Search for: molecular-dynamics
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    Atomistic insight into the behavior of ions at an oil-bearing hydrated calcite surface: implication to ion-engineered waterflooding

    , Article Energy and Fuels ; Volume 35, Issue 16 , 2021 , Pages 13039-13054 ; 08870624 (ISSN) Badizad, M. H ; Koleini, M. M ; Greenwell, H. C ; Ayatollahi, S ; Ghazanfari, M. H ; Sharif University of Technology
    American Chemical Society  2021
    This research provides an atomistic picture of the role of ions in modulating the microstructural features of an oil-contaminated calcite surface. This is of crucial importance for the rational design of ion-engineered waterflooding, a promising technique for enhancing oil recovery from carbonate reservoirs. Inspired by a conventional lab-scale procedure, an integrated series of molecular dynamics (MD) simulations were carried out to resolve the relative contribution of the major ionic constituent of natural brines (i.e., Na+, Cl-, Mg2+, Ca2+, and SO42-) when soaking an oil-bearing calcite surface in different electrolyte solutions of same salinity, namely, CaCl2, MgCl2, Na2SO4, MgSO4, and... 

    α-Helical antimicrobial peptide encapsulation and release from boron nitride nanotubes: A computational study

    , Article International Journal of Nanomedicine ; Pages 4277-4288 , Volume 16 , 2021 ; 11769114 (ISSN) Zarghami Dehaghani, M ; Yousefi, F ; Bagheri, B ; Seidi, F ; Mashhadzadeh, A. H ; Rabiee, N ; Zarrintaj, P ; Mostafavi, E ; Saeb, M. R ; Kim, Y. C ; Sharif University of Technology
    Dove Medical Press Ltd  2021
    Introduction: Antimicrobial peptides are potential therapeutics as anti-bacteria, anti-viruses, anti-fungi, or anticancers. However, they suffer from a short half-life and drug resistance which limit their long-term clinical usage. Methods: Herein, we captured the encapsulation of antimicrobial peptide HA-FD-13 into boron nitride nanotube (BNNT) (20,20) and its release due to subsequent insertion of BNNT (14,14) with molecular dynamics simulation. Results: The peptide-BNNT (20,20) van der Waals (vdW) interaction energy decreased to −270 kcal·mol−1 at the end of the simulation (15 ns). However, during the period of 0.2–1.8 ns, when half of the peptide was inside the nanotube, the... 

    Boron nitride nanotube as an antimicrobial peptide carrier: A theoretical insight

    , Article International Journal of Nanomedicine ; Volume 16 , 2021 , Pages 1837-1847 ; 11769114 (ISSN) Zarghami Dehaghani, M. Z ; Bagheri, B ; Yousefi, F ; Nasiriasayesh, A ; Mashhadzadeh, A. H ; Zarrintaj, P ; Rabiee, N ; Bagherzadeh, M ; Fierro, V ; Celzard, A ; Saeb, M. R ; Mostafavi, E ; Sharif University of Technology
    Dove Medical Press Ltd  2021
    Introduction: Nanotube-based drug delivery systems have received considerable attention because of their large internal volume to encapsulate the drug and the ability to penetrate tissues, cells, and bacteria. In this regard, understanding the interaction between the drug and the nanotube to evaluate the encapsulation behavior of the drug in the nanotube is of crucial importance. Methods: In this work, the encapsulation process of the cationic antimicrobial peptide named cRW3 in the biocompatible boron nitride nanotube (BNNT) was investigated under the Canonical ensemble (NVT) by molecular dynamics (MD) simulation. Results: The peptide was absorbed into the BNNT by van der Waals (vdW)... 

