Search for: van-der-waals-interactions
Molecular dynamics simulation and MM-PBSA calculations of sickle cell hemoglobin in dimer form with Val, Trp, or Phe at the lateral contact, Article Journal of Physical Organic Chemistry ; Volume 23, Issue 9 , March , 2010 , Pages 866-877 ; 08943230 (ISSN) ; Akbarzadeh, H ; Parsafar, G. A ; Sharif University of Technology
As the delay time and hence nuclei formation play a crucial role in the pathophysiology of sickle cell disease, MD simulation and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) calculations have been performed on three systems of hemoglobin; namely dimer of hemoglobin with valine (Hb S), tryptophan (Hbβ6W), and phenylalanine (Hbβ6F) at β6 position. The structural changes due to these aromatic substitutions are investigated. It is shown that β subunits have significant impact on the differences between a dimer and other crystal structures. Transition from a dimer to polymer for Hb S system affects the donor molecule more than that of the acceptor. In the case of donor and...
The effects of geometrical parameters on force distributions and mechanics of carbon nanotubes: A critical study, Article Communications in Nonlinear Science and Numerical Simulation ; Volume 14, Issue 12 , 2009 , Pages 4246-4263 ; 10075704 (ISSN) ; Motevalli, B ; Sharif University of Technology
In this paper, using the continuum approximation together with Lennard-Jones potential, a new semi-analytical expression is given to evaluate the van der Waals interaction between two single-walled carbon nanotubes. Based on this expression, two new formulations are also proposed to model multi-walled carbon nanotubes. In the first one, the interactions between each pair of shells from the inner and outer tubes are summed up over all of the pairs, whereas in the second formulation, a set of correction factors are applied to convert the results of double-walled carbon nanotubes to the correlated multi-walled ones. With respect to the present formulations, extensive studies on the variations...
Article International Journal of Engineering Science ; Volume 44, Issue 17 , 2006 , Pages 1156-1163 ; 00207225 (ISSN) ; Naghdabadi, R ; Sharif University of Technology
In this paper, nanoscale modeling of a multi-shell fullerene embedded in an elastic medium and its application to vibrational analysis is investigated. The spherical layers of the multi-shell fullerene are concentrically nested, with carbon-carbon van der Waals interactions between them. Also, the whole multi-shell fullerene is influenced by polymer-carbon van der Waals forces from the surrounding elastic medium. The elasticity generated by the carbon-carbon bonds is assumed to be distributed isotropically over the fullerene surfaces. Following derivation of explicit equations for the motion of the multi-shell fullerene, vibrational behavior of a double-shell fullerene is analyzed and...
Investigation the stability of SWCNT-polymer composites in the presence of CNT geometrical defects using multiscale modeling, Article 4th International Conference on Multiscale Materials Modeling, MMM 2008, 27 October 2008 through 31 October 2008 ; 2008 , Pages 163-166 ; 9780615247816 (ISBN) ; Naghdabadi, R ; Sharif University of Technology
Department of Scientific Computing, Florida State University 2008
CNT-reinforced polymer composites have attracted attention due to their exceptional high strength. The high strength can be affected by the presence of defects in the nanotubes used as reinforcements in the practical nanocomposites. In this paper, a Molecular Structural Mechanics / Finite Element (MSM/FE) multiscale modeling is used to study the effect of carbon nanotube geometrical defects on the stability of SWCNT-polymer composites. Here, two types of representative volume elements (RVEs) for these nanocomposites are considered with perfect and defected CNT. These RVEs have the same dimensions. The nanotube is modeled at the atomistic scale using molecular structural mechanics whereas the...
Article Journal of Physics D: Applied Physics ; Volume 42, Issue 22 , 2009 ; 00223727 (ISSN) ; Alasty, A ; Sharif University of Technology
The structural instability of an array of cantilevers, each of which interacts with two neighbouring beams through electrostatic and van der Waals forces, is studied. Distributed and lumped parameter modelling of the array result in a set of coupled nonlinear boundary value problems and a set of coupled nonlinear equations, respectively. These coupled nonlinear systems are solved numerically for different numbers of beams in the array to obtain the pull-in parameters. The pull-in parameters converge to constant values with an increase in the number of beams in the array. These constants, which are important in the design of cantilever arrays, are compared for the distributed and lumped...
