Lubricant shear thinning behavior correlated with variation of radius of gyration via molecular dynamics simulations

2017 ◽  
Vol 147 (8) ◽  
pp. 084904 ◽  
Author(s):  
Pinzhi Liu ◽  
Jie Lu ◽  
Hualong Yu ◽  
Ning Ren ◽  
Frances E. Lockwood ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Shear Thinning ◽  
Radius Of Gyration ◽  
Dynamics Simulations

scholarly journals Molecular Dynamics Simulations on the Demolding Process for Nanostructures in Injection Molding

Micromachines ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 636 ◽  
Author(s):  
Can Weng ◽  
Dongjiao Yang ◽  
Mingyong Zhou
Keyword(s):  
Molecular Dynamics ◽  
Injection Molding ◽  
Molecular Dynamics Simulations ◽  
Interaction Mechanism ◽  
Mold Insert ◽  
Sharp Decrease ◽  
Average Density ◽  
Radius Of Gyration ◽  
Good Shape ◽  
Dynamics Simulations

Injection molding is one of the most potential techniques for fabricating polymeric products in large numbers. The filling process, but also the demolding process, influence the quality of injection-molded nanostructures. In this study, nano-cavities with different depth-to-width ratios (D/W) were built and molecular dynamics simulations on the demolding process were conducted. Conformation change and density distribution were analyzed. Interfacial adhesion was utilized to investigate the interaction mechanism between polypropylene (PP) and nickel mold insert. The results show that the separation would first happen at the shoulder of the nanostructures. Nanostructures and the whole PP layer are both stretched, resulting in a sharp decrease in average density after demolding. The largest increase in the radius of gyration and lowest velocity can be observed in 3:1 nanostructure during the separation. Deformation on nanostructure occurs, but nevertheless the whole structure is still in good shape. The adhesion energy gets higher with the increase of D/W. The demolding force increases quickly to the peak point and then gradually decreases to zero. The majority of the force comes from the adhesion and friction on the nanostructure due to the interfacial interaction.

scholarly journals Cavity Closure of 2-Hydroxypropyl-β-cyclodextrin: Replica Exchange Molecular Dynamics Simulations

2019 ◽  
Author(s):  
Khanittha Kerdpol ◽  
Jintawee Kicuntod ◽  
Peter Wolschann ◽  
Seiji Mori ◽  
Chompoonut Rungnim ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Inclusion Complexation ◽  
Water Soluble ◽  
Replica Exchange ◽  
Radius Of Gyration ◽  
Replica Exchange Molecular Dynamics ◽  
Beta Cyclodextrin ◽  
Dynamics Simulations

2-Hydroxypropyl-β-cyclodextrin (HPβCD) has unique properties to enhance the stability and the solubility of low water-soluble compounds by inclusion complexation. Understanding of the structural properties of HPβCD and its derivatives based on the number of 2-hydroxypropyl (HP) substituents at the a-D-glucopyranose subunits is rather important. In this work, replica exchange molecular dynamics simulations were performed to investigate the conformational changes of single- and double-sided HP-substitution called as 6-HPβCDs and 2,6-HPβCDs, respectively. The results show that glucose subunits in both 6-HPβCDs and 2,6-HPβCDs have lower chance to flip than in βCD. Also, HP groups are occasionally blocking the hydrophobic cavity of HPβCDs, thus hindering the drug inclusion. We found that HPβCDs with high number of HP-substitutions are more likely to be blocked, while HPβCDs with double-sided HP-substitution are even more probable to be blocked. Overall, 6-HPβCDs with three and four HP-substitutions are highlighted as the most suitable structures for guest encapsulation based on our conformational analyses such as structural distortion, radius of gyration, circularity and cavity self-closure of the HPβCDs.

scholarly journals Effect of pH on the Supramolecular Structure of Helicobacter pylori Urease by Molecular Dynamics Simulations

Polymers ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 2713
Author(s):  
Haruna L. Barazorda-Ccahuana ◽  
Badhin Gómez ◽  
Francesc Mas ◽  
Sergio Madurga
Keyword(s):  
Molecular Dynamics ◽  
Helicobacter Pylori ◽  
Molecular Dynamics Simulations ◽  
Supramolecular Structure ◽  
Active Sites ◽  
Solvent Accessible Surface Area ◽  
Radius Of Gyration ◽  
Salt Bridges ◽  
Effect Of Ph ◽  
Dynamics Simulations

