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molecular-dynamics-simulations
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Properly-tuned continuum and atomistic models for vibrational analysis of the silicon nanoplates
, Article International Journal of Mechanical Sciences ; Volume 229 , 2022 ; 00207403 (ISSN) ; Nejat Pishkenari, H ; Sharif University of Technology
Elsevier Ltd
2022
Abstract
The high computational costs of atomistic simulations for the investigation of nanostructures, despite their accuracy, necessitate efforts to develop efficient continuum models. Since the classical continuum mechanics assume the matter as continuous and ignore the size dependency of material properties, these theories fail to capture the behavior of materials at the nanoscale. Size-dependencies of nanostructures could result in the emergence of surface effects. This paper, for the first time, aims to develop and tune surface-enhanced continuum models to predict the vibrational properties of nanoplates which are inherently discrete at the nanoscale. Regarding this aim, we use a composite...
Friction reduction in grafted carbon nanochannels by applying an electric field
, Article Computational Materials Science ; Volume 213 , 2022 ; 09270256 (ISSN) ; Moosavi, A ; Hannani, S. K ; Sharif University of Technology
Elsevier B.V
2022
Abstract
Water can be pumped in nanochannels by limiting it between the surfaces with different hydrophobicities and exerting a spinning electric field. The asymmetrical hydrophobicity combined with the spinning electric field and the fact that the water molecules have a dipole moment create a situation in which the angular momentum of water molecules is transformed into a linear momentum and the water is pumped into the nanochannel. The hydrophobicity of the surfaces can be manipulated by using nanostructures to reduce friction. In this study, two types of nanostructures have been used which are hierarchical nanostructures and polymer nanostructures made of Poly(N-isopropylacrylamide). The walls of...
Mechanism understanding of Li-ion separation using a perovskite-based membrane
, Article Membranes ; Volume 12, Issue 11 , 2022 ; 20770375 (ISSN) ; Habibi, M ; Rezvantalab, S ; Mehdizadeh Chellehbari, Y ; Maleki, R ; Razmjou, A ; Sharif University of Technology
MDPI
2022
Abstract
Lithium ions play a crucial role in the energy storage industry. Finding suitable lithium-ion-conductive membranes is one of the important issues of energy storage studies. Hence, a perovskite-based membrane, Lithium Lanthanum Titanate (LLTO), was innovatively implemented in the presence and absence of solvents to precisely understand the mechanism of lithium ion separation. The ion-selective membrane’s mechanism and the perovskite-based membrane’s efficiency were investigated using Molecular Dynamic (MD) simulation. The results specified that the change in the ambient condition, pH, and temperature led to a shift in LLTO pore sizes. Based on the results, pH plays an undeniable role in...
Atomistic study of the effect of crystallographic orientation on the twinning and detwinning behavior of NiTi shape memory alloys
, Article Computational Materials Science ; Volume 203 , 2022 ; 09270256 (ISSN) ; Izadifar, M ; Dolado, J. S ; Ramazani, A ; Sadrnezhaad, S. K ; Sharif University of Technology
Elsevier B.V
2022
Abstract
Understanding the effect of crystallographic orientation on the twinnin/detwinning mechanisms in NiTi shape memory alloys at an atomistic scale can help to control and tune the mechanical properties and failure behavior of such materials. In this work, we employed classical molecular dynamics (MD) and density functional theory (DFT) computational methods to better understand how twinning and detwinning occurs through a combination of slip, twin, and shuffle on 〈0 1 0〉, 〈1 1 0〉, and 〈1 1 1〉 crystallographic orientations under uniaxial tensile test. Elastic constants including Young's Modulus (E), Bulk modulus (B), Poisson's ratio (ν), and Shear Modulus (G) are obtained and computed for...
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 ; Volume 33, Issue 4 , 2022 , Pages 604-616 ; 1045389X (ISSN) ; Taghibakhshi, A ; Nejat Pishkenari, H ; Arghavani, J ; Sharif University of Technology
SAGE Publications Ltd
2022
Abstract
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...
Mechanism of the motion of nanovehicles on hexagonal boron-nitride: A molecular dynamics study
, Article Computational Materials Science ; Volume 207 , 2022 ; 09270256 (ISSN) ; Nejat Pishkenari, H ; Nemati, A ; Sharif University of Technology
Elsevier B.V
2022
Abstract
Nanocars have been proposed to transport nanomaterials on the surface. Study of the mechanism of the motion of nanocars has attracted a lot of interests due to the potential ability of these nano-vehicles in the construction of nanostructures with bottom-up approach. Using molecular dynamics simulations, we study the motion of two nano-vehicles named “Nanocar” and “Nanotruck” on hexagonal boron-nitride monolayer. The obtained results reveals that, boron-nitride is an appropriate option to obtain higher mobility of nanocars compared with metal substrates. Considering different temperatures reveals that nanocars start to move on the BN at 200 K, while long range motions are observed at 400 K...
