scholarly journals Surfactants Enhanced Heavy Oil–Solid Separation from Carbonate Asphalt Rocks-Experiment and Molecular Dynamic Simulation

Nanomaterials ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1835
Author(s):  
Jinjian Hou ◽  
Jinze Du ◽  
Hong Sui ◽  
Lingyu Sun
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Energy Balance ◽  
Aromatic Hydrocarbon ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Saturated Hydrocarbon ◽  
Dynamics Simulation ◽  
Simulation Results

In this study, surfactants were used to enhance heavy oil–solid separation, and a detailed mechanism was explored by SARA (saturates, aromatics, resins, asphaltenes) analysis, element analysis, AFM measurement, and molecular dynamic simulation. Surfactants could effectively decrease oil/solid interaction force and then oil–solid separation would be enhanced. The oil–solid interactive force was in relation to surfactants concentration, pH value, asphaltene content, and salinity. The molecular dynamics simulation results show that the dissociation of saturated hydrocarbon, aromatic hydrocarbon, resin, and asphaltene (SARA) on carbonate minerals is gradually weakened for all surfactants. In the process of molecular dynamics simulation of surfactant stripping SARA, firstly, the surfactant molecules adsorb on the surface of SARA molecules. After that, the surfactant peels SARA molecules off the surface of calcite under the influence of molecular thermal motion. In this process, surfactant molecules will not be directly adsorbed on the surface of trace minerals. The results of energy/temperature balance indicated that saturates, aromatics and resins could remain stable when the molecular dynamics simulation time reached 2000 ps with the phenomenon that saturates, aromatics could liberate from minerals totally within 2000 ps. The molecular dynamics simulation of asphaltenes will not liberate from calcite surface within 6000 ps, meanwhile, they could not reach the energy balance/energy balance within 6000 ps. The functional groups of surfactant molecules would have interactions with the SARA functional group, resulting in different dissociation effects of SARA. The results of molecular dynamics simulation are consistent with the experiment results. The separation effect of saturated hydrocarbon, aromatic hydrocarbon, resin, and asphaltene in five kinds of surfactants were different. The molecular dynamic simulation results were in accordance with the SARA analysis.

Effects of Normal and Aberrant Glycosylation on the Stability of α1-Anti Trypsin Through Molecular Dynamic Simulation

2021 ◽  
Vol 15 (10) ◽  
pp. 3066-3069
Author(s):  
Mujeeb Alam Khan ◽  
Ehtesham . ◽  
Muhammad Shoaib ◽  
Roshan Ali ◽  
Muhammad Idrees
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Dynamics Simulation ◽  
Mean Square ◽  
Glycated Protein ◽  
Alpha 1 Antitrypsin ◽  
The Stability

The Alpha-1 antitrypsin belonging to serpin family is a protease inhibitor, the level of which rises by a factor of ten during inflammation Purpose: To investigate the stability of normal and aberrantly glycosylated α1-antitrypsin through molecular dynamics simulation Study Design: Experimental study Methodology: Current project was conducted in the department of Biochemistry at Institute of Basic Medical Sciences Khyber Medical University, Peshawar. A1AT FASTA sequence was retrieved from UniProt database (UniProt ID: P01009). Post-Translational Modifications (PTM) regions were identified from the same database. GLYCONNECT database was used to understand N-linked glycation with the asparagine residues found at position 70, 107, and 271 amino acid residue regions Statistical analysis: Different bioinformatics analyses such that Root Mean Square Deviation, Radius of gyration, Root Mean Square fluctuation, Hydrogen-bonding, Secondary Structure Determination, and Principal Component Analysis were executed for 100 ns molecular dynamics simulation run Results: RMSd, RMSf, and Rgyr significantly differ between the native type and cancer isoform. More H-bonding and strong protein stability and folding were seen in the native type. PCA analysis further confirms native type compact motion in the parallel direction during MD simulation Conclusion: It was concluded that glycated protein appears to have high structural stability than its aberrant glycated protein. However, it will be utilized for the prompt production of the anti-cancer drugs to effectively treating cancer disease Key Words: Alpha-1 Antitrypsin, Aberrant Glycosylation and Molecular Dynamic Simulation.

scholarly journals Ligand-based design, molecular dynamics and ADMET studies of suggested SARS-CoV-2 Mpro inhibitors

RSC Advances ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 4523-4538
Author(s):  
Nada M. Mohamed ◽  
Eslam M. H. Ali ◽  
Asmaa M. AboulMagd
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Pharmacophore Modeling ◽  
Simulation Results

Compounds I–X were designed to inhibit SARS-CoV-2 Mpro based on pharmacophore modeling of SARS-CoV Mpro inhibitors. Compounds V and VI showed promising molecular docking and molecular dynamic simulation results that surpassed baicalein.

