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1,491 results for “Ione”
POPC @ 310K, 450 mM of CaCl_2. Slipids with ECC-scaled ions
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. <br> The goal was to study the effect of salt on the order <br> parameters of the lipid head group and the glycerol <br> backbone for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The Slipids <br> model [1–3] is employed for lipids, tip3p model for water, <br> and the recent ion parameters by Kohagen et al. [4] for <br> CaCl_2.</p> <p>The Slipids force field parameters were downloaded from<br> http://mmkluster.fos.su.se/slipids/</p> <p>The ion parameters are available at<br> https://bitbucket.org/hseara/ions/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. These data<br> were collected once the adsorption and desorption of <br> CaCl_2 to the surface has reached equilibrium, namely<br> after 500 ns of simulation. Additionally, the initial <br> structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 4.6–> (.tpr) and the energy output file <br> (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined <br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic <br> Force Field for Biological Membranes<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p</p> <p>[4] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions<br> Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth<br> The Journal of Physical Chemistry B 2014 118 (28), 7902-7909<br> DOI: 10.1021/jp5005693</p>
POPC @ 310K, 130 mM of NaCl. Slipids with ions by Smith & Dang
<p>Simulations of a POPC bilayer with 130 mM of NaCl. <br> The goal was to study the effect of salt on the order <br> parameters of the lipid head group and the glycerol <br> backbone. The obtained results are reported in the <br> NMRlipids blog at http://nmrlipids.blogspot.fi</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 130 mM NaCl. The Slipids <br> model [1–3] is employed for lipids, tip3p model for water, <br> and the ion parameters by Smith and Dang [4] for NaCl. </p> <p>The Slipids force field parameters were downloaded from<br> http://mmkluster.fos.su.se/slipids/</p> <p>The ion parameters are available at<br> https://bitbucket.org/hseara/ions/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. Additionally,<br> the initial structure (.gro), topology (.top), index<br> file (.ndx), simulation paremeter file (.mdp), binary <br> run input file for GROMACS v. 4.6–> (.tpr) and the <br> energy output file (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined <br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic <br> Force Field for Biological Membranes<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p</p> <p>[4] Computer simulations of NaCl association in polarizable water<br> David E. Smith and Liem X. Dang <br> The Journal of Chemical Physics 1994 100, 3757-3766<br> DOI: 10.1063/1.466363</p>
POPC @ 310K, 450 mM of CaCl_2. Charmm36 with default Charmm ions
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. <br> The goal was to study the effect of salt on the order <br> parameters of the lipid head group and the glycerol <br> backbone for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The Charmm36 <br> model [1] is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the default Charmm<br> ion parameters (type CAL) for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained from http://mackerell.umaryland.edu/charmm_ff.shtml</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. These data<br> were collected after 1900 ns of simulation Additionally,</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.0–> (.tpr) and the energy output file <br> (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field <br> for Lipids: Validation on Six Lipid Types<br> Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, <br> Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, <br> Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor<br> The Journal of Physical Chemistry B 2010 114 (23), 7830-7843<br> DOI: 10.1021/jp101759q</p>
POPC @ 310K, 450 mM of CaCl_2. Slipids with default Amber ions
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. <br> The goal was to study the effect of salt on the order <br> parameters of the lipid head group and the glycerol <br> backbone for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The Slipids <br> model [1–3] is employed for lipids, tip3p model for water, <br> and the default amber ion parameters (type C0) for CaCl_2.</p> <p>The Slipids force field parameters were downloaded from<br> http://mmkluster.fos.su.se/slipids/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. These data<br> were collected after 1900 ns of simulation. Additionally,</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 4.6–> (.tpr) and the energy output file <br> (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined <br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic <br> Force Field for Biological Membranes<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p</p>
Diffraction images for yeast 5-aminolevulinic acid dehydratase complexed with mercury and lead ions.
