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molecular-dynamics-simulations
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Thermal conductivity of the cell membrane in the presence of cholesterol and amyloid precursor protein
, Article Physical Review E ; Volume 102, Issue 4 , 2020 ; Ejtehadi, M. R ; Sharif University of Technology
American Physical Society
2020
Abstract
The cell membrane is responsible for the transportation of heat between inside and outside the cell. Whether the thermal properties of the cell membrane are affected by the cholesterol concentration or the membrane proteins has not been investigated so far. Although the experimental measurement of the membrane thermal conductivity was not available until very recently, computational methods have been widely used for this purpose. In this study, we carry out molecular dynamics simulations to investigate the relation between the concentration of cholesterol and the thermal conductivity of a model membrane. Our results suggest an increase in the membrane thermal conductivity upon increasing the...
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) ; Yu, J. W ; Lee, W. B ; Rahimi Tabar, M. R ; Rahbari, S. H. E ; Sharif University of Technology
Royal Society of Chemistry
2021
Abstract
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...
Atomic scale interactions between RNA and DNA aptamers with the TNF- α protein
, Article BioMed Research International ; Volume 2021 , 2021 ; 23146133 (ISSN) ; Moosavi, A ; Alexandrakis, G ; Mofrad, M. R. K ; Sharif University of Technology
Hindawi Limited
2021
Abstract
Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for...
Vesicle deformations by clusters of transmembrane proteins
, Article Journal of Chemical Physics ; Volume 134, Issue 8 , 2011 ; 00219606 (ISSN) ; Jalali, M. A ; Sharif University of Technology
2011
Abstract
We carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters change the shapes of their host vesicles. The effects of depletion force and vesiculation on protein clustering are also investigated. By increasing the protein concentration, clusters are fragmented to smaller bundles, which are then redistributed to form more symmetric structures corresponding to lower bending energies. Big clusters and highly aspherical vesicles cannot be formed when the fraction of protein to lipid molecules is large
CO2 /H2 separation using a highly permeable polyurethane membrane: Molecular dynamics simulation
,
Article
Journal of Molecular Structure
;
Volume 1100
,
2015
,
Pages 401-414
;
00222860 (ISSN)
; Mousavi, S. A
;
Sharif University of Technology
Elsevier
2015
Abstract
Abstract In this study, Molecular Dynamics (MD) and Grand Canonical Monte Carlo (GCMC) simulations were conducted to investigate the diffusivity, solubility, and permeability of CO2 , CO, H2 , and H2 O in a polyurethane membrane at three different temperatures. The characterization of the simulated structures was carried out using XRD, FFV, Tg and density calculation, and cavity size distribution. The obtained results were within the expectations reported data in the literature based on the experimental approach, indicating the authenticity of approached in this work. The results showed that the highest diffusivity and permeability coefficients were observed for...
Surface defects characterization with frequency and force modulation atomic force microscopy using molecular dynamics simulations
, Article Current Applied Physics ; Volume 10, Issue 2 , 2010 , Pages 583-591 ; 15671739 (ISSN) ; Meghdari, A ; Sharif University of Technology
2010
Abstract
This paper is devoted to the characterization of the surface defects using a recently developed AFM technique called frequency and force modulation AFM (FFM-AFM). The simulated system includes a recently developed gold coated AFM probe which interacts with a sample including single-atom vacancy and impurities. In order to examine the behavior of the above system on different transition metals, the molecular dynamics (MD) simulation with Sutton-Chen (SC) inter-atomic potential is used. In this study, an online imaging simulation of the probe and sample is performed, and the effects of the horizontal scan speed, the effective frequency set-point, the cantilever stiffness, the tip-sample rest...
