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molecular-dynamics-simulation
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Molecular Dynamics Simulation of Thin Film Growth and Nucleation Processes of Rapid Solidification of Aluminum in Nano-Scale
, M.Sc. Thesis Sharif University of Technology ; Simchi, Abdolreza (Supervisor) ; Ashuri, Hossein (Supervisor)
Abstract
In this project, the melting, solidification and remelting processes and also, the epitaxial growth of thin molten layer on the solidified crystalline substrate is studied using molecular dynamics simulation for the aluminum as an instance for the fcc metals. Sutton-Chen potential is used for energy calculations; the modified version of verlet algorithm is used for determination of position and velocity of atoms; and the berendsen algorithms are used as thermostat and barostat. The effects of pressure and temperature changing rate on the melting and crystallization temperatures and the crystal structure are investigated. The crystal structure of the system is examined using radial...
Numerical Analysis of Underwater and Within Air Sound Generation by using Carbon Nanotube
, M.Sc. Thesis Sharif University of Technology ; Moosavi, Ali (Supervisor)
Abstract
Carbon nanotubes have special thermodynamic properties which makes suitable as a thermo-acoustic sound source. Recently it is shown that by using these nanotubes it is possible to generate strog sound waves in air or water. Experimental analysis of phenomenon can be complicated and expensive. Hence this fact, in this study using molecular dynamic simulation, numerical analysis of sound generation with CNTs in air and water is discussed. For this purpose, the required structue of the system is generated and it has reaced equilibrium. This process has been done for 6 different CNT and for each CNT there are 5 different distances between them. Althogether, 30 different cases has is used for...
Investigation of Dropwise Condensation on Nanostructured Superhydrophobic Surfaces using Molecular Dynamics Simulation
, M.Sc. Thesis Sharif University of Technology ; Moosavi, Ali (Supervisor)
Abstract
Phase change processes have been used in heat transfer industries for decades. However, the heat transfer rate enhancement of the surfaces is still a challenging issue for the researchers. In this path, emerging nanostructured surfaces have shown great potentials. We demonstrate that using nanostructured surfaces in the condensation processes enhances the heat transfer behaviour of the fluid through interfacial contact area increase. In the present study molecular dynamics simulation have been employed to monitor the atomic behaviour of the system components at nanoscale. The argon liquid is considered as the working fluid and the copper surfaces as the phase change site. The effect of...
Investigation of Molecular Interactions of VEGFR and its Inhibitors by Molecular Dynamics Simulation
, M.Sc. Thesis Sharif University of Technology ; Bastani, Daruoosh (Supervisor) ; Mashayekhan, Shohreh (Co-Supervisor) ; Karami, Layla (Co-Supervisor)
Abstract
One of the chief kinds of receptors in cancer angiogenesis is the tyrosine kinase VEGFR-2. This target receptor is presented in both forms; active and inactive. adenosine triphosphate (ATP) residue is the location of deformational change from inactive to active form. Small molecule inhibitors have been designed for various forms of this receptor. In current study, the interaction of small molecular inhibitors including; Regorafenib, Cabozantinib and Thiosanib with dual VEGFR-2 receptor forms was investigated by molecular dynamics with Gromacs software. Cabozantinib and Regorafenib inhibitors had a lower binding energy in interaction with the inactive state however, Thiosanib inhibitors in...
Elucidating the Roles of Interlukin I Receptor Type II (lL-1Rll) in the Regulation of Human Immune System, Atomistic Molecular Dynamics Simulation
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor) ; Azimzadeh Irani, Maryam (Co-Supervisor)
Abstract
IL-1 family of cytokines plays a critical role in the regulation of immune response.These cytokines transfer the signals to the target cells through binding to the IL-1 receptors.Interleukin 1 Receptor Type II (IL-1RII) is the decoy receptor of the IL-1 cytokines. IL-1RII is homologous to the signaling Interleukin 1 Receptor Type I (IL1RI) in its extracellular region and can bind to the same cytokines with higher affinity and the same accessory protein. It down-regulates the signaling and suppresses the downstream pathways due to the lack of the intracellular Toll-Interleukin Receptor (TIR) domain. IL-1RII is decorated by carbohydrate units in-vivo. Dynamics and ligand binding of receptors...
