scholarly journals Analysis of Nanoscratch Mechanism of C-Plane Sapphire with the Aid of Molecular Dynamics Simulation of Hcp Crystal

Nanomaterials ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1739
Author(s):  
Wangpiao Lin ◽  
Naohiko Yano ◽  
Jun Shimizu ◽  
Libo Zhou ◽  
Teppei Onuki ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Basal Slip ◽  
Md Simulation ◽  
Dynamics Simulation ◽  
Machining Efficiency ◽  
Burr Height ◽  
Sapphire Wafer ◽  
Hexagonal Close Packed ◽  
Comparison Results ◽  
Friction Force Microscope

In this study, single groove nanoscratch experiments using a friction force microscope (FFM) with a monocrystalline diamond tip were conducted on a c-plane sapphire wafer to analyze the ductile-regime removal and deformation mechanism including the anisotropy. Various characteristics, such as scratch force, depth, and specific energy for each representative scratch direction on the c-plane of sapphire, were manifested by the FFM, and the results of the specific scratch energy showed a trend of six-fold symmetry on taking lower values than those of the other scratch directions when the scratch directions correspond to the basal slip directions as . Since this can be due to the effect of most probably basal slip or less probably basal twinning on the c-plane, a molecular dynamics (MD) simulation of zinc, which is one of the hexagonal close-packed (hcp) crystals with similar slip/twining systems, was attempted to clarify the phenomena. The comparison results between the nanoscratch experiment and the MD simulation revealed that both the specific scratch energy and the burr height were minimized when scratched in the direction of the basal slip. Therefore, it was found that both the machining efficiency and the accuracy could be improved by scratching in the direction of the basal slip in the single groove nanoscratch of c-plane sapphire.

scholarly journals Molecular dynamics simulation of sI methane hydrate under compression and tension

2020 ◽  
Vol 18 (1) ◽  
pp. 69-76
Author(s):  
Qiang Wang ◽  
Qizhong Tang ◽  
Sen Tian
Keyword(s):  
Molecular Dynamics ◽  
Methane Hydrate ◽  
Fracture Process ◽  
Md Simulation ◽  
Maximum Stress ◽  
Dynamics Simulation ◽  
Tensile Fracture ◽  
Maximum Compressive Stress ◽  
Motion State ◽  
Stress States

AbstractMolecular dynamics (MD) analysis of methane hydrate is important for the application of methane hydrate technology. This study investigated the microstructure changes of sI methane hydrate and the laws of stress–strain evolution under the condition of compression and tension by using MD simulation. This study further explored the mechanical property and stability of sI methane hydrate under different stress states. Results showed that tensile and compressive failures produced an obvious size effect under a certain condition. At low temperature and high pressure, most of the clathrate hydrate maintained a stable structure in the tensile fracture process, during which only a small amount of unstable methane broke the structure, thereby, presenting a free-motion state. The methane hydrate cracked when the system reached the maximum stress in the loading process, in which the maximum compressive stress is larger than the tensile stress under the same experimental condition. This study provides a basis for understanding the microscopic stress characteristics of methane hydrate.

Molecular Dynamics Simulation of AFM-Based Nanomachining Processes

2011 ◽  
Author(s):  
Rapeepan Promyoo ◽  
Hazim El-Mounayri ◽  
Kody Varahramyan ◽  
Ashlie Martini
Keyword(s):  
Molecular Dynamics ◽  
Friction Coefficient ◽  
Md Simulation ◽  
Computational Models ◽  
Dynamics Simulation ◽  
Radius Of Curvature ◽  
Force Microscopy ◽  
Indentation Force ◽  
Atomic Force ◽  
Development And Validation

