Sharif Digital Repository

Water molecules are one of the important molecules in nanofluidics. Its structure and its behavior can change with Temperature and cut-off distance parameters. In this study temperature and cut-off distance effects on the nano-scale water molecules behavior are investigated by molecular dynamics simulations. Many water molecular models have been developed in order to help discover the structure of water molecules. In this study, the flexible three centered (TIP3P-C) water potential is used to model the inter- and intramolecular interactions of the water molecules. In this simulation, we have been studied 512 water molecules with periodic boundary conditions and in a simulation box with 25... 

We investigate heat transfer between parallel plates separated by liquid argon using two-dimensional molecular dynamics (MD) simulations incorporating with 6-12 Lennard-Jones potential between molecule pairs. In molecular dynamics simulation of nanoscale flows through nanochannels, it is customary to fix the wall molecules. However, this approach cannot suitably model the heat transfer between the fluid molecules and wall molecules. Alternatively, we use thermal walls constructed from the oscillating molecules, which are connected to their original positions using linear spring forces. This approach is much more effective than the one which uses a fixed lattice wall modeling to simulate the... 

The Poiseuille flow through slit-like nanochannels is investigated using the nonequilibrium molecular dynamics simulations. To drive a dense flow through the channel, we use two self-adjusting vertical plates strategy. These plates force the liquid to flow through the nanochannel under adjustable inlet and outlet boundary conditions. Comparing with the dual-control-volume grand-canonical molecular dynamics method, the current strategy provides many advantages. The current strategy does not need particle insertion and deletion, therefore, the system dynamics would not be affected at all. Moreover, the number of particles in the simulation system is fixed due to inserting the two... 

Single-cell resolution technologies warrant computational methods that capture cell heterogeneity while allowing efficient comparisons of populations. Here, we summarize cell populations by adding features’ dispersion and covariances to population averages, in the context of image-based profiling. We find that data fusion is critical for these metrics to improve results over the prior alternatives, providing at least ~20% better performance in predicting a compound’s mechanism of action (MoA) and a gene’s pathway. © 2019, The Author(s)  

We use three-dimensional molecular dynamics simulation to investigate the driven flow between two parallel plates separated by argon atoms. Our simulations show that fluids in such channels can be continuously driven. Difference in surface wettability can cause a difference in fluid density along the nano channel. To control the nanochannel temperature walls, we use the thermal wall idea, which models the walls using atoms connected to their original positions by enforcing linear spring forces. In this study, we propose a nanochannel system in which, half of the channel has a low surface wettability, while the other half has a higher surface wettability and that the middle part of channel... 

The nonequilibrium molecular dynamics (NEMD) simulations are performed to calculation the cross drag over a nanotube located in a uniform liquid argon flow. As is known, the behavior of fluid flows in nano-scale sizes is very different from that in microscopic and macroscopic sizes. In this work, our concern is on the flow of argon molecules over a nanotube which occurs in nanoscale sizes. We calculate the cross drag enforced the nanotube at Re<10. In this regard, we use the molecular dynamics and simulate the flow of argon molecules over (6,0), (8,0) and (10,0) nanotubes. The simulations are performed at different velocities and the cross drag coefficient is computed at different Reynolds...