Solvation free energy and solubility of acetaminophen and ibuprofen in supercritical carbon dioxide: Impact of the solvent model
, Article Journal of Supercritical Fluids ; Volume 109 , 2016 , Pages 166-176 ; 08968446 (ISSN) ; Ghotbi, C ; Jahanbin Sardroodi, J ; Karimi Sabet, J ; Robert, M. A ; Sharif University of Technology
Elsevier
2016
Abstract
Classical molecular dynamics simulations are used to compute the solvation free energy of two pharmaceutical solids, namely ibuprofen and acetaminophen in carbon dioxide (CO2), over the density range of interest in supercritical processes. In order to examine the influence of the solvent model on the resulting free energies, three popular CO2 models (Zhang, EPM2, and TraPPE) are studied. Relatively large discrepancies for the solvation free energy exist between these CO2 models, suggesting that the former is sensitive to the different balances between dispersive and electrostatic forces used in these models. In particular, for the solvation of the highly polar (dipole moment of ∼5.2 Debye)...
Calcium chloride adsorption at liquid-liquid interfaces: A molecular dynamics simulation study
, Article Colloids and Surfaces A: Physicochemical and Engineering Aspects ; Volume 527 , 2017 , Pages 70-80 ; 09277757 (ISSN) ; Bahramian, A ; Chen, P ; Pourafshary, P ; Goddard, W.A., III ; Ejtehadi, M. R ; Sharif University of Technology
Abstract
We carried out molecular dynamics simulations (MD) to investigate the adsorption of calcium chloride (CaCl2) at n-hexane-water interfaces. We also measured the interfacial tensions (IFT) of the selected systems making use of the pendant-drop method. The histograms of hexane, water, and the ions indicate an electrical double layer (EDL) near the interface. The trend of the EDL indicates that chloride anions intend to adsorb to the interface more intrinsically than calcium cations. The measured interfacial width of the n-hexane-water interfaces decreases with the salt concentration. The average densities of the interfacial and bulk aqueous solutions demonstrate density heterogeneity in the...
An investigation on tensile properties of coiled carbon nanotubes using molecular dynamics simulation
, Article Diamond and Related Materials ; Volume 74 , 2017 , Pages 154-163 ; 09259635 (ISSN) ; Karimi Taheri, K ; Karimi Taheri, A ; Sharif University of Technology
Elsevier Ltd
2017
Abstract
A coiled carbon nanotube (CCNT) can be formed from the distortion of parent toroidal carbon nanotube with a uniform pitch length and a uniform spring rise angle. In this research molecular dynamics simulation was carried out to assess the tensile properties of three CCNT having indexes of (3,3), (4,4), and (5,5). The results indicated that Stone-Wales defects are necessary for thermodynamic stability of the CCNTs. The stress-strain curves showed that the yield stress, yield strain, and failure strain are decreased with increase in temperature. The force-displacement curves revealed that the spring constant of these materials is highly depended on the tube diameter and rising angle, while it...
Molecular dynamics simulations of orai reveal how the third transmembrane segment contributes to hydration and ca2+ selectivity in calcium release-activated calcium channels
, Article Journal of Physical Chemistry B ; Volume 122, Issue 16 , 2018 , Pages 4407-4417 ; 15206106 (ISSN) ; Berti, C ; Ejtehadi, M. R ; Furini, S ; Sharif University of Technology
American Chemical Society
2018
Abstract
Calcium release-activated calcium (CRAC) channels open upon depletion of Ca2+ from the endoplasmic reticulum, and when open, they are permeable to a selective flux of calcium ions. The atomic structure of Orai, the pore domain of CRAC channels, from Drosophila melanogaster has revealed many details about conduction and selectivity in this family of ion channels. However, it is still unclear how residues on the third transmembrane helix can affect the conduction properties of the channel. Here, molecular dynamics and Brownian dynamics simulations were employed to analyze how a conserved glutamate residue on the third transmembrane helix (E262) contributes to selectivity. The comparison...
A molecular-dynamics study of thermal and physical properties of platinum nanoclusters
, Article Fluid Phase Equilibria ; Volume 280, Issue 1-2 , 2009 , Pages 16-21 ; 03783812 (ISSN) ; Parsafar, G. A ; Sharif University of Technology
2009
Abstract
Metallic nanoclusters are interesting because of their utility in catalysis and sensors. The thermal and physical characteristics of metallic Pt nanoclusters with different sizes were investigated via molecular-dynamics simulations using Quantum Sutton-Chen (QSC) potential. This force field accurately predicts solid and liquid states properties as well as melting of the bulk platinum. Molecular dynamic simulations of Pt nanoclusters with 256, 456, 500, 864, 1372, 2048, 2916, 4000, 5324, 6912, 8788 atoms have been carried out at various temperatures. The Pt-Pt radial distribution function, internal energy, heat capacity, enthalpy, entropy of the nanoclusters were calculated at some...