Recently, atomic force microscopy (AFM) has been widely used for nanomachining and fabrication of micro/ nanodevices. This paper describes the development and validation of computational models for AFM-based nanomachining (nanoindentation and nanoscratching). The Molecular Dynamics (MD) technique is used to model and simulate mechanical indentation and scratching at the nanoscale in the case of gold and silicon. The simulation allows for the prediction of indentation forces and the friction force at the interface between an indenter and a substrate. The effects of tip curvature and speed on indentation force and friction coefficient are investigated. The material deformation and indentation geometry are extracted based on the final locations of atoms, which are displaced by the rigid tool. In addition to modeling, an AFM was used to conduct actual indentation at the nanoscale, and provide measurements to validate the predictions from the MD simulation. The AFM provides resolution on nanometer (lateral) and angstrom (vertical) scales. A three-sided pyramid indenter (with a radius of curvature ∼ 50 nm) is raster scanned on top of the surface and in contact with it. It can be observed from the MD simulation results that the indentation force increases as the depth of indentation increases, but decreases as the scratching speed increases. On the other hand, the friction coefficient is found to be independent of scratching speed.

Molecular dynamics simulation of homogeneous nucleation of supersaturated potassium chloride (KCl) in aqueous solutions

CrystEngComm ◽  
2019 ◽  
Vol 21 (48) ◽  
pp. 7507-7518 ◽  
Author(s):  
Soroush Ahmadi ◽  
Yuanyi Wu ◽  
Sohrab Rohani
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Aqueous Solutions ◽  
Potassium Chloride ◽  
Homogeneous Nucleation ◽  
Md Simulation ◽  
Crystal Nucleation ◽  
Dynamics Simulation

Molecular dynamics (MD) simulation is used to investigate the mechanism of crystal nucleation of potassium chloride (KCl) in a supersaturated aqueous solution at 293 K and 1 atm.

scholarly journals Material Analysis and Molecular Dynamics Simulation for Cavitation Erosion and Corrosion Suppression in Water Hydraulic Valves

Materials ◽  
2020 ◽  
Vol 13 (2) ◽  
pp. 453 ◽  
Author(s):  
Masoud Kamoleka Mlela ◽  
He Xu ◽  
Feng Sun ◽  
Haihang Wang ◽  
Gabriel Donald Madenge
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Essential Role ◽  
Corrosion Inhibitors ◽  
Cavitation Erosion ◽  
Dynamics Simulation ◽  
Preference Ranking ◽  
Water Hydraulics ◽  
The Impact ◽  
Hydraulic Valves

In the milestone of straggling to make water hydraulics more advantageous, the choice of coating polymer for water hydraulics valves plays an essential role in alleviating the impact of cavitation erosion and corrosion, and this is a critical task for designers. Fulfilling the appropriate selection, we conflicted properties that are vital for erosion and corrosion inhibitors, as well as the tribology in the sense of coefficient of friction. This article aimed to choose the best alternative polymer for coating on the selected substrate, that is, Cr2O3, Al2O3, Ti2O3. By applying PROMETHEE (Preference Ranking Organization Method for Enrichment Evaluations), the best polymer obtained with an analyzed performance attribute is Polytetrafluoroethylene (PTFE) that comes up with higher outranking (0.5932052). A Molecular Dynamics (MD) simulation was conducted to identify the stronger bonding with the regards of the better cleave plane between Polytetrafluoroethylene (PTFE) and the selected substrate. Polytetrafluoroethylene (PTFE)/Al2O3 cleaved in (010) plane was observed to be the strongest bond in terms of binding energy (3188 kJ/mol) suitable for further studies.

scholarly journals Molecular Dynamics Simulation and Kinetic Study of Fluoride Binding to V21C/V66C Myoglobin with a Cytoglobin-like Disulfide Bond

2020 ◽  
Vol 21 (7) ◽  
pp. 2512
Author(s):  
Lu-Lu Yin ◽  
Jia-Kun Xu ◽  
Xiao-Juan Wang ◽  
Shu-Qin Gao ◽  
Ying-Wu Lin
Keyword(s):  
Molecular Dynamics ◽  
Disulfide Bond ◽  
Rational Design ◽  
Double Mutant ◽  
Md Simulation ◽  
Experimental Studies ◽  
Heme Iron ◽  
Dynamics Simulation ◽  
Fluoride Ion ◽  
Artificial Proteins