Study the effect of viscoelastic matrix model on the stability of CNT/polymer composites by multiscale modeling, Article Polymer Composites ; Volume 30, Issue 11 , 2009 , Pages 1545-1551 ; 02728397 (ISSN) ; Naghdabadi, R ; Sharif University of Technology
In this article, a Molecular Structural Mechanics/Finite Element (MSM/FE) multiscale modeling of carbon nanotube/polymer composites with viscoelastic (VE) polymer matrix is introduced. The nanotube is modeled at the atomistic scale using structural molecular mechanics. The matrix deformation is analyzed by nonlinear finite element method considering VE behavior. The nanotube and matrix are assumed to be bonded by van der Waals interactions based on the Lennard-Jones potential at the interface. Using the MSM/FE multiscale model, we investigate the effect of carbon nanotube (CNT) on the improvement of mechanical stability of the nanocomposite. Also, the buckling behavior of these...
Investigating the effect of carbon nanotube defects on the column and shell buckling of carbon nanotube-polymer composites using multiscale modeling, Article International Journal for Multiscale Computational Engineering ; Volume 7, Issue 5 , 2009 , Pages 431-444 ; 15431649 (ISSN) ; Naghdabadi, R ; Sharif University of Technology
Carbon nanotube (CNT)-reinforced polymer composites have attracted great attention due to their exceptionally high strength. Their high strength can be affected by the presence of defects in the nanotubes used as reinforcements in practical nanocomposites. In this article, a new three-phase molecular structural mechanics/finite element (MSM/FE) multiscale model is used to study the effect of CNT vacancy defects on the stability of single-wall (SW) CNT-polymer composites. The nanotube is modeled at the atomistic scale using MSM, whereas the interphase layer and polymer matrix are analyzed by the FE method. The nanotube and polymer matrix are assumed to be bonded by van der Waals interactions...
Investigation of the interphase effects on the mechanical behavior of carbon nanotube polymer composites by multiscale modeling, Article Journal of Applied Polymer Science ; Volume 117, Issue 1 , March , 2010 , Pages 361-367 ; 00218995 (ISSN) ; Naghdabadi, R ; Sharif University of Technology
In this article, a multiscale modeling procedure is implemented to study the effect of interphase on the Young's modulus of CNT/polymer composites. For this purpose, a three-phase RVE is introduced which consists of three components, i.e., a carbon nanotube, an interphase layer, and an outer polymer matrix. The nanotube is modeled at the atomistic scale using molecular structural mechanics. Moreover, three-dimensional elements are employed to model the interphase layer and polymer matrix. The nanotube and polymer matrix are assumed to be bonded by van der Waals interactions based on the Lennard-Jones potential at the interface. Using this Molecular Structural Mechanics/Finite Element...
Hybrid finite-element method-molecular dynamics approach for modelling of non-contact atomic force microscopy imaging, Article Micro and Nano Letters ; Volume 6, Issue 6 , June , 2011 , Pages 412-416 ; 17500443 (ISSN) ; Mahboobi, S. H ; Meghdari, A ; Sharif University of Technology
Models capable of accurate simulation of the microcantilever dynamics coupled with complex tip-sample interactions are essential for interpretation of the imaging results in non-contact atomic force microscopy (AFM). In the present research, a combination of finite element and molecular dynamics methods are used for modelling the AFM system to overcome the drawbacks of conventional approaches that use a lumped system with van der Waals interaction. To illustrate the ability of the proposed scheme in providing images with atomic resolution, some simulations have been performed. In the conducted simulations, a diamond tip is interacting with nickel samples having different surface plane...
Article Computational Materials Science ; Volume 69 , 2013 , Pages 335-343 ; 09270256 (ISSN) ; Moshrefzadeh Sani, H ; Sharif University of Technology
In this paper, the molecular structural mechanics method is employed to calculate the mechanical properties of a double-layered carbon graphene sheet more accurately. For this purpose, covalent bonds are modeled using nonlinear beam elements and van der Waals interactions are replaced by nonlinear truss elements. Morse potential and Lennard-Jones potential equations are used to simulate the covalent bonds and van der Waals interactions, respectively. For each atom, van der Waals forces are considered with respect to all the other atoms located in its cut-off radius. In addition to in-plane mechanical properties of single and double-layered graphene sheets some out-of-plane properties like...
