scholarly journals Effect of conductivity, viscosity, and density of water-in-salt electrolytes on the electrochemical behavior of supercapacitors: molecular dynamics simulations and in-situ characterization studies.

2021 ◽  
Author(s):  
Débora Ariana Corrêa da Silva ◽  
Manuel Jonathan Pinzón ◽  
Andresa Messias ◽  
Eudes E. Fileti ◽  
Aline Pascon ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Electrochemical Behavior ◽  
Experimental Studies ◽  
In Situ Characterization ◽  
Advantages And Disadvantages ◽  
Characterization Studies ◽  
Dynamics Simulations ◽  
Density Of Water

It is reported the combination of molecular dynamics simulations and different experimental studies to understand the advantages and disadvantages of departing from conventional (salt-in-water,SiWE) aqueous-based electrolytes to very concentrated (water-in-salt,...

scholarly journals Molecular dynamics simulations and experimental studies reveal differential permeability of withaferin-A and withanone across the model cell membrane

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Renu Wadhwa ◽  
Neetu Singh Yadav ◽  
Shashank P. Katiyar ◽  
Tomoko Yaguchi ◽  
Chohee Lee ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cell Membrane ◽  
Molecular Dynamics Simulations ◽  
Experimental Studies ◽  
Bilayer Membrane ◽  
Withaferin A ◽  
Head Group ◽  
Polar Head Group ◽  
Natural Drugs ◽  
Dynamics Simulations

AbstractPoor bioavailability due to the inability to cross the cell membrane is one of the major reasons for the failure of a drug in clinical trials. We have used molecular dynamics simulations to predict the membrane permeability of natural drugs—withanolides (withaferin-A and withanone) that have similar structures but remarkably differ in their cytotoxicity. We found that whereas withaferin-A, could proficiently transverse through the model membrane, withanone showed weak permeability. The free energy profiles for the interaction of withanolides with the model bilayer membrane revealed that whereas the polar head group of the membrane caused high resistance for the passage of withanone, the interior of the membrane behaves similarly for both withanolides. The solvation analysis further revealed that the high solvation of terminal O5 oxygen of withaferin-A was the major driving force for its high permeability; it interacted with the phosphate group of the membrane that led to its smooth passage across the bilayer. The computational predictions were tested by raising and recruiting unique antibodies that react to withaferin-A and withanone. The time-lapsed analyses of control and treated cells demonstrated higher permeation of withaferin-A as compared to withanone. The concurrence between the computation and experimental results thus re-emphasised the use of computational methods for predicting permeability and hence bioavailability of natural drug compounds in the drug development process.

scholarly journals Nanoformulation-by-design: an experimental and molecular dynamics study for polymer coated drug nanoparticles

RSC Advances ◽  
2020 ◽  
Vol 10 (33) ◽  
pp. 19521-19533 ◽  
Author(s):  
Ioanna Danai Styliari ◽  
Vincenzo Taresco ◽  
Andrew Theophilus ◽  
Cameron Alexander ◽  
Martin Garnett ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Experimental Studies ◽  
High Drug ◽  
Nanoparticle Formation ◽  
Polymer Nanoparticle ◽  
Drug Nanoparticles ◽  
Dynamics Simulations

Experimental studies of drug–polymer nanoparticle formation combined with molecular dynamics simulations provide atomistic explanations for the high drug loadings obtained.

scholarly journals Optimizing the performance of reactive molecular dynamics simulations for many-core architectures

2018 ◽  
Vol 33 (2) ◽  
pp. 304-321 ◽  
Author(s):  
Hasan Metin Aktulga ◽  
Chris Knight ◽  
Paul Coffman ◽  
Kurt A O’Hearn ◽  
Tzu-Ray Shan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Species ◽  
Trajectory Data ◽  
Reactive Molecular Dynamics ◽  
Species Analysis ◽  
Dynamics Simulations ◽  
Many Core ◽  
Molecular Species Analysis

Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this article, we focus on optimizing the performance of the widely used LAMMPS/ReaxC package for many-core architectures. As hybrid parallelism allows better leverage of the increasing on-node parallelism, we adopt thread parallelism in the construction of bonded and nonbonded lists and in the computation of complex ReaxFF interactions. To mitigate the I/O overheads due to large volumes of trajectory data produced and to save users the burden of post-processing, we also develop a novel in situ tool for molecular species analysis. We analyze the performance of the resulting ReaxC-OMP package on two different architectures: (i) Mira, an IBM Blue Gene/Q system and (ii) Cori-II, a Cray XC-40 sytem with Knights Landing processors. For Pentaerythritol tetranitrate (PETN) systems of sizes ranging from 32 thousand to 16.6 million particles, we observe speedups in the range of 1.5–4.5×. We observe sustained performance improvements for up to 262,144 cores (1,048,576 processes) of Mira and a weak scaling efficiency of 91.5% in large simulations containing 16.6 million particles. The in situ molecular species analysis tool incurs only insignificant overheads across various system sizes and runs configurations.

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