Synthesis and molecular dynamics simulation of hyperbranched poly(amine-ester)/neodymium nanocomposites

2016 ◽  
Vol 23 (1) ◽  
pp. 53-60
Author(s):  
Zunli Mo ◽  
Xiaobo Zhu ◽  
Yanzhi Liu ◽  
Ruibin Guo
Keyword(s):  
Molecular Dynamics ◽  
Hyperbranched Polymer ◽  
Md Simulation ◽  
Md Simulations ◽  
Canonical System ◽  
Dynamics Simulation ◽  
Static And Dynamic Characteristics ◽  
Transmission Electron ◽  
Hyperbranched Poly ◽  
The Stability

AbstractFully atomistic molecular dynamics (MD) simulations were employed to examine the static and dynamic characteristics of hyperbranched poly(amine-ester) (HPAE). In this work, use of G2, G3, and G4 HPAE as a template and stabilizer to prepare HPAE/neodymium (Nd) nanocomposites was studied. The results of transmission electron microscopy showed that Nd particles were deposited on the surface of HPAE within nanoscales, the size of nanoparticles was uniform, and there was better dispersion with high generation of hyperbranched polymer. Virtual Materiale software was applied to research the MD simulation of HPAE/Nd nanocomposites. The stability of the system and mechanism was studied from the perspective of molecular structure and energy change in canonical system (constant NVT). G4 HPAE is more suitable for use as template and stabilizer in MD simulation, which is consistent with experimental results.

STUDY OF AFFINITIES BETWEEN SINGLE-WALLED NANOTUBE AND EPOXY RESIN USING MOLECULAR DYNAMICS SIMULATION

2006 ◽  
Vol 05 (01) ◽  
pp. 131-144 ◽  
Author(s):  
JIHUA GOU ◽  
BIN FAN ◽  
GANGBING SONG ◽  
AURANGZEB KHAN
Keyword(s):  
Molecular Dynamics ◽  
Epoxy Resin ◽  
Md Simulation ◽  
Average Distance ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Repulsive Interaction ◽  
Curing Agent ◽  
Single Walled Nanotubes ◽  
Simulation Results

In the processing of carbon nanotube/polymer composites, the interactions between the nanotube and polymer matrix will occur at the molecular level. Understanding their interactions before curing is crucial for nanocomposites processing. In this study, molecular dynamics (MD) simulations were employed to reveal molecular interactions between (10, 10) single-walled nanotube and two kinds of epoxy resin systems. The two kinds of resin systems were EPON 862/EPI-CURE W curing agent (DETDA) and DGEBA (diglycidylether of bisphenol A)diethylenetriamine (DETA) curing agent. The MD simulation results show that the EPON 862, DETDA and DGEBA molecules had strong attractive interactions with single-walled nanotubes and their molecules changed their conformation to align their aromatic rings parallel to the nanotube surface due to π-stacking effect, whereas the DETA molecule had a repulsive interaction with the single-walled nanotubes. The interaction energies of the molecular systems were also calculated. Furthermore, an affinity index (AI) of the average distance between the atoms of the resin molecule and nanotube surface was defined to quantify the affinities between the nanotubes and resin molecules. The MD simulation results show that the EPON 862/EPI-CURE W curing agent system has good affinities with single-walled nanotubes.

Establishing a data-based scattering kernel model for gas–solid interaction by molecular dynamics simulation

2021 ◽  
Vol 928 ◽  
Author(s):  
Zijing Wang ◽  
Chengqian Song ◽  
Fenghua Qin ◽  
Xisheng Luo
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Md Simulation ◽  
Rarefied Gas ◽  
Interaction Model ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Rarefied Gas Flows ◽  
Accommodation Coefficients ◽  
Scattering Kernel

Scattering kernel models for gas–solid interaction are crucial for rarefied gas flows and microscale flows. However, most existing models depend on certain accommodation coefficients (ACs). We propose here to construct a data-based model using molecular dynamics (MD) simulation and machine learning. The gas–solid interaction is first modelled by 100 000 MD simulations of a single gas molecule reflecting on the wall surface, which is fulfilled by GPU parallel technology. The results showed a correlation of the reflection velocity with the incidence velocity in the same direction, and also revealed correlations that may exist in different directions, which are neglected by the traditional gas–solid interaction model. Inspired by the sophisticated Cercignani–Lampis–Lord (CLL) model, two improved scattering kernels were constructed to better reproduce the probability density of velocity determined from MD simulation. The first one adopts variable ACs which depend on the incidence velocity and the second one combines three CLL-like kernels. All the parameters in the improved kernels are automatically chosen by the machine learning method. Compared with the numerical experiments of a molecular beam, the reconstructed scattering kernels are basically consistent with the MD results.

