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molecular-dynamics-simulations
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Molecular dynamics simulation investigation of hexanoic acid adsorption onto calcite (1014)surface
, Article Fluid Phase Equilibria ; Volume 387 , 2015 , Pages 24-31 ; 03783812 (ISSN) ; Koleini, M. M ; Ayatollahi, S ; Sharif University of Technology
Abstract
In this paper we report the results of classical molecular dynamics (MD) simulation of hexanoic acid adsorption on calcite (101-4) surface plane using Pavese and AMBER force fields for calcite and hexanoic acid, respectively. Pair correlation function, strictly suggests a well-structured adsorption. Density profile indicates the adsorption occurs through double-bonded O atom of the acid head group by direct interaction with Ca atom at calcite surface. Adsorption orientation of H and double-bonded O atoms was found to be as lock and key with respect to calcite surface Ca and O atoms, facilitating an effective adsorption. Adsorption time evolution indicates that O atom adsorption is...
Steered molecular dynamic simulation approaches for computing the blood brain barrier (BBB) diffusion coefficient
, Article IFMBE Proceedings ; Volume 51 , 2015 , Pages 1699-1703 ; 16800737 (ISSN) ; 9783319193878 (ISBN) ; Shamloo, A ; Alasti, A ; Zadeh, E. G ; Jaffray D. A ; Sharif University of Technology
Springer Verlag
2015
Abstract
In the recent years a great attention of research deals with different physical and biological aspects of the BBB structure, a robust shield that separates the blood and brain, a recent research held by the authors of this paper has focused on figuring out computing the diffusion coefficient of endothelial cell membrane. In this study, the major efforts have been concentrated on calculating a standardized measure for the amount of permeability and diffusion of this barrier. As a result, this work is dedicated to molecular dynamics (MD) simulation of calculating the interaction force between nano-particle and BBB membrane. data is recorded by using steered molecular dynamics simulation and...
Molecular dynamics simulation study of the effect of temperature and grain size on the deformation behavior of polycrystalline cementite
, Article Scripta Materialia ; Volume 95, Issue 1 , 2015 , Pages 23-26 ; 13596462 (ISSN) ; Karimi Taheri, A ; Kang, K ; Ryu, S ; Sharif University of Technology
Elsevier Ltd
2015
Abstract
Molecular dynamics simulations combined with quantitative atomic displacement analyses were performed to study the deformation behaviors of polycrystalline cementite (Fe3C). At low temperature and large grain size, dislocation glide acts as the preferred deformation mechanism. Due to the limited number of slip systems at low temperature, polycrystalline cementite breaks by forming voids at grain boundaries upon tensile loading. When the temperature rises or the grain size reduces, grain boundary sliding becomes the primary mechanism and plastic deformation is accommodated effectively
Nanoscopic spontaneous motion of liquid trains: Nonequilibrium molecular dynamics simulation
, Article Journal of Chemical Physics ; Volume 132, Issue 2 , 2010 ; 00219606 (ISSN) ; Jalali, M. A ; Sharif University of Technology
Abstract
Macroscale experiments show that a train of two immiscible liquid drops, a bislug, can spontaneously move in a capillary tube because of surface tension asymmetries. We use molecular dynamics simulation of Lennard-Jones fluids to demonstrate this phenomenon for NVT ensembles in submicron tubes. We deliberately tune the strength of intermolecular forces and control the velocity of bislug in different wetting and viscosity conditions. We compute the velocity profile of particles across the tube and explain the origin of deviations from the classical parabolae. We show that the self-generated molecular flow resembles the Poiseuille law when the ratio of the tube radius to its length is less...
Continuum models calibrated with atomistic simulations for the transverse vibrations of silicon nanowires
, Article International Journal of Engineering Science ; Volume 100 , 2016 , Pages 8-24 ; 00207225 (ISSN) ; Afsharmanesh, B ; Tajaddodianfar, F ; Sharif University of Technology
Elsevier Ltd
2016
Abstract
We have conducted Molecular Dynamics (MD) simulations with the Environment-Dependent Interatomic Potential (EDIP) to obtain the natural frequency of ultra-thin Silicon Nanowires (SiNWs) with various crystallographic structures, boundary conditions and dimensions. As expected, results show that the mechanical properties of SiNWs are size-/orientation-dependent. The observed phenomena are ascribed to the surface effects which become dominant due to the large surface-to-volume number of atoms at the investigated range of dimensions. Due to their accuracy, atomistic simulations are widely accepted for the investigations of such nano-scaled systems; however, they suffer from high computational...