The Study on Young's Modulus of Multilayered Cu/Ni Multilayered Nano Thin Films by Molecular Dynamics Simulation

2014 ◽  
Vol 513-517 ◽  
pp. 113-116
Author(s):  
Jen Ching Huang ◽  
Fu Jen Cheng ◽  
Chun Song Yang
Keyword(s):  
Thin Film ◽  
Thin Films ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Strain Rate ◽  
Young’S Modulus ◽  
Potential Function ◽  
Dynamics Simulation ◽  
System Temperature ◽  
Simulation Results

The Youngs modulus of multilayered nanothin films is an important property. This paper focused to investigate the Youngs Modulus of Multilayered Ni/Cu Multilayered nanoThin Films under different condition by Molecular Dynamics Simulation. The NVT ensemble and COMPASS potential function were employed in the simulation. The multilayered nanothin film contained the Ni and Cu thin films in sequence. From simulation results, it is found that the Youngs modulus of Cu/Ni multilayered nanothin film is different at different lattice orientations, temperatures and strain rate. After experiments, it can be found that the Youngs modulus of multilayered nanothin film in the plane (100) is highest. As thickness of the thin film and system temperature rises, Youngs modulus of multilayered nanothin film is reduced instead. And, the strain rate increases, the Youngs modulus of Cu/Ni multilayered nanothin film will also increase.

Study on Nanolithography Process of Polycrystalline Copper Using Molecular Dynamic Simulation

2007 ◽  
Vol 340-341 ◽  
pp. 961-966
Author(s):  
Chan Il Kim ◽  
Young Suk Kim ◽  
Sang Il Hyun ◽  
Seung Han Yang ◽  
Jun Young Park ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Grain Boundary ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Diamond Like Carbon ◽  
Polycrystalline Copper ◽  
Berkovich Indenter ◽  
Contact Surfaces ◽  
Dynamics Simulations

Molecular dynamics simulations are performed to verify the effect of grain boundary on nanolithography process. The model with about two hundred thousand copper (Cu) atoms is composed of two different crystal orientations of which contact surfaces are (101) and (001) planes. The grain boundary is located on the center of model and has 45 degreeangle in xz-plane. The tool is made of diamond-like-carbon with the shape of Berkovich indenter. As the tool is indented and plowed on the surface, dislocations are generated. Moreover, during the plowing process, the steps as well as the typical pile-ups are formed in front of the tool. These defects propagate into the surface of the substrate. As the tool approaches to the grain boundary, the defects are seen to be accumulated near the grain boundary. The shape of the grain boundary is also significantly deformed after the tool passes it. We observed the forces exerted on the tool by the contact with substrate, so that the friction coefficients can be obtained to address the effect of the grain boundary on the friction characteristics.

Nano-Indentation Simulation Study Based on Parallel Computing

2012 ◽  
Vol 500 ◽  
pp. 696-701
Author(s):  
Ying Zhu ◽  
Sen Song ◽  
Ling Ling Xie ◽  
Shun He Qi ◽  
Qian Qian Liu
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computing ◽  
Molecular Dynamics Simulation ◽  
Large Scale ◽  
Dynamics Simulation ◽  
Parallel Computer ◽  
Nano Indentation ◽  
Simulation Results ◽  
The Impact ◽  
Simulation Time

This method of parallel computing into nanoindentation molecular dynamics simulation (MDS), the author uses a nine-node parallel computer and takes the single crystal aluminum as the experimental example, to implement the large-scale process simulation of nanoindentation. Compared the simulation results with experimental results is to verify the reliability of the simulation. The method improves the computational efficiency and shortens the simulation time and the expansion of scale simulation can significantly reduce the impact of boundary conditions, effectively improve the accuracy of the molecular dynamics simulation of nanoindentation.

scholarly journals Nanotribology at high temperatures

2012 ◽  
Vol 3 ◽  
pp. 586-588 ◽  
Author(s):  
Saurav Goel ◽  
Alexander Stukowski ◽  
Gaurav Goel ◽  
Xichun Luo ◽  
Robert L Reuben
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Melting Point ◽  
High Temperatures ◽  
Conceptual Understanding ◽  
Experimental Verification ◽  
Elevated Temperatures ◽  
Dynamics Simulation ◽  
Major Constraint ◽  
Simulation Results

Recent molecular dynamics simulation results have increased conceptual understanding of the grazing and the ploughing friction at elevated temperatures, particularly near the substrate’s melting point. In this commentary we address a major constraint concerning its experimental verification.

scholarly journals Molecular Dynamics Simulation of Grain Growth in Nanocrystalline Ni

