scholarly journals MD-Simulation of Molten (Li, K)Cl at the Eutectic Composition. Self-Exchange Velocities of Li- and K-Isotopes near the Cl--Ions

1987 ◽  
Vol 42 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Isao Okada
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Md Simulation ◽  
Eutectic Composition ◽  
Isotope Effects ◽  
Dynamics Simulation ◽  
Atomic Masses ◽  
The Masses ◽  
Oscillating Motion

Molecular dynamics simulation (MD) has been done for a molten (Li, K)Cl mixture of the eutectic composition at about 700 K, 950 K and 1100 K and, for comparison, also for pure LiCl and KCl at about 950 K and 1100 K The atomic masses of half the Li+ and K+ ions have been set at 6.941 and 39.098, respectively. Self-exchange velocities (SEV’s) of these cations have been calculated. The Chemla effect is reflected by the SEV’s. The isotope effects of the SEV’s in the mixture increase slightly with temperature. The motions of the cations with respect to the adjacent CI- are classified into four modes: (1) an oscillating motion, (2) a leaving motion, (3) a wandering motion and (4) a coming-back motion. It is found that the velocity of the leaving motion is dependent only on the masses and the temperature, and independent of the kind of cations and the composition.

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 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.

Investigation of thermal, structural and dynamical properties of (Aux–Cuy–Niy)N=32,108,256 ternary nanosystems: effect of Au addition to Cu–Ni bimetallic nanoclusters via MD simulation

RSC Advances ◽  
2016 ◽  
Vol 6 (72) ◽  
pp. 67619-67629 ◽  
Author(s):  
Hamed Akbarzadeh ◽  
Mohsen Abbaspour ◽  
Esmat Mehrjouei
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Md Simulation ◽  
Dynamics Simulation ◽  
Heating And Cooling ◽  
Bimetallic Nanoclusters ◽  
Dynamical Properties ◽  
Metallic Nanoclusters

In this work, we have investigated the heating and cooling processes for ternary metallic nanoclusters with different Au mole fractions using molecular dynamics simulation.

Mass Transfer at Atomic Scale in MD Simulation of Friction Stir Welding

2016 ◽  
Vol 683 ◽  
pp. 626-631 ◽  
Author(s):  
Ivan Konovalenko ◽  
Igor S. Konovalenko ◽  
Andrey Dmitriev ◽  
Serguey Psakhie ◽  
Evgeny A. Kolubaev
Keyword(s):  
Molecular Dynamics ◽  
Mass Transfer ◽  
Friction Stir Welding ◽  
Molecular Dynamics Simulation ◽  
Md Simulation ◽  
Atomic Scale ◽  
Dynamics Simulation ◽  
Friction Stir ◽  
Embedded Atom ◽  
Atom Potential

Mass transfer has been studied at atomic scale by molecular dynamics simulation of friction stir welding and vibration-assisted friction stir welding using the modified embedded atom potential. It was shown that increasing the velocity movement and decreasing the angle velocity of the tool reduce the penetration depth of atoms into the opposite crystallite in the connected pair of metals. It was shown also that increasing the amplitude of vibrations applied to the friction stir welding tool results in increasing the interpenetration of atoms belonging to the crystallites joined

Hydration of iron–porphyrins: ab initio quantum mechanical charge field molecular dynamics simulation study

2017 ◽  
Vol 19 (45) ◽  
pp. 30822-30833 ◽  
Author(s):  
Syed Tarique Moin ◽  
Thomas S. Hofer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ab Initio ◽  
Md Simulation ◽  
Dynamics Simulation ◽  
Quantum Mechanical ◽  
Simulation Approach ◽  
Iron Porphyrins ◽  
Charge Field ◽  
Mechanical Charge

The ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulation approach was successfully applied to Fe2+–P and Fe3+–P in water to evaluate their structural, dynamical and energetic properties.

Mechanical property prediction of starch/polymer composites by molecular dynamics simulation

RSC Advances ◽  
2014 ◽  
Vol 4 (22) ◽  
pp. 11475-11480 ◽  
Author(s):  
Yao-Chun Wang ◽  
Shin-Pon Ju ◽  
Chien-Chia Chen ◽  
Hsin-Tsung Chen ◽  
Jin-Yuan Hsieh
Keyword(s):  
Mechanical Properties ◽  
Mechanical Property ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Polymer Composites ◽  
Md Simulation ◽  
Dynamics Simulation ◽  
Property Prediction ◽  
Mechanical Property Prediction

Molecular dynamics (MD) simulation was used to investigate the mechanical properties of several starch composites.

Molecular Dynamics Simulation of Gas Transport in Polyisoprene Matrix

2013 ◽  
Vol 844 ◽  
pp. 209-213
Author(s):  
Natthida Rakkapao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Model ◽  
Material Properties ◽  
Diffusion Coefficients ◽  
Potential Application ◽  
Md Simulation ◽  
Gas Transport ◽  
Dynamics Simulation ◽  
Membrane Properties

Molecular Dynamics (MD) simulation was employed to study the diffusivity of biogas in a PI matrix with the aim to verify simulations as a useful tool to predict PI membrane properties for biogas treatment. The simulation model of PI numerical was reliable and accurate in predicting both the material properties and the diffusivity of gases in PI matrix. The diffusion coefficients (D) of the major components in biogas, namely CH4, CO2, H2O, O2, and N2, were computed by simulating trajectories of each gas in PI matrix at 300 K. The simulations gave DCO2 that was 6 times larger than DCH4, and this agrees well with permeabilities reported in the literature. This suggests that PI membranes could be used to treat biogas by separating CO2 and CH4. However, the diffusivities of N2, H2O, and CH4 are closely similar, so PI membranes are not capable of separating these. The potential application of PI membrane to CO2/CH4 separation seems worth further exploration.

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