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molecular-simulation
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A theoretical and industrial study of component co-adsorption on 3A zeolite: an industrial case
, Article Chemical Papers ; Volume 74, Issue 2 , August , 2020 , Pages 651-661 ; Moradi, H ; Tavan, Y ; Sharif University of Technology
Springer
2020
Abstract
The 3A zeolite is an excellent adsorbent for natural gas dehydration due to low energy requirement in regeneration step and easy operation. To perform a reliable modeling, a good equilibrium adsorption isotherm is mandatory. Accordingly, water, methane, methyl mercaptan (M-mercaptan) and CO2 adsorption isotherms and also the competitive adsorption loading versus temperature are described for the system using molecular simulation and mathematical models. It is found that CO2 competes with water for adsorption on 3A and lower temperature is required for selective removal of water. The mathematical model results showed that M-mercaptan and CO2 quickly adsorb on 3A and capacity of 3A for water...
Molecular dynamics simulation of formation and growth of CdS nanoparticles
, Article Molecular Simulation ; Vol. 40, issue. 5 , Jul , 2014 , p. 361-369 ; ISSN: 08927022 ; Eskandari, Z ; Rahimi Tabar, M. R ; Sahimi, M ; Sharif University of Technology
Abstract
Monodispersed semiconducting nanoparticles are usually synthesised in a liquid medium using injection of an appropriate solution. A key factor in attaining a narrow particle size distribution (PSD) is the temporal separation of the nucleation and growth stages, where the former takes place during the injection. Faster injection produces a larger number of nuclei and a narrower PSD. The injection speed is expected to affect the diffusion of the ions in the solution and to create uniformly high supersaturation for a short period of time. In this paper, we study the growth of CdS nanoparticles during the injection by molecular dynamics simulation. A solution of Cd ions is injected into the...
Toward an equation of state for water inside carbon nanotubes
, Article Journal of Physical Chemistry B ; Volume 116, Issue 16 , April , 2012 , Pages 4943-4951 ; 15206106 (ISSN) ; Parsafar, G. A ; Sharif University of Technology
American Chemical Society
2012
Abstract
Water inside carbon nanotubes as an example of nanoconfined water has gained noticeable attention, in both theoretical and applied aspects. Molecular simulation has played a major role in the studies in this field. Yet, there is a need for systematic study of simulation results and compilation of scientifically reliable predictive relations. Here we present Monte Carlo simulations of water inside carbon nanotubes with different radii. An equation of state which was derived on the basis of the extended Lennard-Jones (12,6,3) as the effective pair potential is chosen for the system of water inside the carbon nanotubes. The equation of state is modified to take the effects of anisotropic...
Investigation on Wettability Alteration of Reservoir Rocks by Functionalized Silica Nanoparticles using Molecular Dynamics Simulations
, M.Sc. Thesis Sharif University of Technology ; Mohammadi, Aliasghar (Supervisor) ; Seyfkordi, Aliakbar (Supervisor)
Abstract
The properties of 3 nm-diameter fluorinated silica nanoparticles with different coverage percent of CF3 groups as water and oil repellents were investigated at the water-rock and decane-rock interface using molecular dynamics simulation. Simulating a pore of rock in presence of water and decane molecules separately, resulted in liquid bridging for both of liquids. The density profiles of liquids in the pore clearly show several highly ordered layers packing of the molecules close to the rock surface. Distribution of liquid molecules around the nanoparticles is much influenced with increasing CF3 groups on the nanoparticle surface. Results show that adsorption of functionalized silica...
Microscopic structure and solubility predictions of multifunctional solids in supercritical carbon dioxide: a molecular simulation study
, Article Journal of Physical Chemistry B ; Volume 121, Issue 7 , 2017 , Pages 1660-1674 ; 15206106 (ISSN) ; Paluch, A. S ; Sharif University of Technology
Abstract
Molecular dynamics simulations were employed to both estimate the solubility of nonelectrolyte solids, such as acetanilide, acetaminophen, phenacetin, methylparaben, and lidocaine, in supercritical carbon dioxide and understand the underlying molecular-level driving forces. The solubility calculations involve the estimation of the solute's limiting activity coefficient, which may be computed using conventional staged free-energy calculations. For the case of lidocaine, wherein the infinite dilution approximation is not appropriate, we demonstrate how the activity coefficient at finite concentrations may be estimated without additional effort using the dilute solution approximation and how...
Extending a hybrid continuum-molecular simulation method to solve the micro/nanoscale gas mixing problems
, Article ASME 2018 5th Joint US-European Fluids Engineering Division Summer Meeting, FEDSM 2018, 15 July 2018 through 20 July 2018 ; Volume 3 , 2018 ; 08888116 (ISSN); 9780791851579 (ISBN) ; Darbandi, M ; Schneider, G. E ; Fluids Engineering Division ; Sharif University of Technology
American Society of Mechanical Engineers (ASME)
2018
Abstract
Despite vast efforts in developing hybrid continuum-molecular methods, there has been no specific work focused on the gas mixture flow simulations including the mixing and/or separation of species. In present study, we extend a hybrid method to analyze such phenomena suitably and study the gas mixing problems in micro/nano length scales reliably. The results of current hybrid simulations are compared against the results of full-molecular simulations to evaluate the physical accuracy of developed hybrid method. The effect of continuum breakdown criterion is investigated to find out the achieved accuracy of developed hybrid simulation method from different perspectives. The current results...