<p>The diffraction images corresponding to the data used to refine the Hg- and Pb- complexes of yeast ALAD as described in this paper: ‘MAD analyses of yeast 5-aminolaevulinate dehydratase. Their use in structure determination and in defining the metal binding sites.’ P.T. Erskine, E.M.H. Duke, I.J. Tickle, N. Senior, M.J.Warren and J.B. Cooper. Acta Crystallogr. D. (2000), D56, 421-430. </p>
POPC with varying amounts of cholesterol, 450 mM of CaCl_2. Charmm36 with default Charmm ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 450 mM of CaCl_2 performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Charmm36 model [1,2] is employed for lipids, the Charmm compatible variant of the tip3p model for water, and the default Charmm ion parameters (type CAL) for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained from http://mackerell.umaryland.edu/charmm_ff.shtml .<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 2 µs long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 5.0->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor, The Journal of Physical Chemistry B 2010 114 (23), 7830–7843, DOI: 10.1021/jp101759q</p> <p>[2] Update of the Cholesterol Force Field Parameters in CHARMM. Joseph B. Lim, Brent Rogaski, and Jeffery B. Klauda, The Journal of Physical Chemistry B 2012 116 (1), 203–210, DOI: 10.1021/jp207925m</p>
POPC with varying amounts of cholesterol, 450 mM of CaCl_2. Charmm36 with ECC-scaled ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 450 mM of CaCl_2 performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Charmm36 model [1,2] is employed for lipids, the Charmm compatible variant of the tip3p model for water, and the recent ion parameters by Kohagen et al. [3] for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained Charmm-GUI [4], and the ion parameters are available at https://bitbucket.org/hseara/ions/ . IMPORTANT: The simulations are performed with version 1.7 obtained from Charmm-GUI, and this version is known to have an issue with the multiplicity of dihedrals in Gromacs output files, see http://www.charmm-gui.org/?doc=log . <br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 800 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 5.0->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor, The Journal of Physical Chemistry B 2010 114 (23), 7830–7843, DOI: 10.1021/jp101759q</p> <p>[2] Update of the Cholesterol Force Field Parameters in CHARMM. Joseph B. Lim, Brent Rogaski, and Jeffery B. Klauda, The Journal of Physical Chemistry B 2012 116 (1), 203–210, DOI: 10.1021/jp207925m</p> <p>[3] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions. Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth, The Journal of Physical Chemistry B 2014 118 (28), 7902-7909, DOI: 10.1021/jp5005693</p> <p>[4] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, <br> Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im, Journal of Chemical Theory and Computation 2016 12 (1), 405-413, DOI: 10.1021/acs.jctc.5b00935</p>
POPC with varying amounts of cholesterol, 130 mM of NaCl. Charmm36 with default Charmm ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 130 mM of NaCl performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Charmm36 model [1,2] is employed for lipids, the Charmm compatible variant of the tip3p model for water, and the standard Charmm ion parameters for NaCl [3].</p> <p>The Charmm36 force field parameters were obtained Charmm-GUI [4]. IMPORTANT: The simulations are performed with version 1.7 obtained from Charmm-GUI, and this version is known to have an issue with the multiplicity of dihedrals in Gromacs output files, see http://www.charmm-gui.org/?doc=log . <br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 200 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 5.0->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor, The Journal of Physical Chemistry B 2010 114 (23), 7830–7843, DOI: 10.1021/jp101759q</p> <p>[2] Update of the Cholesterol Force Field Parameters in CHARMM. Joseph B. Lim, Brent Rogaski, and Jeffery B. Klauda, The Journal of Physical Chemistry B 2012 116 (1), 203–210, DOI: 10.1021/jp207925m</p> <p>[3] Control of Ion Selectivity in LeuT: Two Na+ Binding Sites with Two Different Mechanisms. Sergei Y. Noskov and Benoit Roux, Journal of Molecular Biology 2008 377 (3), 804–818, DOI:10.1016/j.jmb.2008.01.015</p> <p>[4] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, <br> Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im, Journal of Chemical Theory and Computation 2016 12 (1), 405-413, DOI: 10.1021/acs.jctc.5b00935</p>
POPC with varying amounts of cholesterol, 450 mM of CaCl_2. Slipids with ECC-scaled ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 450 mM of CaCl_2 performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. Additionally, simulations with 0% cholesterol are repeated at 330 K, 350 K, and 370 K. The Slipids model [1–3] is employed for lipids, tip3p model for water, and the recent ion parameters by Kohagen et al. [4] for CaCl_2. The Slipids force field parameters are available at http://www.fos.su.se/~sasha/SLipids/ and the ion parameters are available at https://bitbucket.org/hseara/ions/<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 600 ns long (800 ns long for systems at elevated temperatures) with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 4.6->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, The Journal of Physical Chemistry B 2012 116 (10), 3164-3179, DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948, DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2013 9 (1), 774-784, DOI: 10.1021/ct300777p</p> <p>[4] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions. Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth, The Journal of Physical Chemistry B 2014 118 (28), 7902-7909, DOI: 10.1021/jp5005693</p>