An atomistic insight into the implications of ion-tuned water injection in wetting preferences of carbonate reservoirs
, Article Journal of Molecular Liquids ; Volume 293 , 2019 ; 01677322 (ISSN) ; Badizad, M. H ; Ghatee, M. H ; Ayatollahi, S ; Sharif University of Technology
Elsevier B.V
2019
Abstract
The efficiency of water flooding methods is known to improve by applying ion-tuned water injection. Although there is a consensus that such improvement happens through reversing reservoir wettability characteristics to more water-wet state, the true impact of ions is still ambiguous among contradictory debates. The well-known molecular dynamics (MD) simulation techniques would shed light on such ambiguities to gain deep atomic-scale understanding of the process. Results from MD simulations show that the presence of Na+ and Cl¯ ions leads to the formation of an electrical double layer in adjacency of calcite surface while Mg2+ ions dominantly make complexes with hydrocarbons throughout the...
An atomistic insight into interfacial properties of brine nanofilm confined between calcite substrate and hydrocarbon layer
, Article Applied Surface Science ; Volume 490 , 2019 , Pages 89-101 ; 01694332 (ISSN) ; Badizad, M. H ; Ayatollahi, S ; Sharif University of Technology
Elsevier B.V
2019
Abstract
Molecular dynamics simulation was applied in this study to scrutinize the interfacial properties of water nano-film confined between calcite mineral and hydrocarbon layer, as two intrinsically different media. Such system resembles the environment experienced by water molecules in the pore spaces of underground carbonate reservoirs. The interplay between water film and confining phases, oil and mineral, strongly influences hydrocarbon production process; however, there is a lack of detailed understanding of the involved interactions. MD simulations indicate development of several layers with different water densities in the confined brine. Water molecules form well-ordered structure in three...
Investigation of the interactions between Melittin and the PLGA and PLA polymers: Molecular dynamic simulation and binding free energy calculation
, Article Materials Research Express ; Volume 6, Issue 5 , 2019 ; 20531591 (ISSN) ; Moosavi, A ; Sharif University of Technology
Institute of Physics Publishing
2019
Abstract
Nanobiotechnology is the application of nanotechnology in nanomedicine. Recently, the use of antimicrobial peptides as a substitute for antibiotics and anticancer drugs has attracted increasing attention. Therefore, the study of the structural behavior of these peptides such as Melittin and their interactions with biocompatible and biodegradable polymers is important. This study was performed to evaluate the critical interactions in the formation of the Melittin-polymers complexes. The aim of the current study was to investigate molecular mechanisms of Melittin encapsulation in biopolymers by molecular dynamics (MD) simulation. The results indicated that the basic residues of Melittin could...
Investigation of the interactions between Melittin and the PLGA and PLA polymers: Molecular dynamic simulation and binding free energy calculation
, Article Materials Research Express ; Volume 6, Issue 5 , 2019 ; 20531591 (ISSN) ; Moosavi, A ; Sharif University of Technology
Institute of Physics Publishing
2019
Abstract
Nanobiotechnology is the application of nanotechnology in nanomedicine. Recently, the use of antimicrobial peptides as a substitute for antibiotics and anticancer drugs has attracted increasing attention. Therefore, the study of the structural behavior of these peptides such as Melittin and their interactions with biocompatible and biodegradable polymers is important. This study was performed to evaluate the critical interactions in the formation of the Melittin-polymers complexes. The aim of the current study was to investigate molecular mechanisms of Melittin encapsulation in biopolymers by molecular dynamics (MD) simulation. The results indicated that the basic residues of Melittin could...
A temperature-calibrated continuum model for vibrational analysis of the fullerene family using molecular dynamics simulations
, Article Applied Mathematical Modelling ; Volume 80 , April , 2020 , Pages 115-125 ; Golzari, A ; Sharif University of Technology
Elsevier Inc
2020
Abstract
In the present study, a model was proposed to determine the elastic properties of the family of fullerenes at different temperatures (between 300 and 2000 K) using a combination of molecular dynamics simulation and continuum shell theory. The fullerenes molecules examined here are eight spherical fullerenes, including C60, C80, C180, C240, C260, C320, C500, and C720. First, the breathing mode frequency and the radius of gyration of the molecules were obtained at different temperatures by molecular dynamics simulations using AIREBO potential. Then, these data were used in a continuum model to obtain the elastic coefficients of these closed clusters of carbon in terms of temperature changes....
