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#### Complex self-propelled rings: A minimal model for cell motility

, Article Soft Matter ; Volume 13, Issue 35 , 2017 , Pages 5865-5876 ; 1744683X (ISSN) ; Dehghani Ghahnaviyeh, S ; Nejat Pishkenari, H ; Auth, T ; Gompper, G ; Sharif University of Technology
Royal Society of Chemistry
2017

Abstract

Collective behavior of active matter is observed for self-propelled particles, such as vibrated disks and active Brownian particles, as well as for cytoskeletal filaments in motile cells. Here, a system of quasi two-dimensional penetrable self-propelled rods inside rigid rings is used to construct a complex self-propelled particle. The rods interact sterically with each other and with a stationary or mobile ring via a separation-shifted Lennard-Jones potential. They either have a sliding attachment to the inside of the ring at one of their ends, or can move freely within the ring confinement. We study the inner structure and dynamics of the mobile self-propelled rings. We find that these...

#### Calculation of effective pair potential via the volumetric data

, Article Phase Transitions ; Vol. 87, issue. 1 , 2014 , pp. 38-58 ; ISSN: 01411594 ; Parsafar, G ; Sharif University of Technology
Abstract

The concept of effective pair potential (EPP), in which medium effects and contribution of long-range interactions are added to near-neighbor pair interactions, is a useful tool to derive and calculate the thermodynamic quantities. It has been shown that the extended Lennard-Jones (12, 6, 3) potential is an accurate EPP for many systems. However, the parameters of this EPP are not known for any systems. We introduce a new approach to use experimental pvT data of a fluid to calculate its EPP parameters. Such calculation has been carried out for some fluids at some temperatures. Unlike the isolated pair potential, it has been shown that the parameters significantly vary with temperature. We...

#### Bidirectional water transport through non-straight carbon nanotubes

, Article Journal of Molecular Liquids ; Volume 276 , 2019 , Pages 39-46 ; 01677322 (ISSN) ; Moosavi, A ; Sharif University of Technology
Elsevier B.V
2019

Abstract

Natural nanochannels and those used for applied purposes are often several nanometers in diameter and have lengths up to micrometer scales. Since normally no pressure gradient, mechanical force or electrical field is exerted on fluids in these situations, the fluid flow within them is not single-file and can be bidirectional. For this reason, studying the behavior of bidirectional flows in the channels is of paramount importance. In this study, a comprehensive investigation on the straight and non-straight bidirectional water transfer through carbon nanotubes is conducted via extensive molecular dynamics simulations. The results indicate that by changing the length, the diameter and the...

#### Designing an intelligent controller for a molecular valve

, Article 2008 Proceedings of the ASME - 2nd International Conference on Integration and Commercialization of Micro and Nanosystems, MicroNano 2008, 3 June 2008 through 5 June 2008, Kowloon ; 2008 , Pages 195-201 ; 0791842940 (ISBN); 9780791842942 (ISBN) ; Alasty, A ; Sharif University of Technology
2008

Abstract

Too much effort has been done for manipulating individual atoms, using nano-manipulators and Scanning Tunneling Microscopes (STM). On the other hand, characterization and manipulation of nano-flows is of great concern. In the current work a molecular valve has been considered, which is made up of six atoms placed on the circumstance of a circle. A fuzzy controller has been designed for controlling the diameter of this molecular valve. The designed fuzzy controller used singleton fuzzifier, Mamdani inference engine, center average defuzzifier and exponential membership functions. A model based on the classical Molecular Dynamics (MD) is used for modeling the nano-system and passing the states...

#### 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

Abstract

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...

#### 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) ; Taghibakhshi, A ; Nejat Pishkenari, H ; Arghavani, J ; Sharif University of Technology
SAGE Publications Ltd
2021

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...

#### Influence of quantum effect on deviation from linear isotherm regularity

, Article Scientia Iranica ; Volume 19, Issue 3 , June , 2012 , Pages 555-560 ; 10263098 (ISSN) ; Parsafar, G. A ; Sharif University of Technology
2012

Abstract

A general regularity was found based on an effective pair potential of Lennard-Jones LJ (12, 6), for both dense, nonmetallic and nonionic fluids and solids according to which (Z-1) v2 linearly varies with respect to ρ2 for each isotherm, and this equation of state (EoS I) is known as LIR. However, despite the fact that Ne is a simple spherical species, unexpectedly, its solid and liquid phases both show a significant deviation from EoS I. In this work, we have investigated the accuracy of the EoS I for other systems, including quantum light molecules, such as D 2, H 2 and He, in both fluid and solid states at different temperatures. Like Ne, we have noticed that these systems do not well...

#### 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)...

#### 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
Abstract

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...

#### 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
2009

Abstract

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...

#### Simulation of heat transfer in nanoscale flow using molecular dynamics

, Article ASME 2010 8th International Conference on Nanochannels, Microchannels, and Minichannels Collocated with 3rd Joint US-European Fluids Engineering Summer Meeting, ICNMM2010, 1 August 2010 through 5 August 2010, Montreal, QC ; Issue PARTS A AND B , 2010 , Pages 1563-1568 ; 9780791854501 (ISBN) ; Abbasi, H. R ; Sabouri, M ; Khaledi Alidusti, R ; Sharif University of Technology
2010

Abstract

We investigate heat transfer between parallel plates separated by liquid argon using two-dimensional molecular dynamics (MD) simulations incorporating with 6-12 Lennard-Jones potential between molecule pairs. In molecular dynamics simulation of nanoscale flows through nanochannels, it is customary to fix the wall molecules. However, this approach cannot suitably model the heat transfer between the fluid molecules and wall molecules. Alternatively, we use thermal walls constructed from the oscillating molecules, which are connected to their original positions using linear spring forces. This approach is much more effective than the one which uses a fixed lattice wall modeling to simulate the...

#### 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
2010

Abstract

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...

#### 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
2009

Abstract

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...