    Effect of the pyrrolic nitrogen functional group in the selective adsorption of CO2: GCMC, MD, and DFT studies

    , Article Energy and Fuels ; Volume 35, Issue 19 , 2021 , Pages 15918-15934 ; 08870624 (ISSN) Ekramipooya, A ; Mirzaee Valadi, F.M ; Latifi Pour, M ; Rashtchian, D ; Gholami, M. R ; Sharif University of Technology
    American Chemical Society  2021
    In this paper, the pyrrolic nitrogen functional group's presence is investigated in the selective adsorption of CO2. The grand canonical Monte Carlo (GCMC), molecular dynamics (MD), and density functional theory (DFT) were used for this study's goal. GCMC was used to calculate adsorption isotherms, selectivity, and isosteric heats. MD was used to calculate the radial distribution function (RDF) and diffusion. Reactivity parameters, electrostatic potential (ESP), reduced density gradient (RDG), and independent gradient model (IGM) were calculated using DFT. Adsorption isotherms, selectivity, and isosteric heats demonstrated that the NH group caused the selective adsorption of CO2 among CH4,... 

    Effect of the heteroatom presence in different positions of the model asphaltene structure on the self-aggregation: MD and DFT study

    , Article Journal of Molecular Liquids ; Volume 334 , 2021 ; 01677322 (ISSN) Ekramipooya, A ; Mirzaee Valadi, F ; Farisabadi, A ; Gholami, M. R ; Sharif University of Technology
    Elsevier B.V  2021
    In this study, a series of heteroatoms including nitrogen, oxygen, and sulfur were added to different positions of the model asphaltene structure to study the effect of the heteroatom presence in the self-aggregation of the model asphaltenes. Molecular Dynamics was used to calculate Solubility Parameters, Radial Distribution Function, and Relative Solubility Parameters. Additionally, Reactivity Parameters, Electrostatic Potential, Reduced Density Gradient, and Independent Gradient Model were calculated using the Density Functional Theory to further investigate the Molecular Dynamics results. This study indicated that heteroatoms' diversity and their positions in the model asphaltene... 

    Effect of annealing-induced tensions on the mechanical failure of copper/copper interface in wafer-to-wafer hybrid bonding

    , Article ECS Journal of Solid State Science and Technology ; Volume 10, Issue 2 , 2021 ; 21628769 (ISSN) Ghaemi, M ; Jafary Zadeh, M ; Sharif University of Technology
    IOP Publishing Ltd  2021
    The copper/copper (Cu/Cu) interface has an important role in wafer-to-wafer hybrid bonding for 3D integration applications. Reports indicate the possibility of the formation of post-bonding interfacial voids and cracks which must be avoided. Here, we use molecular dynamics simulations to investigate the effect of annealing-induced tensions on the strength and deformation mechanisms of Cu/Cu interfaces. We perform tensile tests on the pristine and defective Cu/Cu interfaces including a prototypical interfacial grain boundary in two defective limits: the presence of a single (isolated) void, and an array of multiple voids. The latter resembles interfacial nanoscale roughness as a result of... 

    Probe into the molecular mechanism of ibuprofen interaction with warfarin bound to human serum albumin in comparison to ascorbic and salicylic acids: Allosteric inhibition of anticoagulant release

    , Article Journal of Chemical Information and Modeling ; Volume 61, Issue 8 , 2021 , Pages 4045-4057 ; 15499596 (ISSN) Kalhor, H. R ; Taghikhani, E ; Sharif University of Technology
    American Chemical Society  2021
    The release of anticoagulant drugs such as warfarin from human serum albumin (HSA) has been important not only mechanistically but also clinically for patients who take multiple drugs simultaneously. In this study, the role of some commonly used drugs, including s-ibuprofen, ascorbic acid, and salicylic acid, was investigated in the release of warfarin bound to HSA in silico. The effects of the aforementioned drugs on the HSA-warfarin complex were investigated with molecular dynamics (MD) simulations using two approaches; in the first perspective, molecular docking was used to model the interaction of each drug with the HSA-warfarin complex, and in the second approach, drugs were positioned... 

