scholarly journals Graphene Adhesion Mechanics on Iron Substrates: Insight from Molecular Dynamic Simulations

Crystals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 579 ◽  
Author(s):  
Wang ◽  
Jin ◽  
Yang ◽  
Zong ◽  
Peng
Keyword(s):  
Molecular Dynamic ◽  
Surface Engineering ◽  
Graphene Nanosheets ◽  
Pair Potential ◽  
Md Simulations ◽  
Adhesion Energy ◽  
Dynamic Simulations ◽  
Embedded Atom ◽  
Adhesion Mechanics ◽  
Eam Potential

The adhesion feature of graphene on metal substrates is important in graphene synthesis, transfer and applications, as well as for graphene-reinforced metal matrix composites. We investigate the adhesion energy of graphene nanosheets (GNs) on iron substrate using molecular dynamic (MD) simulations. Two Fe–C potentials are examined as Lennard–Jones (LJ) pair potential and embedded-atom method (EAM) potential. For LJ potential, the adhesion energies of monolayer GN are 0.47, 0.62, 0.70 and 0.74 J/m2 on the iron {110}, {111}, {112} and {100} surfaces, respectively, compared to the values of 26.83, 24.87, 25.13 and 25.01 J/m2 from EAM potential. When the number of GN layers increases from one to three, the adhesion energy from EAM potential increases. Such a trend is not captured by LJ potential. The iron {110} surface is the most adhesive surface for monolayer, bilayer and trilayer GNs from EAM potential. The results suggest that the LJ potential describes a weak bond of Fe–C, opposed to a hybrid chemical and strong bond from EAM potential. The average vertical distances between monolayer GN and four iron surfaces are 2.0–2.2 Å from LJ potential and 1.3–1.4 Å from EAM potential. These separations are nearly unchanged with an increasing number of layers. The ABA-stacked GN is likely to form on lower-index {110} and {100} surfaces, while the ABC-stacked GN is preferred on higher-index {111} surface. Our insights of the graphene adhesion mechanics might be beneficial in graphene growing, surface engineering and enhancement of iron using graphene sheets.

Spotting Differences in Molecular Dynamic Simulations of Influenza A M2 Protein-Ligand Complexes by Varying M2 construct, Lipid Bilayer and Force Field

2019 ◽  
Author(s):  
Dimitrios Kolokouris ◽  
Iris Kalenderoglou ◽  
Panagiotis Lagarias ◽  
Antonios Kolocouris
Keyword(s):  
Molecular Dynamic ◽  
Lipid Bilayer ◽  
Influenza A ◽  
Md Simulations ◽  
Membrane Curvature ◽  
Buffer Size ◽  
M2 Protein ◽  
Dynamic Simulations ◽  
Amphipathic Helices ◽  
Drug Protein Binding

<p>We studied by molecular dynamic (MD) simulations systems including the inward<sub>closed</sub> state of influenza A M2 protein in complex with aminoadamantane drugs in membrane bilayers. We varied the M2 construct and performed MD simulations in M2TM or M2TM with amphipathic helices (M2AH). We also varied the lipid bilayer by changing either the lipid, DMPC or POPC, POPE or POPC/cholesterol (chol), or the lipids buffer size, 10x10 Å<sup>2 </sup>or 20x20 Å<sup>2</sup>. We aimed to suggest optimal system conditions for the computational description of this ion channel and related systems. Measures performed include quantities that are available experimentally and include: (a) the position of ligand, waters and chlorine anion inside the M2 pore, (b) the passage of waters from the outward Val27 gate of M2 S31N in complex with an aminoadamantane-aryl head blocker, (c) M2 orientation, (d) the AHs conformation and structure which is affected from interactions with lipids and chol and is important for membrane curvature and virus budding. In several cases we tested OPLS2005, which is routinely applied to describe drug-protein binding, and CHARMM36 which describes reliably protein conformation. We found that for the description of the ligands position inside the M2 pore, a 10x10 Å<sup>2</sup> lipids buffer in DMPC is needed when M2TM is used but 20x20 Å<sup>2</sup> lipids buffer of the softer POPC; when M2AH is used all 10x10 Å<sup>2</sup> lipid buffers with any of the tested lipids can be used. For the passage of waters at least M2AH with a 10x10 Å<sup>2</sup> lipid buffer is needed. The folding conformation of AHs which is defined from hydrogen bonding interactions with the bilayer and the complex with chol is described well with a 10x10 Å<sup>2</sup> lipids buffer and CHARMM36. </p>

scholarly journals Investigations on Forming Ether Coated Iron Nanoparticle Materials by First-Principle Calculations and Molecular Dynamic Simulations

