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20 results for “Dynamic cation”

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zenodo40/100

A complete picture of cation dynamics in hybrid perovskite materials from solid-state NMR spectroscopy

Raw, collated NMR and XRD data for the article "A Complete Picture of Cation Dynamics in Hybrid Perovskite Materials from Solid-State NMR Spectroscopy". For further details see the readme.txt file.

opencc-by-4.0Jan 2023View details →

dryad40/100

Correlated nanoimaging of structure and dynamics of cation-polaron coupling in hybrid perovskites

Open the record for dataset details and reuse information.

publicFeb 2025View details →

zenodo36/100

Molecular dynamics simulation trajectory of a cationic lipid bilayer: 6/94 mol% DMTAP/DMPC

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 6 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 94 mol-%) lipids in water. Number of DMPC: 120. Number of DMTAP: 8. Number of Cl--ions: 8. Number of waters: 5099. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)] with DMTAP modification by Gurtovenko et al. [Biophys. J. 86 3461 (2004)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 109 ns. Previously equilibrated for: 32 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm. Van der Waals: Truncated at 1.0 nm. Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.

opencc-by-4.0May 2016View details →

zenodo36/100

Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC in 0.5 M NaCl

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 50 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 50 mol-%) lipids in 0.5 M NaCl solution. Number of DMPC: 64. Number of DMTAP: 64. Number of Na+-ions: 48. Number of Cl--ions: 112. Number of waters: 5240. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)] with DMTAP modification by Gurtovenko et al. [Biophys. J. 86 3461 (2004)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 179 ns. Previously equilibrated for: 21 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm. Van der Waals: Truncated at 1.0 nm. Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.

opencc-by-4.0May 2016View details →

zenodo36/100

Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC in 1.0 M NaCl

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 50 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 50 mol-%) lipids in 1.0 M NaCl solution. Number of DMPC: 64. Number of DMTAP: 64. Number of Na+-ions: 94. Number of Cl--ions: 158. Number of waters: 5148. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)] with DMTAP modification by Gurtovenko et al. [Biophys. J. 86 3461 (2004)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 170 ns. Previously equilibrated for: 21 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm. Van der Waals: Truncated at 1.0 nm. Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.

opencc-by-4.0May 2016View details →

zenodo36/100

Molecular dynamics simulation trajectory of a cationic lipid bilayer: 6/94 mol% DMTAP/DMPC in 1.0 M NaCl

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 6 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 94 mol-%) lipids in 1.0 M NaCl solution. Number of DMPC: 120. Number of DMTAP: 8. Number of Na+-ions: 89. Number of Cl--ions: 97. Number of waters: 4921. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)] with DMTAP modification by Gurtovenko et al. [Biophys. J. 86 3461 (2004)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 230 ns. Previously equilibrated for: 12 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm. Van der Waals: Truncated at 1.0 nm. Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.

opencc-by-4.0May 2016View details →

zenodo36/100

Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC in 1.0 M NaCl

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in 1.0 M NaCl solution. Number of DMPC: 32. Number of DMTAP: 96. Number of Na+-ions: 96. Number of Cl--ions: 192. Number of waters: 5304. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)] with DMTAP modification by Gurtovenko et al. [Biophys. J. 86 3461 (2004)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 110 ns. Previously equilibrated for: 11 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm. Van der Waals: Truncated at 1.0 nm. Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.

opencc-by-4.0May 2016View details →

zenodo36/100

Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 50 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 50 mol-%) lipids in water. Number of DMPC: 64. Number of DMTAP: 64. Number of Cl--ions: 64. Number of waters: 5336. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)] with DMTAP modification by Gurtovenko et al. [Biophys. J. 86 3461 (2004)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 149 ns. Previously equilibrated for: 41 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm. Van der Waals: Truncated at 1.0 nm. Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.