Investigating The Mechanical Properties Of Two-Dimensional Silicon Dioxide With Inherent Negative Poisson's Ratio by Molecular Dynamics Method
,
M.Sc. Thesis
Sharif University of Technology
;
Tavakoli, Ruholah
(Supervisor)
Abstract
Silicon dioxide or silica with the chemical formula SiO2 is the basic component of many minerals. SiO2 films and sheets are widely used in mechanics, optics and electronics due to their outstanding mechanical and electronic performance. The main reason for research in the field of materials with negative Poisson's ratio is their unusual properties, which arise due to the inherent property of negative Poisson's ratio. In this research, the mechanical properties of four two-dimensional silica structures at a temperature of one Kelvin were investigated with the help of molecular dynamics simulation. Also, the sensitivity of the results to the system size and strain rate was studied, and the...
Molecular Dynamic Simulation of Water Desalination Across Porous Single Layer Graphene Membrane
, M.Sc. Thesis Sharif University of Technology ; Moosavi, Ali (Supervisor)
Abstract
In recent years carbon nanotubes and other carbon nanostructures such as graphene sheets have attracted a lot of attention due to their unique mechanical, thermal and electrical properties. These structures can be used in desalination of sea water, removal of hazardous substances from water tanks, gases separation, and so on. The nano porous single layer graphene membranes are very efficient for desalinating water due to their very low thickness. In this study, the mechanism of passing water and salt ions through nano porous single-layer graphene membrane are simulated using classical molecular dynamics. In the simulation, in order to separate salt ions from the water, the effects of applied...
Water electrolyte transport through corrugated carbon nanopores [electronic resource]
, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 90, Issue 1, July 2014, Article number 012304 ; Moosavi. A
Abstract
We investigate the effect of wall roughness on water electrolyte transport characteristics at different temperatures through carbon nanotubes by using nonequilibrium molecular dynamics simulations. Our results reveal that shearing stress and the nominal viscosity increase with ion concentration in corrugated carbon nanotubes (CNTs), in contrast to cases in smooth CNTs. Also, the temperature increase leads to the reduction of shearing stress and the nominal viscosity at moderate degrees of wall roughness. At high degrees of wall roughness, the temperature increase will enhance radial movements and increases resistance against fluid motion. As the fluid velocity increases, the particles do not...
Water electrolyte transport through corrugated carbon nanopores
, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Vol. 90, issue. 1 , July , 2014 ; ISSN: 15393755 ; Moosavi, A ; Sharif University of Technology
Abstract
We investigate the effect of wall roughness on water electrolyte transport characteristics at different temperatures through carbon nanotubes by using nonequilibrium molecular dynamics simulations. Our results reveal that shearing stress and the nominal viscosity increase with ion concentration in corrugated carbon nanotubes (CNTs), in contrast to cases in smooth CNTs. Also, the temperature increase leads to the reduction of shearing stress and the nominal viscosity at moderate degrees of wall roughness. At high degrees of wall roughness, the temperature increase will enhance radial movements and increases resistance against fluid motion. As the fluid velocity increases, the particles do not...
Anomalous diffusion of proteins in sheared lipid membranes
, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 88, Issue 3 , September , 2013 ; 15393755 (ISSN) ; Jalali, M. A ; Sharif University of Technology
2013
Abstract
We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow conditions. Protein embedded membranes behave quite differently: by imposing a simple shear flow and sliding the monolayers of the membrane over each other, the motion of protein clusters becomes strongly superdiffusive in the shear direction. In such a circumstance, the subdiffusion regime is predominant perpendicular to the flow. We show that superdiffusion is a result of accelerated chaotic motions of protein-lipid complexes within the membrane voids,...
Confinement dynamics of a semiflexible chain inside nano-spheres
, Article Journal of Chemical Physics ; Volume 139, Issue 4 , 2013 ; 00219606 (ISSN) ; Heidari, M ; Eslami Mossallam, B ; Ejtehadi, M. R ; Sharif University of Technology
2013
Abstract
We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter procedure is carried out by injecting the chain inside a spherical shell through a hole on the shell surface. The chain is modeled with a rigid body molecular dynamics simulation and its parameters are adjusted to DNA base-pair elasticity. Directional order parameter is employed to analyze and compare the confined chain and the conformations of the...