Planar molecular dynamics simulation of metallic nanoparticles manipulation
, Article 2008 8th IEEE Conference on Nanotechnology, IEEE-NANO, Arlington, TX, 18 August 2008 through 21 August 2008 ; 2008 , Pages 163-164 ; 9781424421046 (ISBN) ; Meghdari, A ; Jalili, N ; Amiri, F ; Sharif University of Technology
2008
Abstract
The aim of this research is to conduct atomistic investigations of physical interaction analysis of nanoscale objects manipulation. The system consists of tip, particle and substrate. The manipulation tool moves with a constant speed while pushing the particle in a desired direction. The focus of the research is on ultra-fine metallic nanoparticles. To perform this research, Nose-Hoover dynamics and Sutton-Chen interatomic potential will be used to investigate the behavior of the aforementioned system which is made from different transition metals. The effects of size, material type and temperature on the success of the process have been investigated by planar molecular dynamics. © 2008 IEEE...
Investigation of Thermodynamic and Dynamic Properties of Some Solids and Fluids with Nano Dimensions Using Molecular Dynamics Simulation
, Ph.D. Dissertation Sharif University of Technology ; Parsafar, Gholam Abbas (Supervisor)
Abstract
The physical characteristics of Pt nanoclusters with different sizes (256-8788 atoms) have been investigated via molecular dynamics simulations. The Pt-Pt radial distribution function, internal energy, heat capacity, enthalpy, entropy of the nanoclusters are calculated at some temperatures. The melting point predicted by the various properties is consistent with each other and shows that the melting temperature increases with the particle size. We have calculated the Gibbs free energy for the Pt bulk and also for its nanoparticle. We have used the thermodynamic integration method to obtain the Gibbs free energy. The total Gibbs free energy is taken as the sum of its central bulk and its...
Sliding Motion of Carbon Nanotube on Graphene Surface
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor) ; Nikamal, Mahdi (Co-Advisor)
Abstract
Unique and interesting properties of Graphene with two dimentional and CarbonNanotubes rod-like and their increasing applications such as application in electronic industry, sensors, displays, supercapasitors, pharmacy, etc, they hase become an important field of condensed matter and nanotechnology. Crystalization process and the distribution of light atoms and molecules on graphene surface hase become one of the reaserche arease of interest and hase attracted much attention. These studies play an important role in design of nanosensors graphene based. Most of the experimental observatins of surface diffusion in the chemical and physics systems have been classically described and...
Computer Simulation of Coiled Carbon Nanotubes Deformation By Molecular Dynamics Approach
, M.Sc. Thesis Sharif University of Technology ; Karimi Taheri, Ali (Supervisor)
Abstract
A Coiled Carbon Nanotube (CCNT) can be geometrically viewed as a graphene sheet whose rolled and twisted to form a helically coiled nanotube. It is the strongest material ever measured with strengthexceeding more than hundred times of steel.The strength of a CCNT iscritically influenced by temperature, tube diameter, strain rate and pitch angle. In this study,a Molecular Dynamics (MD) simulationis performed to understand the effect of temperature, strain rate, tube diameter and pitch angle on the mechanical properties of CCNTs. Results indicate thatexisting the stone-wales defects is necessaryfor thermodynamic stability of CCNTs.According to the stress-strain curves it was observed thatyield...
Investigation of Surfactin Behavior at the Presence of Wate, Oil, and Asphaltene
, M.Sc. Thesis Sharif University of Technology ; Roosta Azad, Reza (Supervisor) ; Yaghmaee, Soheyla (Supervisor)
Abstract
In this research, the behavior of surfactin at the presence of water, decane, and asphaltene is investigated. Decane is chosen instead of crude oil to simplify the model. In the first chapter, basic molecular structures are introduced. Furthermore, in the second chapter molecular dynamics simulation, as the main tool in these simulations, is introduced. In the third chapter, one of the most important quantities in chemical engineering, diffusion coefficient, is chosen to investigate the efficiency and accuracy of molecular dynamics simulation method to calculate such a quantity and results show that molecular dynamics simulation can present accurate quantities, more accurate than common...