Three Major Phosphoacceptor Sites in HIV-1 Capsid Protein Enhances its Structural Stability and Resistance Against the Inhibitor: Explication Through Molecular Dynamics Simulation, Molecular Docking and DFT Analysis

2020 ◽  
Vol 23 (1) ◽  
pp. 41-54 ◽  
Author(s):  
Nouman Rasool ◽  
Waqar Hussain
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Capsid Protein ◽  
Structural Stability ◽  
Md Simulations ◽  
Host Cells ◽  
Dynamics Simulation ◽  
Maximum Stability ◽  
The Stability ◽  
Hiv 1

Background: Human Immunodeficiency Virus 1 (HIV-1) is a lentivirus, which causes various HIV-associated infections. The HIV-1 core dissociation is essential for viral cDNA synthesis and phosphorylation of HIV-1 capsid protein (HIV-1 CA) plays an important role in it. Objective: The aim of this study was to explicate the role of three phosphoserine sites i.e. Ser109, Ser149 and Ser178 in the structural stability of HIV-1 CA, and it’s binding with GS-CA1, a novel potent inhibitor. Method: Eight complexes were analyzed and Molecular Dynamics (MD) simulations were performed to observe the stability of HIV-1 CA in the presence and absence of phosphorylation of serine residues at four different temperatures i.e. 300K, 325K, 340K and 350K, along with molecular docking and DFT analysis. Results: The structures showed maximum stability in the presence of phosphorylated serine residue. However, GS-CA1 docked most strongly with the native structure of HIV-1 CA i.e. binding affinity was -8.5 kcal/mol (Ki = 0.579 µM). Conclusion: These results suggest that the phosphorylation of these three serine residues weakens the binding of GS-CA1 with CA and casts derogatory effect on inhibition potential of this inhibitor, but it supports the stability of HIV-1 CA structure that can enhance regulation and replication of HIV-1 in host cells.

scholarly journals Investigation of vibrational manner of carbon nanotubes in the vicinity of ultrasonic argon flow using molecular dynamics simulation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Iman Karami ◽  
S. Ali Eftekhari ◽  
Davood Toghraie
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Oscillation Amplitude ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Vibrational Behavior ◽  
Atomic Structures ◽  
Argon Flow ◽  
The Stability

AbstractAmong various types of nanostructures, carbon nanotube (CNT) is one of the most important nanostructures. These nanostructures have been considered due to their mechanical, thermal, and vibrational properties. In this research, this nanostructure’s vibrational behavior in the vicinity of argon flow in the vicinity of ultrasonic velocity was investigated. The effect of factors such as the stability of atomic structures, the atomic manner of carbon nanotubes in the presence of ultrasonic fluid, the influence of carbon nanotubes’ length, and the chirality of carbon nanotubes on vibrational behavior was studied by molecular dynamics simulation. The MD simulations display an enhance in amplitude and a decrease in the oscillation frequency. Physically, these simulations’ results indicated the appropriate mechanical strength of carbon nanotubes in the presence of argon fluid. Numerically, the simulated carbon nanotubes’ minimum oscillation amplitude and frequency were equal to 2.02 nm and 10.14 ps−1. On the other hand, the maximum physical quantities were expressed as 4.03 nm and 13.01 ps−1.

Study of Helium Bubble Induced Hardening in BCC-Fe by Molecular Dynamics Simulation

2019 ◽  
Vol 944 ◽  
pp. 378-386
Author(s):  
Li Xia Jia ◽  
Xin Fu He ◽  
Shi Wu ◽  
Dong Jie Wang ◽  
Han Cao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Edge Dislocation ◽  
Reasonable Agreement ◽  
Md Simulation ◽  
Md Simulations ◽  
Defect Size ◽  
Dynamics Simulation ◽  
Helium Bubble ◽  
Increasing Temperature ◽  
Critical Resolved Shear Stress

The interaction between an moving edge dislocation and helium bubble was studied in BCC-Fe using Molecular dynamics（MD）simulation. Edge dislocation passed the bubble via cut mechanism. A step with a length of b is left on both sides of the bubble after dislocation left away. The influence of simulation temperature, defect size and He/V ratio in bubble on critical resolved shear stress (CRSS) for dislocation to shear bubble were investigated. The CRSS increases with increasing defect sizes, and decreases with increasing temperature. When He/V ratio is at the range of 0-1, CRSS depends weakly on the He/V ratio. The estimated obstacle strength of helium bubble based on MD simulations is acceptable and reasonable agreement with one deduced from the dispersion barrier-hardening model applied to experimental results.