Protein design is able to create artificial proteins with advanced functions, and computer simulation plays a key role in guiding the rational design. In the absence of structural evidence for cytoglobin (Cgb) with an intramolecular disulfide bond, we recently designed a de novo disulfide bond in myoglobin (Mb) based on structural alignment (i.e., V21C/V66C Mb double mutant). To provide deep insight into the regulation role of the Cys21-Cys66 disulfide bond, we herein perform molecular dynamics (MD) simulation of the fluoride–protein complex by using a fluoride ion as a probe, which reveals detailed interactions of the fluoride ion in the heme distal pocket, involving both the distal His64 and water molecules. Moreover, we determined the kinetic parameters of fluoride binding to the double mutant. The results agree with the MD simulation and show that the formation of the Cys21-Cys66 disulfide bond facilitates both fluoride binding to and dissociating from the heme iron. Therefore, the combination of theoretical and experimental studies provides valuable information for understanding the structure and function of heme proteins, as regulated by a disulfide bond. This study is thus able to guide the rational design of artificial proteins with tunable functions in the future.

scholarly journals Preparation and Molecular Dynamics Simulation of RDX/MUF Nanocomposite Energetic Microspheres with Reduced Sensitivity

Processes ◽  
2019 ◽  
Vol 7 (10) ◽  
pp. 692
Author(s):  
Jia ◽  
Hu ◽  
Xu ◽  
Liu ◽  
Ma ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Binding Energy ◽  
Emulsion Polymerization ◽  
Md Simulation ◽  
Urea Formaldehyde ◽  
Urea Formaldehyde Resin ◽  
Experimental Results ◽  
Dynamics Simulation ◽  
Formaldehyde Resin ◽  
Process Conditions

In order to improve the general problem of irregular coating morphology and low mechanical strength of the coating layer in existing coating desensitization technology, nano-cyclotrimethylene trinitramine/melamine-urea-formaldehyde (RDX/MUF) composite energetic microspheres were prepared by an improved emulsion polymerization, taking the MUF as the binder and RDX as the main explosive. In order to judge whether RDX/MUF possessed good stability, the combination of differential scanning calorimetry (DSC) and molecular dynamics (MD) simulation was used to determine the level of binding binding energy between urea-formaldehyde resin binder (UF) and RDX. In addition, to investigate the optimal reaction temperature for the preparation of MUF/RDX, the binding energy between UF and RDX at different temperatures was simulated. And then the morphology and thermal properties of the as-prepared composite energetic microspheres were analyzed by scanning electron microscopy (SEM) and DSC, the impact sensitivity and friction sensitivity of the resultant samples were tested as well. Moreover, RDX/MUF with the same MUF content was prepared by physical mixing for comparative analysis. MD simulation demonstrated that UF and RDX possessed good binding ability at 298 K. The DSC method indicatec that UF and RDX had good compatibility, and the comprehensive performance of RDX after coating was not significantly deteriorated; The optimal binding temperature between UF and RDX was 60~70 °C which is consistent with the experimental results. The experimental results showed that the optimum process conditions for the preparation of RDX/MUF could be listed as follows: the temperature for preparing RDX/MUF composite energetic microspheres by the improved emulsion polymerization was 70 °C the optimal pH value of the urea-formaldehyde resin prepolymer solution was 3, and the optimal melamine-urea molar ratio was 0.4.

scholarly journals Molecular Dynamics Simulation reveals the mechanism by which the Influenza Cap-dependent Endonuclease acquires resistance against Baloxavir marboxil

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ryunosuke Yoshino ◽  
Nobuaki Yasuo ◽  
Masakazu Sekijima
Keyword(s):  
Molecular Dynamics ◽  
Aromatic Ring ◽  
Influenza A ◽  
Md Simulation ◽  
Binding Free Energy ◽  
Complex Structure ◽  
Antiviral Drug ◽  
Rna Replication ◽  
Dynamics Simulation ◽  
Dependent Endonuclease