A molecular dynamics simulation study of nanomechanical properties of asymmetric lipid bilayer
, Article Journal of Membrane Biology ; Volume 246, Issue 1 , 2013 , Pages 67-73 ; 00222631 (ISSN) ; Amininasab, M ; Vali, M ; Ejtehadi, M ; Kowsari, F ; Sharif University of Technology
2013
Abstract
A very important part of the living cells of biological systems is the lipid membrane. The mechanical properties of this membrane play an important role in biophysical studies. Investigation as to how the insertion of additional phospholipids in one leaflet of a bilayer affects the physical properties of the obtained asymmetric lipid membrane is of recent practical interest. In this work a coarse-grained molecular dynamics simulation was carried out in order to compute the pressure tensor, the lateral pressure, the surface tension and the first moment of lateral pressure in each leaflet of such a bilayer. Our simulations indicate that adding more phospholipids into one monolayer results in...
Dynamics of nanodroplets on wettability gradient surfaces
, Article Journal of Physics Condensed Matter ; Volume 23, Issue 8 , February , 2011 ; 09538984 (ISSN) ; Mohammadi, A ; Sharif University of Technology
2011
Abstract
A lubrication model is used to study the dynamics of nanoscale droplets on wettability gradient surfaces. The effects of the gradient size, size of the nanodroplets and the slip on the dynamics have been studied. Our results indicate that the position of the center of mass of the droplets can be well described in terms of a third-order polynomial function of the time of the motion for all the cases considered. By increasing the size of the droplets the dynamics increases. It is also shown that the slip can considerably enhance the dynamics. The results have been compared with the results obtained using theoretical models and molecular dynamics simulations
Molecular dynamics simulation of supercoiled DNA rings
, Article Macromolecules ; Volume 48, Issue 1 , December , 2015 , Pages 164-172 ; 00249297 (ISSN) ; Schiessel, H ; Ejtehadi, M. R ; Sharif University of Technology
American Chemical Society
2015
Abstract
DNA supercoiling is a widespread phenomenon in biology. Here we introduce a coarse-grained DNA model and study supercoiled DNA rings via a rigid body molecular dynamics simulation. Our model allows us to investigate these structures in more detail than previously. The simulations are performed on rings of one to six kilobase pairs length and are compared to available experimental data and former simulation studies. The current study provides new additional information about some of the geometrical parameters of the supercoiled DNA rings. It also shows how enforcing a supercoiled DNA ring to two-dimensional space changes its geometrical parameters. Finally, our molecular dynamics method...
Molecular dynamics simulation of manipulation of metallic nanoclusters on double-layer substrates
, Article Physica E: Low-Dimensional Systems and Nanostructures ; Volume 42, Issue 9 , 2010 , Pages 2364-2374 ; 13869477 (ISSN) ; Meghdari, A ; Jalili, N ; Amiri, F ; Sharif University of Technology
2010
Abstract
Molecular dynamics simulations are carried out to investigate the manipulation of metallic clusters on double-layer surfaces. The system parts are made of transition metals. The conditions which are subjected to change in the tests are material combinations for cluster, main substrate and lubricant layer (adlayer). In addition to qualitative observations, two criteria which represent the particle deformation and substrate abrasion are utilized as evaluation tools and are computed for each case. Obtaining this sort of knowledge is highly beneficial for further experiments in order to be able to plan the conditions and routines, which guarantee better success in the manipulation process
Disease-related metabolites affect protein-nanoparticle interactions
, Article Nanoscale ; Volume 10, Issue 15 , 2018 , Pages 7108-7115 ; 20403364 (ISSN) ; Montazeri, A ; Naghdabadi, R ; Hajipour, M. J ; Zanganeh, S ; Caracciolo, G ; Mahmoudi, M ; Sharif University of Technology
Royal Society of Chemistry
2018
Abstract
Once in biological fluids, the surface of nanoparticles (NPs) is rapidly covered with a layer of biomolecules (i.e., the "protein corona") whose composition strongly determines their biological identity, regulates interactions with biological entities including cells and the immune system, and consequently directs the biological fate and pharmacokinetics of nanoparticles. We recently introduced the concept of a "personalized protein corona" which refers to the formation of different biological identities of the exact same type of NP after being exposed to extract plasmas from individuals who have various types of diseases. As different diseases have distinct metabolomic profiles and...