Molecular Dynamics Simulation of Nanobubbles

2003 ◽  
Author(s):  
Shu Takagi ◽  
Gota Kikugawa ◽  
Yoichiro Matsumoto
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Pure Water ◽  
Simulation Method ◽  
Bubble Nucleation ◽  
Liquid Interface ◽  
Dynamics Simulation ◽  
Hydroxyl Groups ◽  
Surfactant System ◽  
The Stability

Some results have been reported recently related to the bubble formation with Molecular Dynamics (MD) simulation method. Some of them conduct the MD simulations of the bubble nucleation including impurity molecules with L-J potential [1,2]. In the present study, we investigate the stability of the nanometer size bubble in water, using molecular dynamics (MD) simulation method. MD simulation of an aqueous surfactant system: water liquid and alcohols below the liquid saturation density is carried out to investigate the stability of “nanobubbles” and the structure of the gas-liquid interface. To analyze the effect of surfactant structure, volume, and polarization on the stability of bubble nuclei, we use water by SPC/E model as the solvent molecules and 1-propanol, 1-pentanol, 1-heptanol as the surfactant molecules. Fig.1 shows the numerical result of instantaneous behavior of nanobubbles under the presence of surfactant in water. The calculation system is the cubic cell which has a side length of 25.057[Å], and a three-dimensional periodic boundary condition is applied. To include the intramolecular motion, AMBER force field [3] is adopted as a potential function. The momentum equations are integrated by velocity-Verlet argorithm [4]. Further, the time integration is extended to the Multi Time Scale algorithm by r-RESPA method [5]. As the surfactant molecules, to evaluate the influence of the hydrophobic effect of surfactants on the stability of bubble nuclei, we adopt 1-propanol (C3H7OH), 1-pentanol (C5H11OH), and 1-heptanol (C7H15OH), and to investigate the influence of the polarization of hydrophilic groups (-OH), “pseudo” 1-pentanol of which charge is cancelled away is also calculated. As a result, it was found that from the MD simulation at the condition that the bubble nuclei could not exist stably in pure water, a stable bubble is formed in aqueous surfactant system and hydroxyl groups of surfactants tend to point to the liquid phase at the gas-liquid interface. It is also shown that the longer hydrophobic chains the surfactants have, the more stably the bubble nuclei can exist.

Molecular Dynamics Simulation on Effect of Nanoparticle Aggregation on Transport Properties of a Nanofluid1

2012 ◽  
Vol 3 (2) ◽  
Author(s):  
Hongbo Kang ◽  
Yuwen Zhang ◽  
Mo Yang ◽  
Ling Li
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Transport Properties ◽  
Periodic Boundary Condition ◽  
Md Simulation ◽  
Periodic Boundary ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Nanoparticle Aggregation ◽  
Nanoparticle Cluster

Effect of nanoparticle aggregation on the transport properties that include thermal conductivity and viscosity of nanofluids is studied by molecular dynamics (MD) simulation. Unlike many other MD simulations on nanofluids which have only one nanoparticle in the simulation box with periodic boundary condition, in this work, multiple nanoparticles are placed in the simulation box which makes it possible to simulate the aggregation of the nanoparticles. Thermal conductivity and viscosity of the nanofluid are calculated using Green–Kubo method and results show that the nanoparticle aggregation induces a significant enhancement of thermal conductivity in nanofluid, while the increase of viscosity is moderate. The results also indicate that different configurations of the nanoparticle cluster result in different enhancements of thermal conductivity and increase of viscosity in the nanofluid.

Molecular docking, molecular dynamics simulation, and ADMET analysis of levamisole derivatives against the SARS-CoV-2 main protease (MPro)

Bioimpacts ◽  
2021 ◽  
Author(s):  
Khalil EL Khatabi ◽  
Ilham Aanouz ◽  
Marwa Alaqarbeh ◽  
Mohammed Aziz Ajana ◽  
Tahar Lakhlifi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Md Simulation ◽  
Antiviral Agents ◽  
Dynamics Simulation ◽  
Main Protease ◽  
In Silico Admet ◽  
Wet Lab ◽  
The Stability ◽  
Drug Leads

Introduction: The new species of coronaviruses (CoVs), SARS-CoV-2, was reported as responsible for an outbreak of respiratory disease. Scientists and researchers are endeavoring to develop new approaches for the effective treatment against of the COVID-19 disease. There are no finally targeted antiviral agents able to inhibit the SARS-CoV-2 at present. Therefore, it is of interest to investigate the potential uses of levamisole derivatives, which are reported to be antiviral agents targeting the influenza virus. Methods: In the present study, 12 selected levamisole derivatives containing imidazo[2,1-b]thiazole were subjected to molecular docking in order to explore the binding mechanisms between these derivatives and the SARS-CoV-2 Mpro (PDB: 7BQY). The levamisole derivatives were evaluated for in silico ADMET properties for wet-lab applicability. Further, the stability of the best-docked complex was checked using molecular dynamics (MD) simulation at 20 ns. Results: Levamisole derivatives and especially molecule N°6 showed more promising docking results, presenting favorable binding interactions as well as better docking energy compared to chloroquine and mefloquine. The results of ADMET prediction and MD simulation support the potential of the molecule N°6 to be further developed as a novel inhibitor able to stop the newly emerged SARS-CoV-2. Conclusion: This research provided an effective first line in the rapid discovery of drug leads against the novel CoV (SARS-CoV-2).

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.

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.

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