Understanding the stability of polypeptide membranes in ionic liquids: a theoretical molecular dynamics study

2019 ◽  
Vol 43 (25) ◽  
pp. 10151-10161 ◽  
Author(s):  
Eyber Domingos Alves ◽  
Leonardo Bruno Assis Oliveira ◽  
Guilherme Colherinhas
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Stability Analysis ◽  
Energy Storage ◽  
Ionic Solution ◽  
The Stability ◽  
New Applications

Stability analysis of polypeptide membranes in ionic liquids can make possible new applications of these membranes in energy storage and ionic solution separation.

scholarly journals Peptides in the presence of aqueous ionic liquids: tunable co-solutes as denaturants or protectants?

2015 ◽  
Vol 17 (39) ◽  
pp. 26049-26053 ◽  
Author(s):  
Volker Lesch ◽  
Andreas Heuer ◽  
Vasileios A. Tatsis ◽  
Christian Holm ◽  
Jens Smiatek
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulations ◽  
Acetate Solution ◽  
Native Conformation ◽  
The Stability ◽  
Dynamics Simulations ◽  
Significant Structure

We studied the stability of a small β-hairpin peptide under the influence of an aqueous 1-ethyl-3-methylimidazolium acetate solution via all-atom molecular dynamics simulations. A significant structure dependent binding of ACE to the peptide was identified as the main reason for the denaturation of the native conformation.

scholarly journals Choline-Based Ionic Liquids-Incorporated IRMOF-1 for H2S/CH4 Capture: Insight from Molecular Dynamics Simulation

Processes ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 412
Author(s):  
Mohamad Adil Iman Ishak ◽  
Mohd Faisal Taha ◽  
Mohd Dzul Hakim Wirzal ◽  
Muhammad Najib Nordin ◽  
Muslim Abdurrahman ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ionic Liquids ◽  
Md Simulation ◽  
Metal Organic Framework ◽  
Dynamics Simulation ◽  
Crowding Effect ◽  
Metal Organic ◽  
The Stability ◽  
Stable Incorporation

The removal of H2S and CH4 from natural gas is crucial as H2S causes environmental contamination, corrodes the gas stream pipelines, and decreases the feedstock for industrial productions. Many scientific researches have shown that the metal-organic framework (MOF)/ionic liquids (ILs) have great potential as alternative adsorbents to capture H2S. In this work, molecular dynamics (MD) simulation was carried out to determine the stability of ILs/IRMOF-1 as well as to study the solubility of H2S and CH4 gases in this ILs/IRMOF-1 hybrid material. Three choline-based ILs were incorporated into IRMOF-1 with different ratios of 0.4, 0.8, and 1.2% w/w, respectively, in which the most stable choline-based ILs/IRMOF-1 composite was analysed for H2S/CH4 solubility selectivity. Among the three choline-based ILs/IRMOF-1, [Chl] [SCN]/IRMOF-1 shows the most stable incorporation. However, the increment of ILs loaded in the IRMOF-1 significantly reduced the stability of the hybrid due to the crowding effect. Solvation free energy was then computed to determine the solubility of H2S and CH4 in the [Chl] [SCN]/IRMOF-1. H2S showed higher solubility compared to CH4, where its solubility declined with the increase of choline-based IL loading.

Stability Analysis of the Nanjung Water Diversion Twin Tunnels based on Convergence Measurement

2019 ◽  
Vol 1 (1) ◽  
pp. 49-60
Author(s):  
Simon Heru Prassetyo ◽  
Ganda Marihot Simangunsong ◽  
Ridho Kresna Wattimena ◽  
Made Astawa Rai ◽  
Irwandy Arif ◽  
...  
Keyword(s):  
Stability Analysis ◽  
Convergence Rate ◽  
Critical Strain ◽  
Convergence Rates ◽  
Strain Analysis ◽  
Water Diversion ◽  
Tunnel Face ◽  
Tunnel Stability ◽  
The Stability ◽  
Twin Tunnels

This paper focuses on the stability analysis of the Nanjung Water Diversion Twin Tunnels using convergence measurement. The Nanjung Tunnel is horseshoe-shaped in cross-section, 10.2 m x 9.2 m in dimension, and 230 m in length. The location of the tunnel is in Curug Jompong, Margaasih Subdistrict, Bandung. Convergence monitoring was done for 144 days between February 18 and July 11, 2019. The results of the convergence measurement were recorded and plotted into the curves of convergence vs. day and convergence vs. distance from tunnel face. From these plots, the continuity of the convergence and the convergence rate in the tunnel roof and wall were then analyzed. The convergence rates from each tunnel were also compared to empirical values to determine the level of tunnel stability. In general, the trend of convergence rate shows that the Nanjung Tunnel is stable without any indication of instability. Although there was a spike in the convergence rate at several STA in the measured span, that spike was not replicated by the convergence rate in the other measured spans and it was not continuous. The stability of the Nanjung Tunnel is also confirmed from the critical strain analysis, in which most of the STA measured have strain magnitudes located below the critical strain line and are less than 1%.

Design of potential IKK-β inhibitors using molecular docking and molecular dynamics techniques for their anti-cancer potential

2020 ◽  
Vol 16 ◽  
Author(s):  
Salam Pradeep Singh ◽  
Iftikar Hussain ◽  
Bolin Kumar Konwar ◽  
Ramesh Chandra Deka ◽  
Chingakham Brajakishor Singh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Md Simulation ◽  
Inflammatory Diseases ◽  
Binding Free Energy ◽  
Anti Cancer ◽  
Dietary Phytochemicals ◽  
Toxicity Analysis ◽  
The Stability ◽  
Stable Trajectory

Aim and Objective: To evaluate a set of seventy phytochemicals for their potential ability to bind the inhibitor of nuclear factor kappaB kinase beta (IKK-β) which is a prime target for cancer and inflammatory diseases. Materials and Methods: Seventy phytochemicals were screened against IKK-β enzyme using DFT-based molecular docking technique and the top docking hits were carried forward for molecular dynamics (MD) simulation protocols. The adme-toxicity analysis was also carried out for the top docking hits. Results: Sesamin, matairesinol and resveratrol were found to be the top docking hits with a total score of -413 kJ/mol, -398.11 kJ/mol and 266.73 kJ/mol respectively. Glu100 and Gly102 were found to be the most common interacting residues. The result from MD simulation observed a stable trajectory with a binding free energy of -107.62 kJ/mol for matairesinol, -120.37 kJ/mol for sesamin and -40.56 kJ/mol for resveratrol. The DFT calculation revealed the stability of the compounds. The ADME-Toxicity prediction observed that these compounds fall within the permissible area of Boiled-Egg and it does not violate any rule for pharmacological criteria, drug-likeness etc. Conclusion: The study interprets that dietary phytochemicals are potent inhibitors of IKK-β enzyme with favourable binding affinity and less toxic effects. In fact, there is a gradual rise in the use of plant-derived molecules because of its lesser side effects compared to chemotherapy. The study has also provided an insight by which the phytochemicals inhibited the IKK-β enzyme. The investigation would also provide in understanding the inhibitory mode of certain dietary phytochemicals in treating cancer.

Prediction of Ionic Liquids Properties through Molecular Dynamics Simulations

2014 ◽  
Vol 4 (2) ◽  
pp. 151-172 ◽  
Author(s):  
Marta L.S. Batista ◽  
Joao A.P. Coutinho ◽  
Jose R.B. Gomes
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations
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