    Atomistic simulation of creep deformation mechanisms in nickel-based single crystal superalloys

    , Article Materials Science and Engineering A ; Volume 809 , 2021 ; 09215093 (ISSN) Khoei, A. R ; Tolooei Eshlaghi, G ; Shahoveisi, S ; Sharif University of Technology
    Elsevier Ltd  2021
    In this paper, the creep deformation mechanisms are investigated in nickel-based single crystal superalloys. Two-dimensional molecular dynamics (MD) simulations are conducted to model various temperatures, stress conditions, and phase interface crystal orientations. Ni-based single-crystal superalloys are of great importance in the aircraft industry due to their excellent high temperature creep resistance. This characteristic mainly originates from two features considered in their structure; firstly, their two-phase micro-structure comprising gamma γ and gamma prime γ′, and secondly the nature of this superalloy itself, which is a single-crystal. MD is a powerful tool to gain insight into... 

    Dynamical time scales of friction dynamics in active microrheology of a model glass

    , Article Soft Matter ; Volume 17, Issue 20 , 2021 , Pages 5162-5169 ; 1744683X (ISSN) Madanchi, A ; Yu, J. W ; Lee, W. B ; Rahimi Tabar, M. R ; Rahbari, S. H. E ; Sharif University of Technology
    Royal Society of Chemistry  2021
    Owing to the local/heterogeneous structures in supercooled liquids, after several decades of research, it is now clear that supercooled liquids are structurally different from their conventional liquid counterparts. Accordingly, an approach based on a local probe should provide a better understanding about the local mechanical properties as well as heterogeneous structures. Recently, the superiority of active microrheology over global rheology has been demonstrated [Yu et al., Sci. Adv., 2020, 6, 8766]. Here, we elaborate this new avenue of research and provide more evidence for such superiority. We report on the results of an extensive molecular dynamics simulation of active microrheology... 

    Defining microRNA signatures of hair follicular stem and progenitor cells in healthy and androgenic alopecia patients

    , Article Journal of Dermatological Science ; Volume 101, Issue 1 , 2021 , Pages 49-57 ; 09231811 (ISSN) Mohammadi, P ; Nilforoushzadeh, M. A ; Youssef, K. K ; Sharifi Zarchi, A ; Moradi, S ; Khosravani, P ; Aghdami, R ; Taheri, P ; Hosseini Salekdeh, G ; Baharvand, H ; Aghdami, N ; Sharif University of Technology
    Elsevier Ireland Ltd  2021
    Background: The exact pathogenic mechanism causes hair miniaturization during androgenic alopecia (AGA) has not been delineated. Recent evidence has shown a role for non-coding regulatory RNAs, such as microRNAs (miRNAs), in skin and hair disease. There is no reported information about the role of miRNAs in hair epithelial cells of AGA. Objectives: To investigate the roles of miRNAs affecting AGA in normal and patient's epithelial hair cells. Methods: Normal follicular stem and progenitor cells, as well as follicular patient's stem cells, were sorted from hair follicles, and a miRNA q-PCR profiling to compare the expression of 748 miRNA (miRs) in sorted cells were performed. Further, we... 

    First principle simulation of coated hydroxychloroquine on Ag, Au and Pt nanoparticles

    , Article Scientific Reports ; Volume 11, Issue 1 , 2021 ; 20452322 (ISSN) Morad, R ; Akbari, M ; Rezaee, P ; Koochaki, A ; Maaza, M ; Jamshidi, Z ; Sharif University of Technology
    Nature Research  2021
    From the first month of the COVID-19 pandemic, the potential antiviral properties of hydroxychloroquine (HCQ) and chloroquine (CQ) against SARS-CoV-2 suggested that these drugs could be the appropriate therapeutic candidates. However, their side effects directed clinical tests towards optimizing safe utilization strategies. The noble metal nanoparticles (NP) are promising materials with antiviral and antibacterial properties that can deliver the drug to the target agent, thereby reducing the side effects. In this work, we applied both the quantum mechanical and classical atomistic molecular dynamics approaches to demonstrate the adsorption properties of HCQ/CQ on Ag, Au, AgAu, and Pt... 

