فهرس المقالات Molecular dynamics simulations

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  1 - Influences of Small-Scale Effect and Boundary Conditions on the Free Vibration of Nano-Plates: A Molecular Dynamics Simulation
  S.F Asbaghian Namin R Pilafkan
  This paper addresses the influence of boundary conditions and small-scale effect on the free vibration of nano-plates using molecular dynamics (MD) and nonlocal elasticity theory. Based on the MD simulations, Large-scale Atomic/Molecular Massively Parallel Simulator (LA أکثر

  This paper addresses the influence of boundary conditions and small-scale effect on the free vibration of nano-plates using molecular dynamics (MD) and nonlocal elasticity theory. Based on the MD simulations, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is used to obtain fundamental frequencies of single layered graphene sheets (SLGSs) which modeled in this paper as the most common nano-plates. On the other hand, governing equations are derived using nonlocal elasticity and the first-order shear deformation theory (FSDT). Afterwards, these equations solved using generalized differential quadrature method (GDQ). The small-scale effect is applied in the governing equations of motion by nonlocal parameter. The effects of different side lengths, boundary conditions, and nonlocal parameter are inspected for the aforementioned methods. The results obtained from the MD simulations are compared with those of nonlocal elasticity theory to calculate appropriate values for the nonlocal parameter. As a result, for the first time, the nonlocal parameter values are suggested for graphene sheets with various boundary conditions. Furthermore, it is shown that nonlocal elasticity approach using classical plate theory (CLPT) assumptions overestimates the natural frequencies. تفاصيل المقالة
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  2 - Molecular dynamics simulation study on the drug discovery in covid-19 disease
  Pejman Shir Ali Poor Elham Tazikeh-Lemeski
  In this study, drug discovery of SARS-CoV-2 nsp-16 effective in Coronavirus (COVID-19) has been accomplished by pharmacophore-based virtual screening among some analogs (FDA approved drugs) and marine natural plants (MNP). The comparison of the binding energies and the أکثر

  In this study, drug discovery of SARS-CoV-2 nsp-16 effective in Coronavirus (COVID-19) has been accomplished by pharmacophore-based virtual screening among some analogs (FDA approved drugs) and marine natural plants (MNP). The comparison of the binding energies and the inhibition constants was determined using molecular docking method. Between selected drugs, three compound were selected for further investigation using the molecular dynamics simulations. The results indicated that Ibrutinib and Idelalisib are oral medications while Kumusine, with proper hydrophilic and solubility properties, is an appropriate candidate for nsp-16 inhibitor and can be effective to control COVID-19 disease. It seems that Kumusine due to its better drug properties including the highest binding, the ability of destroying the secondary structure of the protein can be proposed as the best drug candidate among screened drugs in this research, for further investigations. تفاصيل المقالة
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  3 - Study Effect of Deformation Nanochannel Wall Roughness on The Water-Copper Nano-Fluids Poiseuille Flow Behavior
  محمد میثم امراللهی پورشیرازی داود طغرایی احمدرضا عظیمیان
  In the nanochannel flow behavior with respect to expand their applications in modern systems is of utmost importance. According to the results obtained in this study, the condition of nonslip on the wall of the nanochannel is not acceptable because in the nano dimension أکثر

  In the nanochannel flow behavior with respect to expand their applications in modern systems is of utmost importance. According to the results obtained in this study, the condition of nonslip on the wall of the nanochannel is not acceptable because in the nano dimensions, slip depends on different parameters including surface roughness. In this study, keeping the side area roughness, deformation effects on fluid flow behavior is investigated. Modeling software open source LAMMPS with equilibrium molecular dynamics simulations have been carried out. Unlike previous studies, existence fluid in laboratory conditions as water-copper nanofluids used. The results showed that rectangular was the most effective and triangular was least effective roughness on flow behavior, resulting in a rough triangular nanochannel slip occurs with more intensity.Existence roughness on the surface increases the number of oscillations in the fluid layer but amplitude near the wall is smooth to rough increased. Nanoparticles also increase the impact on the flow properties تفاصيل المقالة