Coatings ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 395 ◽  
Author(s):  
Junlei Sun ◽  
Shixuan Hui ◽  
Pingan Liu ◽  
Ruochen Sun ◽  
Mengjun Wang
Keyword(s):  
Molecular Dynamic ◽  
Md Simulations ◽  
First Principle ◽  
Sphere Model ◽  
Dynamic Simulations ◽  
First Principle Calculations ◽  
Binding Force ◽  
Adsorption Behaviors ◽  
Single Sphere ◽  
To Come

The mechanism of coating effects between ether molecules and iron (Fe) nanoparticles was generally estimated using first-principle calculations and molecular dynamic (MD) simulations coupling with Fe (110) crystal layers and sphere models. In the present work, the optimized adsorption site and its energy were confirmed. The single sphere model in MD simulations was studied for typical adsorption behaviors, and the double sphere model was built to be more focused on the gap impact between two particles. In those obtained results, it is demonstrated that ether molecules were prone to be adsorbed on the long bridge site of the Fe (110) crystal while comparing with other potential sites. Although the coating was not completely uniform at early stages, the formation of ether layer ended up being equilibrated finally. Accompanied with charge transfer, those coated ether molecules exerted much binding force on the shell Fe atoms. Additionally, when free ether molecules were close to the gap between two nanoparticles, they were found to come under double adsorption effects. Although this effect might not be sufficient to keep them adsorbed, the movement of these ether molecules were hindered to some extent.

scholarly journals Molecular Dynamics Study on Deformation Mechanism of Grain Boundaries in Magnesium Crystal: Based on Coincidence Site Lattice Theory

2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Ken-ichi Saitoh ◽  
Kohei Kuramitsu ◽  
Tomohiro Sato ◽  
Masanori Takuma ◽  
Yoshimasa Takahashi
Keyword(s):  
Molecular Dynamics ◽  
Deformation Mechanism ◽  
Coincidence Site Lattice ◽  
Md Simulations ◽  
Uniaxial Tensile ◽  
High Angle ◽  
Site Lattice ◽  
Embedded Atom ◽  
Significant Difference ◽  
Eam Potential

As for magnesium (Mg) alloys, it has been noted that they are inferior to plastic deformation, but improvement in the mechanical properties by further refinement of grain size has been recently suggested. It means the importance of atomistic view of polycrystalline interface of Mg crystal. In this study, to discuss the deformation mechanism of polycrystalline Mg, atomistic grain boundary (GB) models by using coincidence site lattice (CSL) theory are constructed and are simulated for their relaxed and deformatted structures. First, GB structures in which the axis of rotation is in [11¯00] direction are relaxed at 10 Kelvin, and the GB energies are evaluated. Then, the deformation mechanism of each GB model under uniaxial tensile loading is observed by using the molecular dynamics (MD) method. The present MD simulations are based on embedded atom method (EAM) potential for Mg crystal. As a result, we were able to observe atomistically a variety of GB structures and to recognize significant difference in deformation mechanism between low-angle GBs and high-angle GBs. A close scrutiny is made on phenomena of dislocation emission processes peculiar to each atomistic local structure in high-angle GBs.

Spotting Differences in Molecular Dynamic Simulations of Influenza A M2 Protein-Ligand Complexes by Varying M2 construct, Lipid Bilayer and Force Field

2019 ◽  
Author(s):  
Dimitrios Kolokouris ◽  
Iris Kalenderoglou ◽  
Panagiotis Lagarias ◽  
Antonios Kolocouris
Keyword(s):  
Molecular Dynamic ◽  
Lipid Bilayer ◽  
Influenza A ◽  
Md Simulations ◽  
Membrane Curvature ◽  
Buffer Size ◽  
M2 Protein ◽  
Dynamic Simulations ◽  
Amphipathic Helices ◽  
Drug Protein Binding

<p>We studied by molecular dynamic (MD) simulations systems including the inward<sub>closed</sub> state of influenza A M2 protein in complex with aminoadamantane drugs in membrane bilayers. We varied the M2 construct and performed MD simulations in M2TM or M2TM with amphipathic helices (M2AH). We also varied the lipid bilayer by changing either the lipid, DMPC or POPC, POPE or POPC/cholesterol (chol), or the lipids buffer size, 10x10 Å<sup>2 </sup>or 20x20 Å<sup>2</sup>. We aimed to suggest optimal system conditions for the computational description of this ion channel and related systems. Measures performed include quantities that are available experimentally and include: (a) the position of ligand, waters and chlorine anion inside the M2 pore, (b) the passage of waters from the outward Val27 gate of M2 S31N in complex with an aminoadamantane-aryl head blocker, (c) M2 orientation, (d) the AHs conformation and structure which is affected from interactions with lipids and chol and is important for membrane curvature and virus budding. In several cases we tested OPLS2005, which is routinely applied to describe drug-protein binding, and CHARMM36 which describes reliably protein conformation. We found that for the description of the ligands position inside the M2 pore, a 10x10 Å<sup>2</sup> lipids buffer in DMPC is needed when M2TM is used but 20x20 Å<sup>2</sup> lipids buffer of the softer POPC; when M2AH is used all 10x10 Å<sup>2</sup> lipid buffers with any of the tested lipids can be used. For the passage of waters at least M2AH with a 10x10 Å<sup>2</sup> lipid buffer is needed. The folding conformation of AHs which is defined from hydrogen bonding interactions with the bilayer and the complex with chol is described well with a 10x10 Å<sup>2</sup> lipids buffer and CHARMM36. </p>