2012 ◽  
Vol 715-716 ◽  
pp. 599-604 ◽  
Author(s):  
Stephen M. Foiles
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Grain Growth ◽  
High Density ◽  
Dynamics Simulation ◽  
Square Root ◽  
Twin Boundaries ◽  
Parabolic Kinetics ◽  
Simulation Results ◽  
The Creation

Grain growth in nanocrystalline Ni has been simulated by molecular dynamics. The simulations show the creation of a high density of twin boundaries during the growth as well as the formation of vacancies consistent with recent experimental observations. The growth follows parabolic kinetics with the diameter increasing with the square root of time consistent with behavior of conventional scale metals but in disagreement with prior simulation results.

scholarly journals Construction of Novel Aspartokinase Mutant A380I and Its Characterization by Molecular Dynamics Simulation

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3379 ◽  
Author(s):  
Caijing Han ◽  
Li Fang ◽  
Chunlei Liu ◽  
Yunna Gao ◽  
Weihong Min
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
High Throughput Screening ◽  
Model Comparison ◽  
Site Directed Mutagenesis ◽  
Dynamics Simulation ◽  
Wild Type ◽  
Open Conformation ◽  
Simulation Results ◽  
Optimal Ph

In this study, a novel monomer aspartokinase (AK) from Corynebacterium pekinense was identified, and its monomer model was constructed. Site 380 was identified by homologous sequencing and monomer model comparison as the key site which was conserved and located around the binding site of the inhibitor Lys. Furthermore, the mutant A380I with enzyme activity 11.32-fold higher than wild type AK (WT-AK), was obtained by site-directed mutagenesis and high throughput screening. In the mutant A380I, the optimal temperature was raised from 26 °C (WT-AK) to 28 °C, the optimal pH remained unchanged at 8.0, and the half-life was prolonged from 4.5 h (WT-AK) to 6.0 h, indicating enhanced thermal stability. The inhibition of A380I was weakened at various inhibitor concentrations and even activated at certain inhibitor concentrations (10 mM of Lys, 5 mM or 10 mM of Lys + Thr, 10 mM of Lys + Met, 5 mM of Lys + Thr + Met). Molecular dynamics simulation results indicated that the occupancy rate of hydrogen bond between A380I and ATP was enhanced, the effect of Lys (inhibitor) on the protein was weakened, and the angle between Ser281-Tyre358 and Asp359-Gly427 was increased after mutation, leading to an open conformation (R-state) that favored the binding of substrate.

Identification of New Hsp90 Inhibitors: Structure Based Virtual Screening, Molecular Dynamic Simulation, Synthesis and Biological Evaluation

2021 ◽  
Vol 21 ◽  
Author(s):  
Maryam Abbasi ◽  
Massoud Amanlou ◽  
Mahmoud Aghaei ◽  
Farshid Hassanzadeh ◽  
Hojjat Sadeghi-Aliabadi
Keyword(s):  
Virtual Screening ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Md Simulations ◽  
Biological Evaluation ◽  
Dynamics Simulation ◽  
Hsp70 Expression ◽  
Hsp90 Inhibitors ◽  
Screening Study

Background: Heat shock protein90 (Hsp90) is overexpressed in tumor cells, thus the inhibition of the Hsp90 ATPase activity would be a meaningfully an effective strategy in cancer therapy. Objective: The present work was aimed at four steps: designing new Hsp90 inhibitors as anti-cancer by a virtual screening study; synthesize designed compounds; biological evaluation of them and finally molecular dynamic (MD) simulations of best compounds. Methods: A virtual screening study was performed on a library (100 compounds) of the ZINC database with benzimidazole scaffold; then an extracted compound and two derivatives were synthesized. The anti-proliferative and ATPase inhibitory activities of these compounds were evaluated by MTT and ATPase inhibition assays, respectively. The western blot analysis was performed to the evaluation of the expression level of Hsp70 and Her2 proteins. Finally, 200 ns molecular dynamic simulation was carried out to confirm stability the strongest synthesized compound in Hsp90 active site. Results: ZINC00173501 compound with an aminobenzimidazole scaffold was chosen by the virtual screening study. ZINC00173501 compound and two of its derivatives were synthesized. ATPase inhibitory activity of three synthesized compounds shown that ZINC00173501 compound was the most potent inhibitor (IC50= 8.6 μM) with the anti-proliferative activity 14.41 μM, 19.07 μM and more than 100 μM against MCF-7, HeLa and HUVEC cell lines, respectively. The high level of Hsp70 expression and low level of Her2 expression confirmed ZINC00173501 as an Hsp90 inhibitor. Finally, molecular dynamics simulation showed that ZINC00173501 was stable in Hsp90 active cite during 200 ns simulation. Conclusion: The biological evaluation results show that 2-aminobenzimidazole scaffold could be suggested as a lead for inhibition of Hsp90.

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