    Study of microstructural growth under cyclic martensite phase transition in shape memory alloys; A molecular dynamics approach

    , Article Journal of Intelligent Material Systems and Structures ; 2021 ; 1045389X (ISSN) Moravej, S. A ; Taghibakhshi, A ; Nejat Pishkenari, H ; Arghavani, J ; Sharif University of Technology
    SAGE Publications Ltd  2021
    Shape memory alloys are referred to as a group of alloys that can retrieve the permanent deformation and strain applied to them and eventually return to their original form. So far, various studies have been done to determine the behavior of these alloys under cyclic loading. Most of the studies have mainly been conducted by using the foundations of Continuum Mechanics in order to examine the properties of memory alloys. In this study, instead of using the Continuum Mechanics, a Molecular Dynamics simulation method using Lennard-Jones potential is utilized. The changes in the behavior and properties of memory alloy under cyclic loading are being examined. First, the functional form... 

    Study and Simulation of Nanoparticle Translocation Through Cell Membrane

    , Article Iranian Journal of Science and Technology - Transactions of Mechanical Engineering ; Volume 45, Issue 4 , 2021 , Pages 939-960 ; 22286187 (ISSN) Nejat Pishkenari, H ; Barzegar, M. R ; Taghibakhshi, A ; Sharif University of Technology
    Springer Science and Business Media Deutschland GmbH  2021
    In this research, nanoparticle translocation through cell membrane has been studied and simulated. To this end, gold nanoparticles have been selected as the main carrier of the drug and have been functionalized with some selected ligands. The partial charges of the ligands have been calculated using quantum mechanics based on HF technique with 6-31Gd basis set. To achieve the realistic shape of a drug, the number and arrangement of ligands loaded on the gold nanoparticle have been optimized. After determining the properties such as diffusion coefficient and validating the results with experimental data, a MARTINI coarse-grained mapping of the drugs is created. The coarse-grained model of the... 

    Modeling vibrational behavior of silicon nanowires using accelerated molecular dynamics simulations

    , Article Scientia Iranica ; Volume 27, Issue 2 , 2021 , Pages 819-827 ; 10263098 (ISSN) Nejat Pishkenari, H ; Delafrouz, P ; Sharif University of Technology
    Sharif University of Technology  2021
    The classical methods utilized for modeling nano-scale systems are not practical because of the enlarged surface e ects that appear at small dimensions. Contrarily, implementing more accurate methods is followed by prolonged computations as these methods are highly dependent on quantum and atomistic models, and they can be employed for very small sizes in brief time periods. In order to speed up the Molecular Dynamics (MD) simulations of the silicon structures, Coarse-Graining (CG) models are put forward in this research. The procedure involves establishing a map between the main structure's atoms and the beads comprising the CG model and modifying the parameters of the system so that the... 

    On the theoretical and molecular dynamic methods for natural frequencies of multilayer graphene nanosheets incorporating nonlocality and interlayer shear effects

    , Article Mechanics of Advanced Materials and Structures ; 2021 ; 15376494 (ISSN) Nikfar, M ; Taati, E ; Asghari, M ; Sharif University of Technology
    Bellwether Publishing, Ltd  2021
    In this paper, a multiplate nonlocal shear model and molecular dynamic simulations are presented to investigate the effects of interlayer shear and nonlocality on the natural frequencies of multilayer graphene sheets (MLGSs). From one aspect in the optimal design of such structures, the interaction between graphene layers, which can significantly vary the static and dynamic behavior due to lack of solidity of layers stack, should be considered. On the other hand, it is requied that the nonlocality phenomenon which has an effective role in the mechanical analysis of nanostructures is taken into account. To this aim, the equation of motion along with corresponding boundary conditions is... 

    Enhanced local viscosity around colloidal nanoparticles probed by equilibrium molecular dynamics simulations

    , Article Journal of Chemical Physics ; Volume 155, Issue 17 , 2021 ; 00219606 (ISSN) Rabani, R ; Saidi, M. H ; Joly, L ; Merabia, S ; Rajabpour, A ; Sharif University of Technology
    American Institute of Physics Inc  2021
    Nanofluids - dispersions of nanometer-sized particles in a liquid medium - have been proposed for a wide variety of thermal management applications. It is known that a solid-like nanolayer of liquid of typical thicknesses of 0.5-1 nm surrounding the colloidal nanoparticles can act as a thermal bridge between the nanoparticle and the bulk liquid. Yet, its effect on the nanofluid viscosity has not been elucidated so far. In this article, we compute the local viscosity of the nanolayer using equilibrium molecular dynamics based on the Green-Kubo formula. We first assess the validity of the method to predict the viscosity locally. We apply this methodology to the calculation of the local... 