Detection and characterization at nM concentration of oligomers formed by hIAPP, Aβ(1–40) and their equimolar mixture using SERS and MD simulations

2018 ◽  
Vol 20 (31) ◽  
pp. 20588-20596 ◽  
Author(s):  
Luisa D’Urso ◽  
Marcello Condorelli ◽  
Orazio Puglisi ◽  
Carmelo Tempra ◽  
Fabio Lolicato ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Structural Investigation ◽  
Md Simulations ◽  
Equimolar Mixture ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations

We report a structural investigation on IAPP, Aβ(1–40) and their equimolar mixture at nM concentration using SERS spectroscopy and molecular dynamic simulations.

scholarly journals Molecular Dynamic Simulations of Bromodomain and Extra-Terminal Protein 4 Bonded to Potent Inhibitors

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 118
Author(s):  
Siao Chen ◽  
Yi He ◽  
Yajiao Geng ◽  
Zhi Wang ◽  
Lu Han ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Md Simulations ◽  
Docking Studies ◽  
Molecular Dynamic Simulations ◽  
Terminal Protein ◽  
Dynamic Simulations ◽  
Binding Effect ◽  
Computational Alanine Scanning ◽  
Α Helix ◽  
Effect Of Inhibitors

Bromodomain and extra-terminal domain (BET) subfamily is the most studied subfamily of bromodomain-containing proteins (BCPs) family which can modulate acetylation signal transduction and produce diverse physiological functions. Thus, the BET family can be treated as an alternative strategy for targeting androgen-receptor (AR)-driven cancers. In order to explore the effect of inhibitors binding to BRD4 (the most studied member of BET family), four 150 ns molecular dynamic simulations were performed (free BRD4, Cpd4-BRD4, Cpd9-BRD4 and Cpd19-BRD4). Docking studies showed that Cpd9 and Cpd19 were located at the active pocket, as well as Cpd4. Molecular dynamics (MD) simulations indicated that only Cpd19 binding to BRD4 can induce residue Trp81-Ala89 partly become α-helix during MD simulations. MM-GBSA calculations suggested that Cpd19 had the best binding effect with BRD4 followed by Cpd4 and Cpd9. Computational alanine scanning results indicated that mutations in Phe83 made the greatest effects in Cpd9-BRD4 and Cpd19-BRD4 complexes, showing that Phe83 may play crucial roles in Cpd9 and Cpd19 binding to BRD4. Our results can provide some useful clues for further BCPs family search.

Pressure-induced metallization of condensed-phase RDX: molecular dynamic simulations in conjunction with MSST method

2019 ◽  
Vol 97 (4) ◽  
pp. 245-253
Author(s):  
Zi-Qiu Bai ◽  
Jing Chang ◽  
Guang-Fu Ji ◽  
Ni-Na Ge
Keyword(s):  
Electronic Properties ◽  
Molecular Dynamic ◽  
Shock Loading ◽  
Md Simulations ◽  
Impact Sensitivity ◽  
Lower Sensitivity ◽  
Dynamic Simulations ◽  
Multi Scale ◽  
Cyclotrimethylene Trinitramine ◽  
The Impact

The anisotropy of impact sensitivity and microscopic electron properties of the cyclotrimethylene trinitramine (C3H6N6O6) (RDX) under shock loading are investigated in our work. The simulation is performed using molecular dynamic (MD) simulations in conjunction with multi-scale shock technique (MSST). By calculating the microscopic electronic properties and combining the thermodynamic properties, we predict that the metallization pressure of the RDX crystal is approximately 170 GPa under shock loading, which is slightly less than the metallization pressure under hydrostatic pressure. We also found that the microscopic electronic properties are related to the impact sensitivity. When the shock loading is along the z direction, the time of the transition from the insulating state to the metallization of the RDX crystal lags behind the shock loading along the x or y direction. Therefore, we predict that the RDX crystal has a lower sensitivity when the shock loading is along the z direction.