On the glass-forming ability of (Zr0.5Cu0.5)100−xAlx ternary alloys: A molecular dynamics study
, Article Materials Today Communications ; Volume 31 , 2022 ; 23524928 (ISSN) ; Shabestari, S. G ; Tavakoli, R ; Sharif University of Technology
Elsevier Ltd
2022
Abstract
In this research, the atomic scale local structures in (Zr0.5Cu0.5)100−xAlx (x = 0,2,4,6,8,10,12) bulk metallic glass was studied using molecular dynamics simulation method. The pair distribution function, Voronoi analysis and mean squared displacement (MSD) were adopted for investigation of the local structures. It was found that Cu- and Al-centered full icosahedra possess the most frequency accompanied by the most changes during the glass transition process in the supercooled liquid region temperature. Moreover, it was observed that the Al-centered full icosahedra (Al-FI) and Cu-centered full icosahedra (Cu-FI) clusters with 2.5% and 1.9% increase (relative to total atoms), respectively,...
Water desalination by charged multilayer graphene membrane: A molecular dynamics simulation
, Article Journal of Molecular Liquids ; Volume 355 , 2022 ; 01677322 (ISSN) ; Moosavi, A ; Nouri Borujerdi, A ; Sharif University of Technology
Elsevier B.V
2022
Abstract
Graphene, due to its unique excellent properties, is proposed as a developing method with high efficiency compared to classical water desalination methods. In this regard, charging the membrane is considered a promising and effective approach to enhance the performance of the graphene membrane. In this research, by using molecular dynamics simulations, the water desalination by charged multilayer graphene is evaluated and the influence of electric charge amount and geometric parameters, including the pore diameter and the interlayer distance, are investigated. According to the results, the multilayer nanoporous graphene with 16.35 Å pore diameter, in which the electric charge is distributed...
A theoretical investigation into the effects of functionalized graphene nanosheets on dimethyl sulfoxide separation
, Article Chemosphere ; Volume 297 , 2022 ; 00456535 (ISSN) ; Alizadeh, M ; Hasanzadeh, A ; Khataee, A ; Azamat, J ; Sharif University of Technology
Elsevier Ltd
2022
Abstract
The potential of carbon-based nanosheet membranes with functionalized pores is great as water treatment membranes. Using the molecular dynamic simulation technique, the dimethyl sulfoxide (DMSO) separation from the water/DMSO binary solution is investigated, and the functionalized graphene nanosheets are used as a membrane. This membrane was functionalized by –F (fluorine) and –H (hydrogen) functional groups. For the separation of DMSO, external hydrostatic pressures up to 100 MPa were applied to the considered systems. The separation mechanism was based on molecular size. Multiple analyses were done to study the capability of considered membranes for the separation of DMSO molecules from...
Effects of the temperature and the ph on the main protease of sars-cov-2: A molecular dynamics simulation study
, Article Biointerface Research in Applied Chemistry ; Volume 12, Issue 6 , 2022 , Pages 7239-7248 ; 20695837 (ISSN) ; Saadatabadi, A. R ; Sharif University of Technology
AMG Transcend Association
2022
Abstract
The novel coronavirus, recognized as COVID-19, is the cause of an infection outbreak in December 2019. The effect of temperature and pH changes on the main protease of SARS-CoV-2 were investigated using all-atom molecular dynamics simulation. The obtained results from the root mean square deviation (RMSD) and root mean square fluctuations (RMSF) analyses showed that at a constant temperature of 25℃ and pH=5, the conformational change of the main protease is more significant than that of pH=6 and 7. Also, by increasing temperature from 25℃ to 55℃ at constant pH=7, a remarkable change in protein structure was observed. The radial probability of water molecules around the main protease was...