Universal correlation between the thermodynamic potentials and some physical quantities of metallic glasses as a function of cooling rate during molecular dynamics simulation
, Article Journal of Non-Crystalline Solids ; Volume 536 , 2020 ; Tavakoli, R ; Sharif University of Technology
Elsevier B.V
2020
Abstract
The existence of universal semi-log linear relation between potential energy and cooling rate during the molecular dynamics simulations of metallic glasses for Cu-Zr system was formerly reported. For this purpose, different classes of metallic glasses are considered and the validity of this correlation is studied. It is shown that it holds for other thermodynamics potentials and some physical quantities like density and Wendt and Abraham parameter, too. This observation enables us to economically construct atomic scale metallic glass structures equivalent to very low cooling rates, more consistent to experimental works, not accessible using classic molecular simulations. © 2020 Elsevier B.V
Molecular simulation of protein dynamics in nanopores. I. Stability and folding
, Article Journal of Chemical Physics ; Volume 128, Issue 11 , 2008 ; 00219606 (ISSN) ; Rahimi Tabar, M. R ; Sahimi, M ; Sharif University of Technology
2008
Abstract
Discontinuous molecular dynamics simulations, together with the protein intermediate resolution model, an intermediate-resolution model of proteins, are used to carry out several microsecond-long simulations and study folding transition and stability of α -de novo-designed proteins in slit nanopores. Both attractive and repulsive interaction potentials between the proteins and the pore walls are considered. Near the folding temperature Tf and in the presence of the attractive potential, the proteins undergo a repeating sequence of folding/partially folding/unfolding transitions, with Tf decreasing with decreasing pore sizes. The unfolded states may even be completely adsorbed on the pore's...
Mass transfer through PDMS/zeolite 4A MMMs for hydrogen separation: Molecular dynamics and grand canonical Monte Carlo simulations
, Article International Communications in Heat and Mass Transfer ; Volume 108 , 2019 ; 07351933 (ISSN) ; Amirkhani, F ; Khadem, S. A ; Rezakazemi, M ; Asghari, M ; Shirazian, S ; Sharif University of Technology
Elsevier Ltd
2019
Abstract
In industry, utilizing membrane separation technology to purify natural gas streams is of remarkable significance. Molecular Simulation was used in the current article to study the structural and gas separation properties of polydimethylsiloxane (PDMS)/zeolite 4A Mixed Matrix Membranes (MMMs). To explore the optimal performance of MMMs, several structural analyses, namely Fractional Free Volume (FFV), Radial Distribution Function (RDF), X-Ray Diffraction (XRD) and also Glass Transition Temperature (Tg) as one of the most important properties of membranes have been evaluated. Also, the solubilities and diffusivities of periodic cells were respectively measured using MSD and adsorption...
Developing a Hybrid Continuum-Molecular Method to Analyze Binary Gas Mixing and Separation Processes
, Ph.D. Dissertation Sharif University of Technology ; Darbandi, Masoud (Supervisor)
Abstract
The co-existance of rarefied and near-continuum flow regimes is widelyencountered in analyzing the multiscale flow problems, e.g., micro-and nanoflows. Previous investigations have revealed that the continuum-based simulation methods would suffer from the lack of accuracy to predict the rarefied flow regimes. On the other hand, the molecular simulation methods are not computationally efficient in simulating the near-continuum flow regimes. Therefore, the use of hybrid simulation methods has been recommended as a serious alternative to simulate the multiscale flow problems. These methods apply the molecular methods in solving the rarefied flow regions and the continuum methods in solving the...
Molecular simulation of protein dynamics in nanopores. II. Diffusion
, Article Journal of Chemical Physics ; Volume 130, Issue 8 , 2009 ; 00219606 (ISSN) ; Tabar, M.R.R ; Sahimi, M ; Sharif University of Technology
2009
Abstract
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model of proteins, is used to carry out long (several microsecond) simulations in order to study transport of proteins in nanopores. We simulated single-domain proteins with the α-helical native structure. Both attractive and repulsive interaction potentials between the proteins and the pores' walls are considered. The diffusivity D of the proteins is computed not only under the bulk conditions but also as a function of their "length" (the number of the amino-acid groups), temperature T, pore size, and interaction potentials with the walls. Compared with the...
Lipid membranes with transmembrane proteins in shear flow
, Article Journal of Chemical Physics ; Volume 132, Issue 2 , 2010 ; 00219606 (ISSN) ; Noguchi, H ; Gompper, G ; Sharif University of Technology
Abstract
The effects of embedded proteins on the dynamical properties of lipid bilayer membranes are studied in shear flow. Coarse-grained molecular simulations are employed, in which lipids are modeled as short polymers consisting of hydrophilic head groups and hydrophobic tail monomers; similarly, transmembrane proteins are modeled as connected hydrophobic double- or triple-chain molecules with hydrophilic groups at both ends. In thermal equilibrium, rigid proteinlike molecules aggregate in a membrane of flexible lipids, while flexible proteins do not aggregate. In shear flow parallel to the membrane, the monolayers of lipid bilayer slide over each other. The presence of transmembrane proteins...