A Simple Palladium Hydride Embedded Atom Method Potential for Hydrogen Energy Applications

2019 ◽  
Vol 141 (6) ◽  
Author(s):  
Iyad Hijazi ◽  
Yang Zhang ◽  
Robert Fuller
Keyword(s):  
Elevated Temperatures ◽  
Clean Energy ◽  
Md Simulations ◽  
Miscibility Gap ◽  
Embedded Atom Method ◽  
Hydrogen Energy ◽  
Hydrogen Purification ◽  
Palladium Hydride ◽  
Embedded Atom ◽  
Eam Potential

When hydrogen is produced from a biomass or coal gasifier, it is necessary to purify it from syngas streams containing components such as CO, CO2, N2, CH4, and other products. Therefore, a challenge related to hydrogen purification is the development of hydrogen-selective membranes that can operate at elevated temperatures and pressures, provide high fluxes, long operational lifetime, and resistance to poisoning while still maintaining reasonable cost. Palladium-based membranes have been shown to be well suited for these types of high-temperature applications and have been widely utilized for hydrogen separation. Palladium's unique ability to absorb a large quantity of hydrogen can also be applied in various clean energy technologies, like hydrogen fuel cells. In this paper, a fully analytical interatomic embedded atom method (EAM) potential for the Pd-H system has been developed, that is easily extendable to ternary Palladium-based hydride systems, such as Pd-Cu-H and Pd-Ag-H. The new potential has fewer fitting parameters than previously developed EAM Pd-H potentials and is able to accurately predict the cohesive energy, lattice constant, bulk modulus, elastic constants, melting temperature, and the stable Pd-H structures in molecular dynamics (MD) simulations with various hydrogen concentrations. The EAM potential also well predicts the miscibility gap, the segregation of the palladium hydride system into dilute (α), and concentrated (β) phases.

The foundation and study of a new type of lattice inversion potential for Iridium

2015 ◽  
Vol 29 (30) ◽  
pp. 1550220 ◽  
Author(s):  
Xianli Ren ◽  
Song Chen ◽  
Ming Xie ◽  
Song Wang ◽  
Jieqiong Hu ◽  
...  
Keyword(s):  
Exponential Function ◽  
First Principles ◽  
Pair Potential ◽  
Inversion Method ◽  
Energy Curve ◽  
Embedded Atom ◽  
Phonon Spectra ◽  
Double Exponential ◽  
Eam Potential ◽  
Double Exponential Function

In this paper, the lattice cohesive curve of iridium is investigated through first-principles calculations. The double-exponential function to fit the curve is presented. The inversion pair potential curve is generated through Chen’s inversion method. The accurate pair potential function is obtained through fitting by the new double-exponential function. The phonon spectra are calculated using the inversion potential data, the embedded atom method (EAM) potential theory and first-principles method, respectively, to verify the reliability of the inversion potential. The method combining Boltzmann statistics equation with accuracy fitting of lattice cohesive energy curve is proposed to calculate the thermal expansion coefficient. In addition, the bulk modulus and Grüneisen constant in the room temperature are calculated. The results are in good agreement with experiment results, which imply that the inversion potential is effective and accurate.

scholarly journals Dynamic Coupling of Tyrosine 185 with the Bacteriorhodopsin Photocycle, as Revealed by Chemical Shifts, Assisted AF-QM/MM Calculations and Molecular Dynamic Simulations

2021 ◽  
Vol 22 (24) ◽  
pp. 13587
Author(s):  
Sijin Chen ◽  
Xiaoyan Ding ◽  
Chao Sun ◽  
Anthony Watts ◽  
Xiao He ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Molecular Mechanism ◽  
Chemical Shifts ◽  
Proton Translocation ◽  
Md Simulations ◽  
Binding Pocket ◽  
Dynamic Coupling ◽  
Dynamic Simulations ◽  
Dynamic Regulation ◽  
Aromatic Residues

Aromatic residues are highly conserved in microbial photoreceptors and play crucial roles in the dynamic regulation of receptor functions. However, little is known about the dynamic mechanism of the functional role of those highly conserved aromatic residues during the receptor photocycle. Tyrosine 185 (Y185) is a highly conserved aromatic residue within the retinal binding pocket of bacteriorhodopsin (bR). In this study, we explored the molecular mechanism of the dynamic coupling of Y185 with the bR photocycle by automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) calculations and molecular dynamic (MD) simulations based on chemical shifts obtained by 2D solid-state NMR correlation experiments. We observed that Y185 plays a significant role in regulating the retinal cis–trans thermal equilibrium, stabilizing the pentagonal H-bond network, participating in the orientation switch of Schiff Base (SB) nitrogen, and opening the F42 gate by interacting with the retinal and several key residues along the proton translocation channel. Our findings provide a detailed molecular mechanism of the dynamic couplings of Y185 and the bR photocycle from a structural perspective. The method used in this paper may be applied to the study of other microbial photoreceptors.

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