GAG positioning on IL-1RI; A mechanism regulated by dual effect of glycosylation
, Article Glycobiology ; Volume 29, Issue 11 , 2019 , Pages 803-812 ; 14602423 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
NLM (Medline)
2019
Abstract
IL-1RI is the signaling receptor for the IL-1 family of cytokines that are involved in establishment of the innate and acquired immune systems. Glycosylated extracellular (EC) domain of the IL-1RI binds to agonist such as IL-1β or antagonist ligands and the accessory protein to form the functional signaling complex. Dynamics and ligand binding of the IL-1RI is influenced by presence of the glycosaminoglycans (GAGs) of the EC matrix. Here a combination of molecular dockings and molecular dynamics simulations of the unglycosylated, partially N-glycosylated and fully N-glycosylated IL-1RI EC domain in the apo, GAG-bound and IL-1β-bound states were carried out to explain the co-occurring...
Microscopic insight into kinetics of inorganic scale deposition during smart water injection using dynamic quartz crystal microbalance and molecular dynamics simulation
, Article Industrial and Engineering Chemistry Research ; Volume 59, Issue 2 , 2020 , Pages 609-619 ; Kargozarfard, Z ; Najafi, B ; Taghikhani, V ; Ayatollahi, S ; Sharif University of Technology
American Chemical Society
2020
Abstract
Inorganic scale deposition has been found to affect many industrial processes, including water injection into the oil reservoirs. The incompatibility of high sulfate ion content of seawater with formation water containing calcium ions results in formation damage and production decline. In this study, several simultaneous techniques are utilized for qualitative and quantitative analyses of calcium sulfate scale to get more insight into the formation damage during smart water flooding at micro and nanoscales. In the experimental section, calcium sulfate deposition due to the mixing of the formation water and seawater samples was investigated using the dynamic quartz crystal microbalance...
Enhancing water desalination in graphene-based membranes via an oscillating electric field
, Article Desalination ; Volume 495 , December , 2020 ; Moosavi, A ; Nouri Borujerdi, A ; Sharif University of Technology
Elsevier B.V
2020
Abstract
Water desalination methods on the basis of newly developed graphene-based membrane have been introduced as a more efficient alternative for the conventional water purification technologies such as classical thermal desalination and reverse osmosis (RO). However, the increase of water permeation rate and ion rejection are still the main subjects in this field. In this study, a new method based on using oscillating electric field is proposed to improve the performance of nanoporous graphene. The effects of the amplitude and oscillation frequency of the electric field and the pore size of the membrane on the water permeation and salt rejection are studied by conducting molecular dynamics...
Compatibilization of clays and hydrophobic polymers: the case of montmorillonite and polyetheretherketone
, Article Polymer Bulletin ; Volume 77, Issue 10 , 2020 , Pages 5505-5527 ; Akbari, B ; Mehrnejad, F ; Bagheri, R ; Sharif University of Technology
Springer
2020
Abstract
In the last three decades, nanoclay fillers have been increasingly used to improve the mechanical, thermal, barrier and biological properties of the polymers. Nevertheless, incorporation of clays into the hydrophobic polymer matrices leads to the formation of the microcomposites with the minimal improvement in properties. To overcome the intrinsic incompatibility between the clays and the hydrophobic polymers, clay particles are organophilized using organic modifiers. The organic modifier should be thermodynamically miscible with the polymer. In the case of the composites prepared at high temperatures, the organic modifier should also have a high thermal stability to withstand the processing...
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...
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) ; Jamali, Y ; Tajkhorshid, E ; Bavi, O ; Pishkenari, H. N ; Sharif University of Technology
Elsevier Ltd
2021
Abstract
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...
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...
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...