'e superlattice formed in a bilayer graphene/BN has different electronic properties at 0$^{\circ}$ and 60$^{\circ}$ of alignment. Although the existence of these non-identical moir\'e twins is explained by different relaxation of the atomic structures for each alignment, the origin of the observed valley Hall effect remains to be explained. A simple Berry curvature argument do not hold to explain the hundred and twenty degrees periodicity of this observation. Our results highlight the complexity of the interplay between mechanical and electronic properties on moir\'e structure and the importance of taking into account atomic structure relaxation to understand its electronic properties.

opencc-by-4.0Sep 2023View details →

NAMD Trajectory of a Palmitoyl Sphingomyelin Bilayer

All-atom PSM bilayer simulated in NPT ensemble with NAMD and the CHARMM36 force field from Doktorova et al. 2020 J. Phys. Chem. B. article (DOI 10.1021/acs.jpcb.0c03389). The trajectory represents the last 117 ns used for analysis where the area per lipid is equilibrated (the file has 5874 frames output every 20 ps). The bilayer has 200 lipids total (100 lipids per leaflet) and is hydrated with 45 waters/lipid. The simulation was done at 55C (328.15K) and the trajectory is centered on the bilayer midplane.

opencc-by-4.0Sep 2023View details →

NAMD Trajectory of a Tetraoleoyl Cardiolipin Bilayer

All-atom TOCL (tetraoleoyl cardiolipin) bilayer simulated in NPT ensemble with NAMD and the CHARMM36 force field from Doktorova et al. 2017 Phys. Chem. Chem. Phys. article (DOI 10.1039/c7cp01921a). The trajectory represents the last 155 ns used for analysis where the area per lipid is equilibrated (the file has 7752 frames output every 20 ps). The bilayer has 100 lipids total (50 lipids per leaflet) and is hydrated with 60 waters/lipid and 140mM NaCl. The simulation was done at 30C (303.15K) and the trajectory is centered on the bilayer midplane.

opencc-by-4.0Sep 2023View details →

NAMD Trajectory of a DLiPC (di18:2PC) bilayer

All-atom DLiPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine) bilayer simulated in NPT ensemble with NAMD and the CHARMM36 force field from Doktorova et al. 2017 Phys. Chem. Chem. Phys. article (DOI 10.1039/c7cp01921a). The trajectory represents the last 245 ns used for analysis where the area per lipid is equilibrated (the file has 12250 frames output every 20 ps). The bilayer has 200 lipids total (100 lipids per leaflet) and is hydrated with 45 waters/lipid. The simulation was done at 25C (298.15K) and the trajectory is centered on the bilayer midplane.

opencc-zeroJul 2015View details →

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r System: 80 wt% C12E5, T=298K Other files available: http://dx.doi.org/10.6084/m9.figshare.861071

opencc-by-4.0Oct 2023View details →

Gaussian-accelerated Molecular Dynamics simulations of CCR8-CCL1-Gprotein complex in a POPC lipid bilayer

Gaussian-accelerated Molecular Dynamics simulations of the CCR8-CCL1-Gprotein complex in a POPC lipid bilayer. Simulation system was prepared with OpenMM v7.7 and simulations were performed using the GaMD-OpenMM package (https://github.com/MiaoLab20/gamd-openmm) with a modification to include the MDTraj h5 file formate reporter as the output file format. These simulations were then converted to pdb topologies and dcd trajectories using MDTraj. Files include:CCL1_CCR8_noSer23_oriented_repaired1_system.pdb : system topologyCCL1_CCR8_config.xml : config for running GaMD-OpenMMCCL1_CCR8_N_1ns_imaged_structure.pdb : initial topology/structureCCL1_CCR8_N_1ns_imaged_trajectory.dcd : trajectory file Simulations can be loaded in python using MDTraj:import mdtrajtrj = mdtraj.load(<dcd file>, top=<pdb file>)

opencc-by-4.0Nov 2023View details →

Coherent Charge Oscillations in a Bilayer Graphene Double Quantum Dot

This repository contains the experimental data and the scripts for evaluating the data of the publication "Coherent Charge Oscillations in a Bilayer Graphene Double Quantum Dot".

opencc-by-4.0Dec 2023View details →

Quantitative results of the analysis of relevant components of artificial bilayered substitutes developed by tissue engineering

This dataset corresponds to the quantification results carried out for artificial bilayered substitutes developed by tissue engineering and control tissues analyzed in the manuscript entitled "Spatiotemporal characterization of extracellular matrix maturation in human artificial stromal-epithelial tissue substitutes". Tissue engineering techniques offer new strategies to understand complex processes in a controlled and reproducible system. In this study, we generated bilayered human tissue substitutes consisting of a cellular connective tissue with a suprajacent epithelium (full-thickness stromal-epithelial substitutes or SESS), and human tissue substitutes with an epithelial layer generated on top of an acellular biomaterial (epithelial substitutes or ESS). Both types of artificial tissues were studied at sequential time periods to analyze the maturation process of the extracellular matrix (ECM) using histochemical and immunohistochemical techniques. Results showed that both models were able to exhibit a partial development of the epithelial layer. ESS cells showed active proliferation, positive expression of KRT5 and low expression of differentiation markers, whereas SESS epithelium showed higher differentiation levels, with a progressive positive expression of KRT10 and claudin, although the differentiation levels of control native tissues were not reached. Despite the typical rete-ridges and papillae of native tissues were not found, stromal cells in SESS tended to accumulate and actively synthetize ECM components such as collagens and proteoglycans in the stromal area in direct contact with the epithelium (Z1 zone), whereas these components were very scarce in ESS. Regarding the basement membrane (BM), ESS showed a partially-differentiated structure containing fibronectin-1 (FN1) and perlecan (HSPG2), although the PAS staining signal was significantly lower than control native tissues. However, SESS showed higher BM differentiation, with positive expression of FN1, HSPG2, nidogen 1 (NID1), chondroitin-6-sulfate proteoglycans (CH6S), agrin (AGRN), and collagens types IV (COL-IV) and VII (COL-VII), although this structure was negative for lumican (LUM). These results confirm the relevance of epithelial-stromal interaction for ECM development and differentiation, especially regarding BM components, and suggest the usefulness of bilayered artificial tissue substitutes to reproduce ex vivo the ECM maturation and development process of human tissues. The original data obtained for the quantitative analyses of each component are shown in this dataset.

opencc-by-4.0Mar 2024View details →

Topological superconductivity in twisted bilayer WSe2: single band t-J model

Dataset of results related with the theoretical analysis of topological unconventional superconducting state within the t-J model as applied to the description of the twisted bilayer WSe2. The code in c++ which was used to produce the data is also provided. This data set is a result of research which was founded by National Science Centre, Poland (NCN) according to decision 2021/42/E/ST3/00128.

opencc-by-4.0Apr 2024View details →

Infrared Spectroscopy for Diagnosing Superlattice Minibands in Magic-angle Twisted Bilayer Graphene

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