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203 results for “NaCl”
Outdoor mesocosm study evaluating how mass, NaCl tolerance, and pesticide tolerance affect oxidative stress biomarkers (CAT, SOD, GR, GPx, TBARS) in larval wood frogs (Rana sylvatica) exposed to baseline and NaCl-contaminated conditions, 2019
Biomarkers of oxidative stress can aid in wildlife monitoring by allowing conservationists to detect sublethal environmental shifts. However, interpretation of stress responses can be complicated by multiple interacting factors (e.g., individual development, evolved physiological tolerance to stressors) which alter biomarker expression. Here, we investigated how individual ontogenetic traits and population-level tolerance traits influence oxidative stress responses under baseline and contaminated environmental conditions. For our model contaminant, we used NaCl (common freshwater contaminant due to factors such as coastal flooding, irrigation, airborne salt circulation, drought, runoff from road deicing salts). For our model wildlife populations, we used larval wood frogs (Rana sylvatica) from six noninteracting populations known to vary in two population-level tolerance traits: NaCl tolerance (calculated as average time to death from lethal NaCl exposure) and pesticide tolerance (determined by proxy of distance to agriculture - a consistent and highly repeatable relationship). At an outdoor research facility, R. sylvatica tadpoles were exposed to either baseline conditions (0 g/L NaCl added) or NaCl-contaminated conditions (1 g/L NaCl added for 21 days, then reduced to 0.5 g/L NaCl). Exposures were conducted in individual units with 40 replicates per population for each treatment. The experiment was terminated per individual to capture the full term of larval development (Developmental stage: Gosner stage 36), lasting between 33-48 days. For each individual, we measured mass, Snout-Vent-Length, and developmental stage before processing for biomarker expression. Individual homogenates were assayed for oxidative stress biomarkers superoxide dismutase (SOD; responsible for Reactive Oxygen Species capture and peroxide production), glutathione peroxidase (GPx; responsible for high-affinity peroxide reduction), catalase (CAT; responsible for low-affinity peroxide reducti
Amber Lipid17 Simulations of POPC/POPS Membranes with NaCl Counterions
<p><strong>System: </strong>Simulations of POPC/POPS (5:1, 144 lipids in total) membranes with NaCl counterions.</p> <p><strong>Number of POPS:</strong> 24.</p> <p><strong>Number of POPC</strong> 120.</p> <p><strong>Number of waters:</strong> 5760.</p> <p><strong>Number of NaCl ions: </strong>24</p> <p><strong>Lipid model:</strong> 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)].</p> <p><strong>Ion models: </strong> Amber ff99 [J Åqvist <em>J. Phys. Chem.</em> <strong>94</strong> 8021 (1990)].</p> <p><strong>Water model:</strong> TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein <em>J. Chem. Phys.</em> <strong>79</strong> 926 (1983)].</p> <p><strong>Simulation engine:</strong> Amber16 [DA Case et al. <em>AMBER 2017</em> UCSF (2017)].</p> <p><strong>Number of independent repeats per setup: </strong>2.<br> <strong>Trajectory lengths per repeat:</strong> 200 ns.<br> <strong>Previously equilibrated for:</strong> 300 ns.<br> <strong>Sampling rate:</strong> every 10 ps.</p> <p><strong>Time integration step:</strong> 2 fs.</p> <p><strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Langevin' at T = 298 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984); <em>J. Chem. Phys.</em> <strong>103</strong> 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993);<em> J. Chem. Theory Comput.</em> <strong>9</strong> 3878 (2013)].<br> <strong>Van der Waals:</strong> Turned off between 1.0 nm and 1.5 nm.</p> <p><strong>Constraints: </strong>Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [<em>J. Comput. Phys.</em> <strong>23</strong> 327 (1977)], in water using SETTLE [<em>J. Comput. Chem. </em><strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).</p>
Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep4)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong>Year publication: </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.1<br> <br> </p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2184 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> SOL 29366<br> NA 89<br> CL 79</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep2)
<p><strong>Title publication:</strong> <em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.1</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2080 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> SOL 29366<br> NA 89<br> CL 79</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep3)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 5.1.3-dev-20160627-f16daab<br> <br> </p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2068 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> SOL 29366<br> NA 89<br> CL 79</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep1)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication:</strong> 10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.1</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2018 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> SOL 29366<br> NA 89<br> CL 79</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep6)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong> 2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides and 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2018</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 609 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep1)
<p><strong>Title publication:</strong> <em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong>Year publication:</strong> 2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides and 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2134 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep4)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides and 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2018</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 648 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_NaCl_150mM_310K (rep1)