Article Journal of the Royal Society Interface ; Volume 12, Issue 109 , 2015 ; 17425689 (ISSN) ; Mehrbod, M ; Ejtehadi, M. R ; Mofrad, M. R ; Sharif University of Technology
Royal Society of London 2015
von Willebrand factor (VWF) is a naturally collapsed protein that participates in primary haemostasis and coagulation events. The clotting process is triggered by the adsorption and conformational changes of the plasma VWFs localized to the collagen fibres found near the site of injury. We develop coarse-grained models to simulate the adsorption dynamics of VWF flowing near the adhesive collagen fibres at different shear rates and investigate the effect of factors such as interaction and cooperativity of VWFs on the success of adsorption events. The adsorption probability of a flowing VWF confined to the receptor field is enhanced when it encounters an adhered VWF in proximity to the...
A novel model for analysis of multilayer graphene sheets taking into account the interlayer shear effect, Article Meccanica ; Volume 53, Issue 11-12 , 2018 , Pages 3061-3082 ; 00256455 (ISSN) ; Asghari, M ; Sharif University of Technology
Springer Netherlands 2018
In this study, a multiplate shear model is developed for dynamic analysis of multilayer graphene sheets with arbitrary shapes considering the interlayer shear effect. By utilizing the model, then some free-vibration analysis is presented. According to the experimental results, the weak interlayer van der Waals interaction cannot maintain the integrity of carbon atoms in adjacent layers. Therefore, it is required that the interlayer shear effect is accounted to study multilayer graphene mechanical behavior. The governing differential equation of motion is derived for the multilayer graphene sheets utilizing a variational approach based on the Kirchhoff plate model. The essential and natural...
Analytical and molecular dynamics simulation approaches to study behavior of multilayer graphene-based nanoresonators incorporating interlayer shear effect, Article Applied Physics A: Materials Science and Processing ; Volume 124, Issue 2 , 2018 ; 09478396 (ISSN) ; Asghari, M ; Sharif University of Technology
Springer Verlag 2018
Analytical and molecular dynamics simulation approaches are used in this paper to study free-vibration behavior of multilayer graphene-based nanoresonators considering interlayer shear effect. According to experimental observations, the weak interlayer van der Waals interaction cannot maintain the integrity of carbon atoms in the adjacent layers. Hence, it is vital that the interlayer shear effect is taken into account to design and analyze multilayer graphene-based nanoresonators. The differential equation of motion and the general form of boundary conditions are first derived for multilayer graphene sheets with rectangular shape using the Hamilton’s principle. Then, by pursuing an...
Mechanistic understanding of the interactions between nano-objects with different surface properties and α-synuclein, Article ACS Nano ; Volume 13, Issue 3 , 2019 , Pages 3243-3256 ; 19360851 (ISSN) ; Hosseini, A ; Adeli, M ; Ejtehadi, M. R ; Christiansen, G ; Sahin, C ; Tu, Z ; Tavakol, M ; Dilmaghani Marand, A ; Nabipour, I ; Farzadfar, F ; Otzen, D. E ; Mahmoudi, M ; Hajipour, M. J ; Sharif University of Technology
American Chemical Society 2019
Aggregation of the natively unfolded protein α-synuclein (α-syn) is key to the development of Parkinson's disease (PD). Some nanoparticles (NPs) can inhibit this process and in turn be used for treatment of PD. Using simulation strategies, we show here that α-syn self-assembly is electrostatically driven. Dimerization by head-to-head monomer contact is triggered by dipole-dipole interactions and subsequently stabilized by van der Waals interactions and hydrogen bonds. Therefore, we hypothesized that charged nano-objects could interfere with this process and thus prevent α-syn fibrillation. In our simulations, positively and negatively charged graphene sheets or superparamagnetic iron oxide...
Article Physical Chemistry Chemical Physics ; Volume 23, Issue 10 , 2021 , Pages 5999-6008 ; 14639076 (ISSN) ; Zakertabrizi, M ; Habibnejad Korayem, A ; Carbone, P ; Esfandiar, A ; Shahsavari, R ; Sharif University of Technology
Royal Society of Chemistry 2021
Decoding behavioral aspects associated with the water molecules in confined spaces such as an interlayer space of two-dimensional nanosheets is key for the fundamental understanding of water-matter interactions and identifying unexpected phenomena of water molecules in chemistry and physics. Although numerous studies have been conducted on the behavior of water molecules in confined spaces, their reach stops at the properties of the planar ice-like formation, where van der Waals interactions are the predominant interactions and many questions on the confined space such as the possibility of electron exchange and excitation state remain unsettled. We used density functional theory and...