POPC with varying amounts of cholesterol, 450 mM of CaCl_2. Slipids with default Amber ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 450 mM of CaCl_2 performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Slipids model [1–3] is employed for lipids, tip3p model for water, and the default amber ion parameters (type C0) for CaCl_2. The Slipids force field parameters are available at http://www.fos.su.se/~sasha/SLipids/ .<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 2 µs long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 4.6->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, The Journal of Physical Chemistry B 2012 116 (10), 3164-3179, DOI: 10.1021/jp212503e<br> [2] An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948, DOI: 10.1021/ct300342n<br> [3] Another Piece of the Membrane Puzzle: Extending Slipids Further. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2013 9 (1), 774-784, DOI: 10.1021/ct300777p</p> <p> </p>
POPC with varying amounts of cholesterol, 1 M of NaCl. Slipids with ions by Smith & Dang
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 1 M of NaCl. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Slipids model [1–3] is employed for lipids, tip3p model for water, and the ion parameters by Smith and Dang [4] for NaCl. The Slipids force field parameters are available at http://www.fos.su.se/~sasha/SLipids/ and the ion parameters are available at https://bitbucket.org/hseara/ions/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 200 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 4.6->) (.tpr) are provided for each system. The common simulation parameter file (md.mdp) is also provided.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, The Journal of Physical Chemistry B 2012 116 (10), 3164-3179, DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948, DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2013 9 (1), 774-784, DOI: 10.1021/ct300777p</p> <p>[4] Computer simulations of NaCl association in polarizable water. David E. Smith and Liem X. Dang, The Journal of Chemical Physics 1994 100, 3757-3766, DOI: 10.1063/1.466363</p>
POPC with varying amounts of cholesterol, 130 mM of NaCl. Slipids with ECC-scaled ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 130 mM of NaCl performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Slipids model [1–3] is employed for lipids, tip3p model for water, and the and the recent ion parameters by Kohagen et al. [4] for NaCl. The Slipids force field parameters are available at http://www.fos.su.se/~sasha/SLipids/ and the ion parameters are available at https://bitbucket.org/hseara/ions/<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 200 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 4.6->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, The Journal of Physical Chemistry B 2012 116 (10), 3164-3179, DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948, DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2013 9 (1), 774-784, DOI: 10.1021/ct300777p</p> <p>[4] Accounting for Electronic Polarization Effects in Aqueous Sodium Chloride via Molecular Dynamics Aided by Neutron Scattering. Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth, The Journal of Physical Chemistry B 2016 120 (8), 1454–1460, DOI: 10.1021/acs.jpcb.5b05221</p> <p> </p>
POPC with varying amounts of cholesterol, 130 mM of NaCl. Slipids with ions by Smith & Dang
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 130 mM of NaCl performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. Additionally, simulations with 0% cholesterol are repeated at 330 K, 350 K, and 370 K. The Slipids model [1–3] is employed for lipids, tip3p model for water, and the ion parameters by Smith and Dang [4] for NaCl. The Slipids force field parameters are available at http://www.fos.su.se/~sasha/SLipids/ and the ion parameters are available at https://bitbucket.org/hseara/ions/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 200 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 4.6->) (.tpr) are provided for each system. The common simulation parameter file can be downloaded from another entry at https://doi.org/10.5281/zenodo.259341.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, The Journal of Physical Chemistry B 2012 116 (10), 3164-3179, DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948, DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2013 9 (1), 774-784, DOI: 10.1021/ct300777p</p> <p>[4] Computer simulations of NaCl association in polarizable water. David E. Smith and Liem X. Dang, The Journal of Chemical Physics 1994 100, 3757-3766, DOI: 10.1063/1.466363</p>
Pore-Opening and Ion-Conduction Mechanism in Channelrhodopsins C1C2, ChR2, and iChloC by Computational Electrophysiology and Constant-pH Simulations
<p>The simulation run input files, comprising the starting configuration and all necessary parameters for performing the<br>MD simulations.</p>
Continuous new particle formation in a Mediterranean coastal environment: Insights from atmospheric ions behaviour analysis
<p>data used for: </p> <p><strong><span lang="EN-GB">Continuous new particle formation in a Mediterranean coastal environment: Insights from atmospheric ions behaviour analysis</span></strong></p>
Supplementary material 3 from: Satmari A, Miok K, Ion MC, Zaharia C, Schrimpf A, Pârvulescu L (2023) Headwater refuges: Flow protects Austropotamobius crayfish from Faxonius limosus invasion. NeoBiota 89: 71-94. https://doi.org/10.3897/neobiota.89.110085
Overview of the results from the eDNA analysis for the detection of A. bihariensis/A. torrentium, F. limosus and A. astaci
Supplementary material 2 from: Satmari A, Miok K, Ion MC, Zaharia C, Schrimpf A, Pârvulescu L (2023) Headwater refuges: Flow protects Austropotamobius crayfish from Faxonius limosus invasion. NeoBiota 89: 71-94. https://doi.org/10.3897/neobiota.89.110085
Results of two samples Welch t-tests for comparisons between species with respect to the geospatial variables in occurrence sites
Validating the simulation of beam-ion charge exchange in MAST Upgrade
<p>The data that support the findings of the scientific article: P. Ollus et al. (2023) "Validating the simulation of beam-ion charge exchange in MAST Upgrade", Plasma Phys. Control. Fusion.</p>
Supporting Data for "Coupling trapped ions to a nanomechanical oscillator"
Open the record for dataset details and reuse information.
Dataset for "Observation and Numerical Simulation of Cold Ions Energized by EMIC Waves"
<p>* Reduced datasets for figures in the manuscript.</p>
ScienceDex guides
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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.