    S494 O-glycosylation site on the SARS-CoV-2 RBD affects the virus affinity to ACE2 and its infectivity; a molecular dynamics study

    , Article Scientific Reports ; Volume 11, Issue 1 , 2021 ; 20452322 (ISSN) Rahnama, S ; Azimzadeh Irani, M ; Amininasab, M ; Ejtehadi, M. R ; Sharif University of Technology
    Nature Research  2021
    SARS-CoV-2 is a strain of Coronavirus family that caused the ongoing pandemic of COVID-19. Several studies showed that the glycosylation of virus spike (S) protein and the Angiotensin-Converting Enzyme 2 (ACE2) receptor on the host cell is critical for the virus infectivity. Molecular Dynamics (MD) simulations were used to explore the role of a novel mutated O-glycosylation site (D494S) on the Receptor Binding Domain (RBD) of S protein. This site was suggested as a key mediator of virus-host interaction. By exploring the dynamics of three O-glycosylated models and the control systems of unglcosylated S4944 and S494D complexes, it was shown that the decoration of S494 with elongated O-glycans... 

    Mechanical properties of ester- and ether-DPhPC bilayers: A molecular dynamics study

    , Article Journal of the Mechanical Behavior of Biomedical Materials ; Volume 117 , 2021 ; 17516161 (ISSN) Rasouli, A ; Jamali, Y ; Tajkhorshid, E ; Bavi, O ; Pishkenari, H. N ; Sharif University of Technology
    Elsevier Ltd  2021
    In addition to its biological importance, DPhPC lipid bilayers are widely used in droplet bilayers, study of integral membrane proteins, drug delivery systems as well as patch-clamp electrophysiology of ion channels, yet their mechanical properties are not fully measured. Herein, we examined the effect of the ether linkage on the mechanical properties of ester- and ether-DPhPC lipid bilayers using all-atom molecular dynamics simulation. The values of area per lipid, thickness, intrinsic lateral pressure profile, order parameter, and elasticity moduli were estimated using various computational frameworks and were compared with available experimental values. Overall, a good agreement was... 

    Oriented hyperlens based on passivated porous graphene phases for sub-diffraction visible imaging

    , Article Optical Materials Express ; Volume 11, Issue 9 , 2021 , Pages 2839-2853 ; 21593930 (ISSN) Sadeghi, M. N ; Yazdanfar, P ; Rashidian, B ; Sharif University of Technology
    The Optical Society  2021
    The performance of conventional imaging lenses, relying on the phase transformation of propagating waves, is impairing due to the aberration and diffraction limits. For imaging beyond the diffraction limit, different superlens designs have been proposed. Although subdiffraction resolution imaging in the near field has been realized by the superlenses with negative refractive index, magnification of the subwavelength objects into the far field has not been fulfilled. Imaging using “hyperlens” is promising to overcome the energy spreading associated with diffraction, by utilizing negative permittivity parallel to the optical axis, and positive permittivity perpendicular to it. Among various... 

    Friction reduction in a nanochannel with grafted poly(N-isopropylacrylamide) oligomers: A molecular dynamics study

    , Article Physics of Fluids ; Volume 33, Issue 5 , 2021 ; 10706631 (ISSN) Saleki, O ; Moosavi, A ; Hannani, S. K ; Sharif University of Technology
    American Institute of Physics Inc  2021
    Superhydrophobic surfaces have been used for reducing friction in micro- and nanochannels. In the present work, water flow between two carbon walls with nanostructures made of poly(N-isopropylacrylamide) via the molecular dynamics method has been studied. The structure of this polymer can change based on the temperature of the environment, so that by increasing the temperature the structure becomes hydrophobic. This property has been studied and the effect of multiple factors on the slip length is presented. The effects of the number of monomers in the polymer, the distance between the polymers, and the temperature on the flow field are investigated. The results reveal that the slip length...