Numerical study on interactions of atmospheric plasmas and vegetable oils by reactive molecular dynamic simulations

Author(s):  
Shu‐Qi Tian ◽  
Xiao‐Long Wang ◽  
Yuan‐Tao Zhang
Author(s):  
Hoang Hai ◽  
Sangmo Kang ◽  
Yong Kweon Suh

In this paper, we present the numerical study on the properties of aqueous solution confined between uniformly charged hydrophobic plates using the molecular-dynamic simulations. Two kinds of aqueous solutions used in our study are aqueous sodium and aqueous chloride. The SPC/E model and combination of quaternion coordinates with Euler angles are used to model the water molecules and constraint the structure of water molecules, respectively. The hydrophobic plates are separated by 2.6 nm and the space contains 680 water molecules and 20 ions. The charge density on each surface of the plate is the same with each other and satisfies the charge-neutralization criterion over the whole domain. We employed the modified Ewald summation for the uniformly charged surface PPPM method (particle-particle-particle-mesh) to compute the long-range interactions. The static and dynamic properties of solvent and ions are computed. We also compare our results with those provided by solving the Poisson-Boltzmann equation.


2021 ◽  
Vol 125 (5) ◽  
pp. 1487-1502
Author(s):  
Stephan Mohr ◽  
Felix Hoevelmann ◽  
Jonathan Wylde ◽  
Natascha Schelero ◽  
Juan Sarria ◽  
...  

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pranay Asai ◽  
Palash Panja ◽  
Raul Velasco ◽  
Milind Deo

AbstractThe pressure-driven flow of long-chain hydrocarbons in nanosized pores is important in energy, environmental, biological, and pharmaceutical applications. This paper examines the flow of hexane, heptane, and decane in carbon nanotubes (CNTs) of pore diameters 1–8 nm using molecular dynamic simulations. Enhancement of water flow in CNTs in comparison to rates predicted by continuum models has been well established in the literature. Our work was intended to observe if molecular dynamic simulations of hydrocarbon flow in CNTs produced similar enhancements. We used the OPLS-AA force field to simulate the hydrocarbons and the CNTs. Our simulations predicted the bulk densities of the hydrocarbons to be within 3% of the literature values. Molecular sizes and shapes of the hydrocarbon molecules compared to the pore size create interesting density patterns for smaller sized CNTs. We observed moderate flow enhancements for all the hydrocarbons (1–100) flowing through small-sized CNTs. For very small CNTs the larger hydrocarbons were forced to flow in a cork-screw fashion. As a result of this flow orientation, the larger molecules flowed as effectively (similar enhancements) as the smaller hydrocarbons.


Author(s):  
Chiara Luise ◽  
Dina Robaa ◽  
Wolfgang Sippl

AbstractSome of the main challenges faced in drug discovery are pocket flexibility and binding mode prediction. In this work, we explored the aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction by means of in silico approaches. We first investigated the Spindlin1 aromatic cage plasticity by analyzing the available crystal structures and through molecular dynamic simulations. Then we assessed the ability of rigid docking and flexible docking to rightly reproduce the binding mode of a known ligand into Spindlin1, as an example of a reader protein displaying flexibility in the binding pocket. The ability of induced fit docking was further probed to test if the right ligand binding mode could be obtained through flexible docking regardless of the initial protein conformation. Finally, the stability of generated docking poses was verified by molecular dynamic simulations. Accurate binding mode prediction was obtained showing that the herein reported approach is a highly promising combination of in silico methods able to rightly predict the binding mode of small molecule ligands in flexible binding pockets, such as those observed in some reader proteins.


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