The effect of pH on the supramolecular structure of Helicobacter pylori urease was studied by means of molecular dynamics simulations at seven different pHs. Appropriate urease charge distributions were calculated using a semi-grand canonical Monte Carlo (SGCMC) procedure that assigns each residue’s charge state depending on the assigned individual pKa obtained by PROPKA. The effect of pH on protein stability has been analyzed through root-mean-square deviation (RMSD), radius of gyration (RG), solvent-accessible surface area (SASA), hydrogen bonds (HB) and salt bridges (SB). Urease catalyses the hydrolysis of urea in 12 active sites that are covered by mobile regions that act like flaps. The mobility of these flaps is increased at acidic pHs. However, extreme acidic conditions cause urease to have the least number of stabilizing interactions. This initiates the process of denaturalization, wherein the four (αβ)3 subunits of the global structure ((αβ)3)4 of urease start to separate.

scholarly journals Critical Thickness of Free-Standing Nanothin Films Made of Melted Polyethylene Chains via Molecular Dynamics

Polymers ◽  
2021 ◽  
Vol 13 (20) ◽  
pp. 3515
Author(s):  
José Antonio González-Mijangos ◽  
Enrique Lima ◽  
Roberto Guerra-González ◽  
Fernando Iguazú Ramírez-Zavaleta ◽  
José Luis Rivera
Keyword(s):  
Molecular Dynamics ◽  
Film Thickness ◽  
Molecular Dynamics Simulations ◽  
Critical Thickness ◽  
Mechanical Stability ◽  
Radius Of Gyration ◽  
Free Standing ◽  
Thermal Limit ◽  
Density Profiles ◽  
Dynamics Simulations

The mechanical stability of nanothin free-standing films made of melted polyethylene chains was predicted via molecular dynamics simulations in the range of 373.15–673.15 K. The predicted critical thickness, tc, increased with the square of the temperature, T, with additional chains needed as T increased. From T = 373.15 K up to the thermal limit of stability for polyethylene, tc values were in the range of nanothin thicknesses (3.42–5.63 nm), which approximately corresponds to 44–55 chains per 100 nm2. The density at the center of the layer and the interfacial properties studied (density profiles, interfacial thickness, and radius of gyration) showed independence from the film thickness at the same T. The polyethylene layer at its tc showed a lower melting T (<373.15 K) than bulk polyethylene.

scholarly journals Cavity Closure of 2-Hydroxypropyl-β-Cyclodextrin: Replica Exchange Molecular Dynamics Simulations

Polymers ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 145 ◽  
Author(s):  
Khanittha Kerdpol ◽  
Jintawee Kicuntod ◽  
Peter Wolschann ◽  
Seiji Mori ◽  
Chompoonut Rungnim ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Inclusion Complexation ◽  
Water Soluble ◽  
Replica Exchange ◽  
Radius Of Gyration ◽  
Replica Exchange Molecular Dynamics ◽  
Cavity Closure ◽  
Dynamics Simulations

2-Hydroxypropyl-β-cyclodextrin (HPβCD) has unique properties to enhance the stability and the solubility of low water-soluble compounds by inclusion complexation. An understanding of the structural properties of HPβCD and its derivatives, based on the number of 2-hydroxypropyl (HP) substituents at the α-d-glucopyranose subunits is rather important. In this work, replica exchange molecular dynamics simulations were performed to investigate the conformational changes of single- and double-sided HP-substitution, called 6-HPβCDs and 2,6-HPβCDs, respectively. The results show that the glucose subunits in both 6-HPβCDs and 2,6-HPβCDs have a lower chance of flipping than in βCD. Also, HP groups occasionally block the hydrophobic cavity of HPβCDs, thus hindering drug inclusion. We found that HPβCDs with a high number of HP-substitutions are more likely to be blocked, while HPβCDs with double-sided HP-substitutions have an even higher probability of being blocked. Overall, 6-HPβCDs with three and four HP-substitutions are highlighted as the most suitable structures for guest encapsulation, based on our conformational analyses, such as structural distortion, the radius of gyration, circularity, and cavity self-closure of the HPβCDs.

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