opencc-by-4.0May 2016View details →

zenodo36/100

Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC in 0.1 M NaCl

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 50 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 50 mol-%) lipids in 0.1 M NaCl solution. Number of DMPC: 64. Number of DMTAP: 64. Number of Na+-ions: 10. Number of Cl--ions: 74. Number of waters: 5316. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)] with DMTAP modification by Gurtovenko et al. [Biophys. J. 86 3461 (2004)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 190 ns. Previously equilibrated for: 21 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm. Van der Waals: Truncated at 1.0 nm. Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.

opencc-by-4.0May 2016View details →

zenodo36/100

Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC in 0.1 M NaCl

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in 0.1 M NaCl solution. Number of DMPC: 32. Number of DMTAP: 96. Number of Na+-ions: 10. Number of Cl--ions: 106. Number of waters: 5476. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)] with DMTAP modification by Gurtovenko et al. [Biophys. J. 86 3461 (2004)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 110 ns. Previously equilibrated for: 11 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm. Van der Waals: Truncated at 1.0 nm. Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.

opencc-by-4.0May 2016View details →

zenodo36/100

Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC in 0.5 M NaCl

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in 0.5 M NaCl solution. Number of DMPC: 32. Number of DMTAP: 96. Number of Na+-ions: 49. Number of Cl--ions: 145. Number of waters: 5398. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)] with DMTAP modification by Gurtovenko et al. [Biophys. J. 86 3461 (2004)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 110 ns. Previously equilibrated for: 11 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm. Van der Waals: Truncated at 1.0 nm. Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.

opencc-by-4.0May 2016View details →

zenodo36/100

Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in water. Number of DMPC: 32. Number of DMTAP: 96. Number of Cl--ions: 96. Number of waters: 5496. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)] with DMTAP modification by Gurtovenko et al. [Biophys. J. 86 3461 (2004)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 109 ns. Previously equilibrated for: 31 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm. Van der Waals: Truncated at 1.0 nm. Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.

opencc-by-4.0May 2016View details →

zenodo36/100

Revisiting the allosteric regulation of sodium cation on the binding of adenosine at the human A2A adenosine receptors: insights from Supervised Molecular Dynamics (SuMD) simulations.

SuMD trajectories Videos   Video 1: Sodium binding pathway on the antagonist-bound state of A2AR. The video is composed of four synchronized and animated panels that depict the molecular trajectory obtained by the SuMD simulation considering different aspects of the simulation. The time evolution is reported in a nanosecond. In the first panel (upper-left), the molecular representation of the macromolecular system is shown. The A2AR antagonist-bound state backbone is represented by the ribbon style (cyan colour) and the residues within 4 Å of sodium ion during the entire simulation are dynamically shown. Na+ is rendered showing its VdW volume in yellow. In the second panel (upper-right), the dynamic distance of sodium center of mass (CM) from the A2AR allosteric binding site during the trajectory is reported. In the third panel (lower-left), the MMGBSA energy profile is reported. The animated red circle highlights the value of the corresponding frame. The trend is depicted by a continuous black line obtained by smoothing the raw data (grey circles) using a Bezier curve procedure. In the fourth panel (lower-right) cumulative electrostatic interactions are reported for the 15 A2AR residues most contacted by sodium during the whole simulation.   Video 2: Adenosine different binding pathways collection on the two relevant states of A2AR The video is composed of two panels, which summarizes the recognition process of the adenosine agonist, sampled by means of the supervised molecular dynamics methodology, in the two pharmacologically relevant states of the receptor. In particular, on the right side are shown simultaneously all ten replicas collected starting from the agonist-bound conformation of the A2AR (pink ribbon). The meta-binding site located at the level of the ECL2 and the orthosteric binding site were highlighted. On the left side are represented simultaneously all ten replicas collected starting from the antagonist-bound conformation of the A2AR (cyan ribbon). The meta-binding site located at the level of the ECL2 and the extracellular receptor vestibule were highlighted.   Video 3: Adenosine binding pathway on the agonist-bound state of A2AR. The video is composed of four synchronized and animated panels that depict the molecular trajectory obtained by the SuMD simulation considering different aspects of the simulation. The time evolution is reported in a nanosecond. In the first panel (upper-left), the molecular representation of the macromolecular system is shown. The A2AR agonist-bound state backbone is represented by the ribbon style (pink colour) and the residues within 4 Å of sodium ion during the entire simulation are dynamically shown. Adenosine molecule is rendered by orange carbon atoms and by a transparent surface. In the second panel (upper-right), the dynamic distance of agonist center of mass (CM) from the A2AR allosteric binding site during the trajectory is reported. In the third panel (lower-left), the MMGBSA energy profile is reported. The animated red circle highlights the value of the corresponding frame. The trend is depicted by a continuous black line obtained by smoothing the raw data (grey circles) using a Bezier curve procedure. In the fourth panel (lower-right) cumulative electrostatic interactions are reported for the 15 A2AR residues most contacted by adenosine during the whole simulation.