AbstractBaloxavir marboxil (BXM), an antiviral drug for influenza virus, inhibits RNA replication by binding to RNA replication cap-dependent endonuclease (CEN) of influenza A and B viruses. Although this drug was only approved by the FDA in October 2018, drug resistant viruses have already been detected from clinical trials owing to an I38 mutation of CEN. To investigate the reduction of drug sensitivity by the I38 mutant variants, we performed a molecular dynamics (MD) simulation on the CEN-BXM complex structure to analyze variations in the mode of interaction. Our simulation results suggest that the side chain methyl group of I38 in CEN engages in a CH-pi interaction with the aromatic ring of BXM. This interaction is abolished in various I38 mutant variants. Moreover, MD simulation on various mutation models and binding free energy prediction by MM/GBSA method suggest that the I38 mutation precludes any interaction with the aromatic ring of BXA and thereby reduces BXA sensitivity.

scholarly journals High-Throughput Virtual Screening, Molecular Dynamics Simulation, and Enzyme Kinetics Identified ZINC84525623 as a Potential Inhibitor of NDM-1

2019 ◽  
Vol 20 (4) ◽  
pp. 819 ◽  
Author(s):  
Md Rehman ◽  
Mohamed AlAjmi ◽  
Afzal Hussain ◽  
Gulam Rather ◽  
Meraj Khan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Virtual Screening ◽  
Enzyme Kinetics ◽  
High Throughput ◽  
Md Simulation ◽  
Dynamics Simulation ◽  
Multi Drug Resistance ◽  
Stable Complex ◽  
High Throughput Virtual Screening

The bacteria expressing New Delhi Metallo-β-lactamase-1 (NDM-1) can hydrolyze all β-lactam antibiotics including carbapenems, causing multi-drug resistance. The worldwide emergence and dissemination of gene blaNDM-1 (produces NDM-1) in hospital and community settings, rising problems for public health. Indeed, there is an urgent need for NDM-1 inhibitors to manage antibiotic resistance. Here, we have identified novel non-β-lactam ring-containing inhibitors of NDM-1 by applying a high-throughput virtual screening of lead-like subset of ZINC database. The screened compounds were followed for the molecular docking, the molecular dynamics simulation, and then enzyme kinetics assessment. The adopted screening procedure funnels out five novel inhibitors of NDM-1 including ZINC10936382, ZINC30479078, ZINC41493045, ZINC7424911, and ZINC84525623. The molecular mechanics-generalized born surface area and molecular dynamics (MD) simulation showed that ZINC84525623 formed the most stable complex with NDM-1. Furthermore, analyses of the binding pose after MD simulation revealed that ZINC84525623 formed two hydrogen bonds (electrostatic and hydrophobic interaction) with key amino acid residues of the NDM-1 active site. The docking binding free energy and docking binding constant for the ZINC84525623 and NDM-1 interaction were estimated to be −11.234 kcal/mol, and 1.74 × 108 M−1 respectively. Steady-state enzyme kinetics in the presence of ZINC84525623 show the decreased catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics. The findings of this study would be helpful in identifying novel inhibitors against other β-lactamases from a pool of large databases. Furthermore, the identified inhibitor (ZINC84525623) could be developed as efficient drug candidates.

AFM-Based Nanoscratching: A 3D Molecular Dynamics Simulation With Experimental Verification

2014 ◽  
Author(s):  
Rapeepan Promyoo ◽  
Hazim El-Mounayri ◽  
Kody Varahramyan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Md Simulation ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Dimensional Model ◽  
Gold Substrate ◽  
Three Dimensional Model ◽  
Friction Forces ◽  
Defect Mechanism

In this paper, a developed three-dimensional model for AFM-based nanomachining is applied to study mechanical scratching at the nanoscale. The correlation between the scratching conditions, including applied force, scratching depth, and distant between any two scratched grooves, and the defect mechanism in the substrate/workpiece is investigated. The simulations of nanoscratching process are performed on different crystal orientations of single-crystal gold substrate, Au(100), Au(110), and Au(111). The material deformation and groove geometry are extracted from the final locations of atoms, which are displaced by the rigid indenter. The simulation also allows for the prediction of normal and friction forces at the interface between the indenter and substrate. An AFM is used to conduct actual scratching at the nanoscale, and provide measurements to which the MD simulation predictions are compared. The predicted forces obtained from MD simulation compares qualitatively with the experimental results.

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