<p><strong>Title publication: </strong><strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></strong></p> <p><strong><strong>Year publication:</strong></strong><strong> 2018</strong></p> <p><strong>DOI publication: </strong><strong>10.1021/acscentsci.7b00582</strong></p> <p><strong>Description:</strong> Simulation POPC membrane containing 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.5</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 3038 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:<br> POPC 512<br> CER160 9<br> SOL 34258<br> NA 92<br> CL 92</p>
Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep3)
<p><strong>Title publication:</strong> <em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides and 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 1980 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep2)
<p><strong>Title publication:</strong> <em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong> 2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides and 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 4583 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep5)
<p><strong>Title publication:</strong> <em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 peptides and 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2018</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 318 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_9_POPC_512_NaCl_150mM_310K (rep2)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication:</strong> 10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing 9 ceramide (CER160) originally in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.5</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 3038 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:<br> POPC 512<br> CER160 9<br> SOL 34258<br> NA 92<br> CL 92</p>
Amber Lipid17 Simulations of POPC/POPS Membranes with NaCl
<p><strong>System: </strong>Simulations of POPC/POPS (5:1, 144 lipids in total) membranes with 500, 1000, 2000, 3000, and 4000 mM of NaCl.</p> <p><strong>Number of POPS:</strong> 24.</p> <p><strong>Number of POPC</strong> 120.</p> <p><strong>Number of waters:</strong> 5760 (not present in the uploaded trajectories) . </p> <p><strong>Number of Na+ ions: </strong>52 (500mm), 104 (1000mm), 208 (2000mm), 311 (3000mm), 415 (4000mm)</p> <p><strong>Lipid model:</strong> 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)].</p> <p><strong>Ion models: </strong> Amber ff99 [J Åqvist <em>J. Phys. Chem.</em> <strong>94</strong> 8021 (1990)].</p> <p><strong>Water model:</strong> TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein <em>J. Chem. Phys.</em> <strong>79</strong> 926 (1983)].</p> <p><strong>Simulation engine:</strong> Amber16 [DA Case et al. <em>AMBER 2017</em> UCSF (2017)].</p> <p><strong>Number of independent repeats per setup: </strong>1.<br> <strong>Trajectory lengths per repeat:</strong> 200 ns.<br> <strong>Previously equilibrated for:</strong> 100 ns.<br> <strong>Sampling rate:</strong> every 10 ps.</p> <p><strong>Time integration step:</strong> 2 fs.</p> <p><strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Langevin' at T = 298 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984); <em>J. Chem. Phys.</em> <strong>103</strong> 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993);<em> J. Chem. Theory Comput.</em> <strong>9</strong> 3878 (2013)].<br> <strong>Van der Waals:</strong> Turned off between 1.0 nm and 1.5 nm.</p> <p><strong>Constraints: </strong>Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [<em>J. Comput. Phys.</em> <strong>23</strong> 327 (1977)], in water using SETTLE [<em>J. Comput. Chem. </em><strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).</p>
Pure POPC Membrane with 1000mM NaCl simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 115 NaCl, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p>
Pure POPC Membrane with 450mM NaCl simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 51 NaCl, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p>
Example NaCl, Vanadium, and background datasets from ISIS SXD
<p>Example datasets of NaCl, Vanadium, and an empty background run generated using <a href="https://www.isis.stfc.ac.uk/Pages/sxd.aspx">SXD at the ISIS Neutron and Muon Source</a>.</p> <p>Each dataset is given in the <a href="https://www.nexusformat.org/TOFRaw.html">TOFRAW format</a> (.nxs), and original ISIS RAW format (.raw) (see <a href="https://www.isis.stfc.ac.uk/Pages/ISIS-Raw-File-Format.aspx">ISIS file formats</a>).</p> <p>Datasets were recorded 12/2020.</p> <p>Files can be read using <a href="http://www.opengenie.org/Main_Page">Open Genie</a> (RAW only), <a href="https://www.mantidproject.org/Main_Page">Mantid</a>, and <a href="https://github.com/dials/isis_utils">DIALS/isis_utils</a>. The main purpose of this dataset is for use in automated testing for <a href="https://github.com/dials/isis_utils">DIALS/isis_utils</a>.</p> <p> </p>
DPPC_Berger_NaCl_scaled
<p>MD simulation trajectory and related files for fully hydrated DPPC bilayer with 150 mM NaCl. Berger-DPPC-98 force field delivered by Peter Tieleman (http://wcm.ucalgary.ca/tieleman/downloads) was used with Gromacs 5.0.4. Ions were described by the gromos force field. Ion charges were scaled by a factor 0.7. Conditions: T=323K, 72 lipids, 2880 SPC waters, 8 Na, 8 Cl. 120 ns trajectory, last 60 ns analyzed.</p>
DPPC_Berger_NaCl
<p>MD simulation trajectory and related files for fully hydrated DPPC bilayer with 150 mM NaCl. Berger-DPPC-98 force field delivered by Peter Tieleman (http://wcm.ucalgary.ca/tieleman/downloads) was used with Gromacs 5.0.4. Ions were described by the gromos force field. Conditions: T=323K, 72 lipids, 2880 SPC waters, 8 Na, 8 Cl. 120 ns trajectory, last 60 ns analyzed.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
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.
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.
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.
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.