In silico design of novel anticancer drugs with amino acid and carbohydrate building blocks to inhibit PIM kinases
, Article Molecular Simulation ; Volume 48, Issue 6 , 2022 , Pages 526-540 ; 08927022 (ISSN) ; Fattahi, A ; Sharif University of Technology
Taylor and Francis Ltd
2022
Abstract
PIM-1 is a serine-threonine kinase mainly expressed in tissues like the Thymus, spleen, bone marrow, and liver. Overexpression of PIM kinases occurs in various types of human tumours, such as lymphomas, prostate cancer, and oral cancer. As a result, the design of drugs to inhibit PIM-1 in cancerous cells has attracted much attention in recent years. This study aimed to design the alternative inhibitors for PIM-1 kinase, which are based on carbohydrates and amino acids and are expected to be non-toxic with the same chemotherapeutic effects as the traditional known anticancer drugs. The combinatorial use of quantum mechanics (QM) and molecular dynamic simulation (MD) has enabled us to...
Dynamics of antimicrobial peptide encapsulation in carbon nanotubes: the role of hydroxylation
, Article International Journal of Nanomedicine ; Volume 17 , 2022 , Pages 125-136 ; 11769114 (ISSN) ; Yousefi, F ; Seidi, F ; Sajadi, S. M ; Rabiee, N ; Habibzadeh, S ; Esmaeili, A ; Mashhadzadeh, A. H ; Spitas, C ; Mostafavi, E ; Saeb, M. R ; Sharif University of Technology
Dove Medical Press Ltd
2022
Abstract
Introduction: Carbon nanotubes (CNTs) have been widely employed as biomolecule carriers, but there is a need for further functionalization to broaden their therapeutic application in aqueous environments. A few reports have unraveled biomolecule–CNT interactions as a measure of response of the nanocarrier to drug-encapsulation dynamics. Methods: Herein, the dynamics of encapsulation of the antimicrobial peptide HA-FD-13 (accession code 2L24) into CNTs and hydroxylated CNTs (HCNTs) is discussed. Results: The van der Waals (vdW) interaction energy of CNT–peptide and HCNT–peptide complexes decreased, reaching −110.6 and −176.8 kcal.Mol−1, respectively, once encapsulation of the peptide inside...
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 ; Volume 29, Issue 20 , 2022 , Pages 2873-2883 ; 15376494 (ISSN) ; Taati, E ; Asghari, M ; Sharif University of Technology
Taylor and Francis Ltd
2022
Abstract
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...
Glycan-mediated functional assembly of IL-1RI: structural insights into completion of the current description for immune response
, Article Journal of Biomolecular Structure and Dynamics ; Volume 40, Issue 6 , 2022 , Pages 2575-2585 ; 07391102 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
Taylor and Francis Ltd
2022
Abstract
Interleukin 1 Receptor type I (IL-1RI) is a multi-domain transmembrane receptor that triggers the inflammatory response. Understanding its detailed mechanism of action is crucial for treating immune disorders. IL-1RI is activated upon formation of its functional assembly that occurs by binding of the IL-1 cytokine and the accessory protein (Il-1RAcP) to it. X-ray crystallography, small-Angle X-ray Scattering and molecular dynamics simulation studies showed that IL-1RI adopts two types of ‘compact’ and ‘extended’ conformational states in its dynamical pattern. Furthermore, glycosylation has shown to play a critical role in its activation process. Here, classical and accelerated atomistic...
A modified Jarzynski free-energy estimator to eliminate non-conservative forces and its application in nanoparticle-membrane interactions
, Article Physical Chemistry Chemical Physics ; Volume 24, Issue 6 , 2022 , Pages 3647-3654 ; 14639076 (ISSN) ; Lund, M ; Ejtehadi, M. R ; Sharif University of Technology
Royal Society of Chemistry
2022
Abstract
Computational methods to understand interactions in bio-complex systems are however limited to time-scales typically much shorter than in Nature. For example, on the nanoscale level, interactions between nanoparticles (NPs)/molecules/peptides and membranes are central in complex biomolecular processes such as membrane-coated NPs or cellular uptake. This can be remedied by the application of e.g. Jarzynski's equality where thermodynamic properties are extracted from non-equilibrium simulations. Although, the out of equilibrium work leads to non-conservative forces. We here propose a correction Pair Forces method, that removes these forces. Our proposed method is based on the calculation of...
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) ; Koleini, M. M ; Greenwell, H. C ; Ayatollahi, S ; Ghazanfari, M. H ; Sharif University of Technology
American Chemical Society
2021
Abstract
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) ; 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
Abstract
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) ; 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
Abstract
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 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) ; Jafary Zadeh, M ; Sharif University of Technology
IOP Publishing Ltd
2021
Abstract
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) ; Taghikhani, E ; Sharif University of Technology
American Chemical Society
2021
Abstract
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...