Molecular Simulation of Methane Hydrate Formation Investigation of [Emim][BF4] Ionic Liquid effects on Growth and Dissociation of Methane Hydrate Crystal Using Molecular Dynamics Simulation
,
M.Sc. Thesis
Sharif University of Technology
;
Ghotbi , Cyrus
(Supervisor)
;
Taghikhani, Vahid
(Supervisor)
;
Jalili, Amir Hossein
(Supervisor)
Abstract
Formation of gas hydrates is a challenge in the oil and gas industry. Gas hydrate formation can be prevented by several methods. One of these methods is to utilize of inhibitor components. The gas hydrate inhibitors can affect hydrate formation from two aspects, i.e., thermodynamic or kinetic. In this work, thermodynamic and kinetic effects of [Emim][BF4] ionic liquid on growth and dissociation of methane hydrate crystal were investigated using molecular dynamics simulation. Molecular dynamics simulation is powerful tool to investigate the thermophysical, structural, and dynamic properties of methane hydrate and the formation, dissociation, and inhibition mechanisms at the molecular scale....
Study the Effect of Ionic Liquids on the Formation and Growth of Methane Clathrate Hydrates Using Molecular Dynamics Simulation
, M.Sc. Thesis Sharif University of Technology ; hikhani, Vahid (Supervisor) ; Ghotbi, Siroos (Supervisor) ; Jalili, Amir Hossein (Supervisor)
Abstract
The formation of gas hydrates in oil and gas industries has been the subject of long-standing problems. For example, the hydrate formation may occur and block gas pipelines which can lead to safety hazards. All of these will result in catastrophic economic losses and ecological risks. Therefore, various methods were developed to mitigate the formation of gas hydrate. In many cases, the hydrate inhibition by adding kinetic and thermodynamic inhibitors to the system is the only viable option. But recently using ionic liquids as novel hydrate inhibitors and the discovery of dual function thermo-kinetic inhibitors have been studied. In this project the performance of six imidazolium-based ionic...
Study of Thermal Behavior and mechanical properties of Phenolic/Clay Nanocomposits by Molecular Dynamics Simulations
, M.Sc. Thesis Sharif University of Technology ; Hosseni Kordkheili, Ali (Supervisor)
Abstract
Polymer/clay nanocomposites (PCNs) are multifunctional materials that have superior mechanical and thermal properties than polymer-based materials. These materials are obtained by adding small amounts of nanoclays to a polymer matrix. In this work, a molecular dynamics simulation was carried out to investigate the thermomechanical properties of thermosetting clay nanocomposites. The polymer matrix was composed of phenolic molecules with the crosslink density of 0.74, and different structures of PCNS were considered by varying the amount of polymer molecules. Molecular dynamics simulations of different nanocomposite structures were used to provide the atomistic insights, the molecular...
Directed motion of C60 on a graphene sheet subjected to a temperature gradient
, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 83, Issue 4 , 2011 ; 15393755 (ISSN) ; Neek Amal, M ; Ejtehadi, M. R ; Sharif University of Technology
Abstract
Nonequilibrium molecular dynamics simulations are used to study the motion of a C60 molecule on a graphene sheet subjected to a temperature gradient. The C60 molecule is actuated and moves along the system while it just randomly dances along the perpendicular direction. Increasing the temperature gradient increases the directed velocity of C60. It is found that the free energy decreases as the C60 molecule moves toward the cold end. The driving mechanism based on the temperature gradient suggests the construction of nanoscale graphene-based motors
Molecular dynamics modeling of a nanomaterials-water surface interaction
, Article Journal of Applied Physics ; Volume 119, Issue 16 , 2016 ; 00218979 (ISSN) ; Keramati, R ; Abdi, A ; Minary Jolandan, M ; Sharif University of Technology
American Institute of Physics Inc
2016
Abstract
In this article, we study the formation of nanomeniscus around a nanoneedle using molecular dynamics simulation approach. The results reveal three distinct phases in the time-evolution of meniscus before equilibrium according to the contact angle, meniscus height, and potential energy. In addition, we investigated the correlation between the nanoneedle diameter and nanomeniscus characteristics. The results have applications in various fields such as scanning probe microscopy and rheological measurements