Ionic conductivity along transmembrane-electropores in human aquaporin 4: calcium effects from non-equilibrium molecular dynamics

2019 ◽  
Vol 117 (23-24) ◽  
pp. 3783-3790 ◽  
Author(s):  
Mario Bernardi ◽  
Mohammad Reza Ghaani ◽  
Niall J. English
Keyword(s):  
Molecular Dynamics ◽  
Ionic Conductivity ◽  
Aquaporin 4 ◽  
Calcium Effects ◽  
Non Equilibrium Molecular Dynamics ◽  
Non Equilibrium

Controlling ionic conductivity through transprotein electropores in human aquaporin 4: a non-equilibrium molecular-dynamics study

2019 ◽  
Vol 21 (6) ◽  
pp. 3339-3346 ◽  
Author(s):  
Mario Bernardi ◽  
Paolo Marracino ◽  
Micaela Liberti ◽  
José-Antonio Gárate ◽  
Christian J. Burnham ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Conductivity ◽  
Membrane Proteins ◽  
Research Interest ◽  
Aquaporin 4 ◽  
Ongoing Research ◽  
Potential Applications ◽  
In Trans ◽  
Non Equilibrium Molecular Dynamics ◽  
Non Equilibrium

Electroporation is a matter of intensive ongoing research interest, and a much-neglected topic in trans-membrane proteins, particularly in view of such promising potential applications in medicine and biotechnology.

scholarly journals Ionic conductivity in Sm-doped ceria from first-principles non-equilibrium molecular dynamics

2016 ◽  
Vol 296 ◽  
pp. 47-53 ◽  
Author(s):  
Johan Klarbring ◽  
Olga Yu. Vekilova ◽  
Johan O. Nilsson ◽  
Natalia V. Skorodumova ◽  
Sergei I. Simak
Keyword(s):  
Molecular Dynamics ◽  
Ionic Conductivity ◽  
First Principles ◽  
Doped Ceria ◽  
Non Equilibrium Molecular Dynamics ◽  
Non Equilibrium

Human aquaporin 4 gating dynamics under axially oriented electric-field impulses: A non-equilibrium molecular-dynamics study

2018 ◽  
Vol 149 (24) ◽  
pp. 245102 ◽  
Author(s):  
Mario Bernardi ◽  
Paolo Marracino ◽  
Mohammad Reza Ghaani ◽  
Micaela Liberti ◽  
Federico Del Signore ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
Aquaporin 4 ◽  
Non Equilibrium Molecular Dynamics ◽  
Non Equilibrium

A Theoretical Study of the Temperature Gradient Effect on the Soret Coefficient in n-Pentane/n-Decane Mixtures Using Non-Equilibrium Molecular Dynamics

2020 ◽  
Vol 45 (4) ◽  
pp. 319-332
Author(s):  
Xiaoyu Chen ◽  
Ruquan Liang ◽  
Yong Wang ◽  
Ziqi Xia ◽  
Lichun Wu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Temperature Gradient ◽  
Thermal Gradient ◽  
Linear Response ◽  
Theoretical Study ◽  
Soret Coefficient ◽  
Thermal Gradients ◽  
Gradient Effect ◽  
Non Equilibrium Molecular Dynamics ◽  
Non Equilibrium

AbstractThe effect of the temperature gradient on the Soret coefficient in n-pentane/n-decane (n-C5/n-C10) mixtures was investigated using non-equilibrium molecular dynamics (NEMD) with the heat exchange (eHEX) algorithm. n-Pentane/n-decane mixtures with three different compositions (0.25, 0.5, and 0.75 mole fractions, respectively) and the TraPPE-UA force field were used in computing the Soret coefficient ({S_{T}}) at 300 K and 1 atm. Added/removed heat quantities (ΔQ) of 0.002, 0.004, 0.006, 0.008, and 0.01 kcal/mol were employed in eHEX processes in order to study the effect of different thermal gradients on the Soret coefficient. Moreover, a phenomenological description was applied to discuss the mechanism of this effect. Present results show that the Soret coefficient values firstly fluctuate violently and then become increasingly stable with increasing ΔQ (especially in the mixture with a mole fraction of 0.75), which means that ΔQ has a smaller effect on the Soret coefficient when the temperature gradient is higher than a certain thermal gradient. Thus, a high temperature gradient is recommended for calculating the Soret coefficient under the conditions that a linear response and constant phase are ensured in the system. In addition, the simulated Soret coefficient obtained at the highest ΔQ within three different compositions is in great agreement with experimental data.

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