Coarse-graining models for molecular dynamics simulations of FCC metals
, Article Journal of Theoretical and Applied Mechanics (Poland) ; Volume 56, Issue 3 , 2018 , Pages 601-614 ; 14292955 (ISSN) ; Nejat Pishkenari, H ; Sharif University of Technology
Polish Society of Theoretical and Allied Mechanics
2018
Abstract
In this paper, four coarse-graining (CG) models are proposed to accelerate molecular dynamics simulations of FCC metals. To this aim, at first, a proper map between beads of the CG models and atoms of the all-atom (AA) system is assigned, afterwards mass of the beads and the parameters of the CG models are determined in a manner that the CG models and the original all-atom model have the same physical properties. To evaluate and compare precision of these four CG models, different static and dynamic simulations are conducted. The results show that these CG models are at least 4 times faster than the AA model, while their errors are less than 1 percent. © 2018 Polish Society of Theoretical...
Computation of some thermodynamic properties of nitrogen using a new intermolecular potential from molecular dynamics simulation
, Article Chemical Physics ; Volume 358, Issue 3 , 2009 , Pages 185-195 ; 03010104 (ISSN) ; Abbaspour, M ; Namayandeh Jorabchi, M ; Nahali, M ; Sharif University of Technology
2009
Abstract
A new pair-potential energy function of nitrogen has been determined via the inversion of reduced viscosity collision integrals and fitted to obtain an analytical potential form. The pair-potential reproduces the second virial coefficient, viscosity, thermal conductivity, self-diffusion coefficient, and thermal diffusion factor of nitrogen in a good accordance with experimental data over wide ranges of temperatures and densities. We have also performed the molecular dynamics simulation to obtain pressure, internal energy, heat capacity at constant volume, and self-diffusion coefficient of nitrogen at different temperatures and densities using our calculated pair-potential and some other...
Charge asymmetry effect in ion transport through angstrom-scale channels
, Article Journal of Physical Chemistry C ; Volume 123, Issue 2 , 2019 , Pages 1462-1469 ; 19327447 (ISSN) ; Fan, J ; Esfandiar, A ; Zhu, Y ; Wu, H ; Wang, F ; Sharif University of Technology
American Chemical Society
2019
Abstract
Structural and dynamic properties of ions confined in nanoslits are crucial to understand the fundamental mechanism underlying a wide range of chemical and biological phenomena. K + and Cl - show similar ion mobilities in a bulk aqueous solution, whereas they exhibit a remarkable difference when transporting through an angstrom-scale channel. Our molecular dynamics simulations uncover that such discrepancy originates from the subtle differences in their hydration structures and preferable locations across the channel. Opposite charge causes different water dipolar orientations around ions, mediating the distance and tribological interactions between hydrated ions and channel's walls....
Effects of topological constraints on linked ring polymers in solvents of varying quality
, Article Soft Matter ; Volume 16, Issue 12 , 2020 , Pages 3029-3038 ; Chubak, I ; Likos, C. N ; Ejtehadi, M. R ; Sharif University of Technology
Royal Society of Chemistry
2020
Abstract
We investigate the effects of topological constraints in catenanes composed of interlinked ring polymers on their size in a good solvent as well as on the location of their θ-point when the solvent quality is worsened. We mainly focus on poly[n]catenanes consisting of n ring polymers each of length m interlocked in a linear fashion. Using molecular dynamics simulations, we study the scaling of the poly[n]catenane's radius of gyration in a good solvent, assuming in general that Rg ∼ mμnν and we find that μ = 0.65 ± 0.02 and ν = 0.60 ± 0.01 for the range of n and m considered. These findings are further rationalized with the help of a mean-field Flory-like theory yielding the values of μ =...