scholarly journals Molecular Dynamics Simulation of Octacosane for Phase Diagrams and Properties via United Atom Scheme

2021 ◽  
Author(s):  
Ling Dai ◽  
Pavlo Rutkevych ◽  
Souvik Chakraborty ◽  
Gang Wu ◽  
Jun Ye ◽  
...  
Keyword(s):  
Liquid Phase ◽  
Numerical Study ◽  
Annealing Process ◽  
Dynamics Simulation ◽  
Heat Of Fusion ◽  
Condensed Phases ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Rotator Phase ◽  
Cell Anisotropy

We used united atom scheme to build three types of crystalline structures for octacosane (C28H58) and carried out molecular dynamic simulations to investigate their properties. By gradual heating the three polymorphs, we successfully reproduced the sequence of experimentally reported crystalline phase, intermediate rotator phase and liquid phase. The obtained structural properties of the phases, such as molecule chain morphology, density, chain tilt angle, cell anisotropy. We revealed three mechanisms which well described the kinetic deformation and expansion during the annealing process. Furthermore, our model successfully predicted the melting temperature and the heat of fusion. We also reproduced characteristics of the rotator phases and the liquid phase, indicating the transferability of the united atom scheme among different condensed phases of octacosane. Our methodology represents an effective and efficient means of numerical study for octacosane and may have implication for other members of the n-alkane family.

scholarly journals Comparative study of melting points of 3,4-bis(3-nitrofurazan-4-yl)furoxan (DNTF)/1,3,3-trinitroazetidine (TNAZ) eutectic compositions using molecular dynamic simulations

RSC Advances ◽  
2016 ◽  
Vol 6 (64) ◽  
pp. 59141-59149 ◽  
Author(s):  
Ning Liu ◽  
Svatopluk Zeman ◽  
Yuan-jie Shu ◽  
Zong-kai Wu ◽  
Bo-zhou Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Comparative Study ◽  
Molecular Dynamic ◽  
Dynamics Simulation ◽  
Molecular Dynamic Simulations ◽  
Melting Points ◽  
Dynamic Simulations

The melting points of 3,4-bis(3-nitrofurazan-4-yl)furoxan/1,3,3-trinitroazetidine eutectic compositions are precisely predicted by molecular dynamics simulation with different methods.

scholarly journals Insight into the Self-Assembling Properties of Peptergents: A Molecular Dynamics Simulation Study

2018 ◽  
Vol 19 (9) ◽  
pp. 2772 ◽  
Author(s):  
Jean Crowet ◽  
Mehmet Nasir ◽  
Nicolas Dony ◽  
Antoine Deschamps ◽  
Vincent Stroobant ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Molecular Dynamic ◽  
Beta Sheets ◽  
Dynamics Simulation ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Amphipathic Peptide ◽  
Self Assembling ◽  
Ordered Nanostructures

By manipulating the various physicochemical properties of amino acids, the design of peptides with specific self-assembling properties has been emerging for more than a decade. In this context, short peptides possessing detergent properties (so-called “peptergents”) have been developed to self-assemble into well-ordered nanostructures that can stabilize membrane proteins for crystallization. In this study, the peptide with “peptergency” properties, called ADA8 and extensively described by Tao et al., is studied by molecular dynamic simulations for its self-assembling properties in different conditions. In water, it spontaneously forms beta sheets with a β barrel-like structure. We next simulated the interaction of this peptide with a membrane protein, the bacteriorhodopsin, in the presence or absence of a micelle of dodecylphosphocholine. According to the literature, the peptergent ADA8 is thought to generate a belt of β structures around the hydrophobic helical domain that could help stabilize purified membrane proteins. Molecular dynamic simulations are here used to image this mechanism and provide further molecular details for the replacement of detergent molecules around the protein. In addition, we generalized this behavior by designing an amphipathic peptide with beta propensity, which was called ABZ12. Both peptides are able to surround the membrane protein and displace surfactant molecules. To our best knowledge, this is the first molecular mechanism proposed for “peptergency”.

Molecular-Dynamic Simulations on Aqueous Solutions Confined Between Uniformly Charged Hydrophobic Plates

2009 ◽  
Author(s):  
Hoang Hai ◽  
Sangmo Kang ◽  
Yong Kweon Suh
Keyword(s):  
Aqueous Solutions ◽  
Molecular Dynamic ◽  
Numerical Study ◽  
Dynamic Properties ◽  
Water Molecules ◽  
Molecular Dynamic Simulations ◽  
Ewald Summation ◽  
Dynamic Simulations ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

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.

scholarly journals Molecular Dynamics Simulations and Empirical Observations on Soy Lecithin Liposome Preparation

2018 ◽  
Vol 16 (2) ◽  
pp. 222 ◽  
Author(s):  
Rini Dwiastuti ◽  
Muhammad Radifar ◽  
Marchaban Marchaban ◽  
Sri Noegrohati ◽  
Enade Perdana Istyastono
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Molecular Dynamic Simulations ◽  
Soy Lecithin ◽  
Dynamic Simulations ◽  
Liposome Size ◽  
Dynamics Simulations

Soy lecithin is a phospholipid often used in liposome formulations. Determination of water and phospholipid composition is one of the problems in the liposome formulation. This study is using molecular dynamics simulation and empirical observation in producing liposome preparations. Phospholipids 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine (DLPE) were objected in molecular dynamics simulations using Coarse Grained Molecular Dynamics (CGMD) approaches. The result showed that the molecular dynamic simulations could be employed to predict the liposome size. The molecular dynamic simulations resulted in liposome size of 71.22 ± 2.54 nm, which was located within the range of the liposome size resulted from the empirical observations (95.99 ± 43.02 nm). Moreover, similar liposome forms were observed on both results of molecular dynamics simulations and empirical approaches.

scholarly journals Ranking the Efficiency of Gas Hydrate Anti-agglomerants through Molecular Dynamic Simulations

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