opencc-by-4.0Jun 2019View details →

zenodo36/100

Data supporting Mixed-anion mixed-cation perovskite (FAPbI3)0.875(MAPbBr3)0.125: an ab initio molecular dynamics study

Data of a molecular dynamics simulation of the mixed cation and mixed halide perovskite (FAPbI3)0.875(MAPbBr3)0.125 , as well as the end compounds FAPbI3 and MAPbBr3. Related article:  J. Mater. Chem. A, 2022,10, 9592-9603, <a href="https://doi.org/10.1039/D1TA10860C">https://doi.org/10.1039/D1TA10860C</a> arXiv:2112.09795 [cond-mat.mtrl-sci] arXiv: 2112.09795 <a href="https://doi.org/10.48550/arXiv.2112.09795">https://doi.org/10.48550/arXiv.2112.09795</a>

opencc-byDec 2020View details →

dryad36/100

Data from: Tropical tree species traits drive soil cation dynamics via effects on pH: a proposed conceptual framework

Open the record for dataset details and reuse information.

publicJul 2017View details →

zenodo32/100

Phonon Properties and Lattice Dynamics of Two- and Tri-Layered Lead Iodide Perovskites Comprising Butylammonium and Methylammonium Cations—Temperature-Dependent Raman Studies

Open the record for dataset details and reuse information.

opencc-by-4.0May 2024View details →

zenodo32/100

Laser-Induced Electronic and Vibronic Dynamics in the Pyrene Molecule and its Cation

We provide the codes and data required to generate each of the figures in our paper "Laser-Induced Electronic and Vibronic Dynamics in the Pyrene Molecule and its Cation". As well, the input files and key output files of the calculations are included.

opencc-by-4.0Sep 2021View details →

zenodo28/100

Supplementary Information for Publication: Cation Dynamics as Structure Explorer in Hybrid Perovskites – the Case of MAPbI3

Collection of CASTEP *.phonon files according to IKUR-PVP-1 dataset, delivered as a part of the publication: Cation Dynamics as Structure Explorer in Hybrid Perovskites – the Case of MAPbI3 by Kacper Druzbicki, Pablo Gila-Herranz, Pelayo Marin-Villa, Mattia Gaboardi, Jeff Armstrong, and Felix Fernandez-Alonso.

opencc-by-4.0Sep 2023View details →

geo24/100

A cataract-causing mutation in the TRPM3 cation channel disrupts calcium dynamics in the lens

GEO Series GSE250518. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.

openGEO-OpenFeb 2024View details →

zenodo20/100

Molecular Dynamics simulation data for the article "Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism"

Zipped archives with MD simulation data for the article "Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism" (eLife, accepted).

opencc-by-nc-nd-4.0Dec 2018View details →

ScienceDex guides

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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.

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Allen Brain Atlas

Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

Annotated Behaviour and Observability Dataset (ABODe)

ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

DANDI Archive for NWB datasets

DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

International Brain Laboratory public data

The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

OpenNeuro

OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record