Study of the Gating Mechanism of Mechanosensitive Membrane Channels

, M.Sc. Thesis Sharif University of Technology Rasouli, Ali (Author) ; Nejat Pishkenari, Hoessein (Supervisor) ; Zohour, Hassan (Supervisor) ; Jamali, Yousef (Co-Advisor)

Abstract

Mechanosensitive membrane channels are indispensable part of cells that sense and respond to mechanical signals. Hence, malfunction of these channels may cause various diseases. Despite numerous studies of these channels, there are still many unanswered questions surrounding these channels and their gating mechanism. Although there have been valuable experimental studies in this field, the need for modelling and computational studies are still felt since experiments face many limitations in this area. Thus, a channel that its crystallographic structure has been recently determined was chosen and studied using computational tools. In this study, gating of the channel under surface tension has...

Temperature dependence study of nonocontact AFM images using molecular dynamics simulations [electronic resource]

, Article Int. Journal of Modern Physics ; 2012, Vol. 5, pp. 418-432 Nejat Pishkenari, H. (Hossein) ; Meghdar, Ali ; Sharif University of Technology

Abstract

The effect of temperature on the noncontact atomic force microscopy (NC-AFM) surface imaging is investigated with the aid of molecular dynamics (MD) analysis based on the Sutton-Chen (SC) interatomic potential. Particular attention is devoted to the tip and sample flexibility at different temperatures. When a gold coated probe is brought close to the Au (001) surface at high temperatures, the tip and surface atoms are pulled together and their distance becomes smaller. The tip and sample atoms displacement varies in the different environment temperatures and this leads to the different interaction forces. Along this line, to study the effect of temperature on the resulting images, we have...

Investigation of the atomic-scale hysteresis in NC-AFM using atomistic dynamics

, Article Physica E: Low-Dimensional Systems and Nanostructures ; Volume 42, Issue 8 , 2010 , Pages 2069-2077 ; 13869477 (ISSN) Nejat Pishkenari, H ; Meghdari, A ; Sharif University of Technology

2010

Abstract

In this paper, the hysteresis in the tipsample interaction force in noncontact force microscopy (NC-AFM) is measured with the aid of atomistic dynamics simulations. The observed hysteresis in the interaction force and displacement of the system atoms leads to the loss of energy during imaging of the sample surface. Using molecular dynamics simulations it is shown that the mechanism of the energy dissipation occurs due to bistabilities caused by atomic jumps of the surface and tip atoms in the contact region. The conducted simulations demonstrate that when a gold coated nano-probe is brought close to the Au(0 0 1) surface, the tip apex atom jumps to the surface, and instantaneously, four...

Tip geometry effects in surface characterization with amplitude modulation AFM

, Article Scientia Iranica ; Volume 17, Issue 1 F , 2010 , Pages 27-34 ; 10263098 (ISSN) Nejat Pishkenari, H ; Meghdari, A ; Sharif University of Technology

2010

Abstract

In the present work, characterization of the surface trenches and vacancies with Amplitude Modulation AFM (AM-AFM) using Molecular Dynamics (MD) is simulated and the effects of the tip shape on the resulting images are investigated. The simulated system includes a recently developed gold coated AFM probe which interacts with a sample including a surface trench or a single-atom vacancy. In order to examine the behavior of the above system, including different transition metals, a Molecular Dynamics (MD) simulation with Sutton-Chen (SC) interatomic potential is used. Special attention is dedicated to the study of tip geometry effects such as the tip apex radius, the tip cone angle, the probe...

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) Nejat Pishkenari, H ; 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...

Characterization of silicon surface elastic constants based on different interatomic potentials

, Article Thin Solid Films ; Volume 626 , 2017 , Pages 104-109 ; 00406090 (ISSN) Nejat Pishkenari, H ; Rezaei, S ; Sharif University of Technology

2017

Abstract

Mechanical properties of materials are an important factor in designing nanoscale systems. Several researches and experiments have shown that the mechanical properties of the nano-scale materials are different from those of bulk. One of the major reasons for this difference is that the ratio of surface to volume increases at the nano-scale, and the effects of free surfaces become very important. In this paper, we have measured the surface elastic constants of silicon crystalline structure using different interatomic potentials. The potentials employed here are EDIP (Environment-Dependent Interatomic Potential), Stillinger-Weber and Tersoff, and also different crystalline orientations are...

A novel computer-oriented dynamical approach with efficient formulations for multibody systems including ignorable coordinates

, Article Applied Mathematical Modelling ; Volume 62 , 2018 , Pages 461-475 ; 0307904X (ISSN) Nejat Pishkenari, H ; Heidarzadeh, S ; Sharif University of Technology

Elsevier Inc 2018

Abstract

Based on Lagrangian mechanics, we present a novel and computationally efficient set of equations of motion in the matrix notation, for unconstrained or constrained mechanical systems including ignorable coordinates. The equations are applicable to multibody systems including holonomic or nonholonomic constraints. It is shown that by appropriate selection of generalized speeds as a new set of motion variables, the constraint reaction forces can be automatically eliminated from the set of developed reduced dynamical equations in a straightforward manner, resulting in a minimal set of dynamic equations. We present simulation results on one constrained and one unconstrained system to demonstrate...

A temperature-calibrated continuum model for vibrational analysis of the fullerene family using molecular dynamics simulations

, Article Applied Mathematical Modelling ; Volume 80 , April , 2020 , Pages 115-125 Nejat Pishkenari, H ; Golzari, A ; Sharif University of Technology

Elsevier Inc 2020

Abstract

In the present study, a model was proposed to determine the elastic properties of the family of fullerenes at different temperatures (between 300 and 2000 K) using a combination of molecular dynamics simulation and continuum shell theory. The fullerenes molecules examined here are eight spherical fullerenes, including C60, C80, C180, C240, C260, C320, C500, and C720. First, the breathing mode frequency and the radius of gyration of the molecules were obtained at different temperatures by molecular dynamics simulations using AIREBO potential. Then, these data were used in a continuum model to obtain the elastic coefficients of these closed clusters of carbon in terms of temperature changes....

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

Abstract

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...

Adaptive backstepping control of uncertain lorenz system

, Article Proceeding of the 5th International Symposium on Mechatronics and its Applications, ISMA 2008, 27 May 2008 through 29 May 2008, Amman ; 2008 ; 9781424420346 (ISBN) Nejat Pishkenari, H ; Meghdari, A ; Sharif University of Technology

2008

Abstract

In this paper, a novel robust adaptive control method is proposed for controlling the well-known Lorenz chaotic attractor. Firstly, we design a new Backstepping controller for controlling the Lorenz system based on the Lyapunov stability theorem. The proposed method is different from the typical Backstepping control method and it can overcome the singularity problem appeared in using the typical Backstepping control method. So by exploiting the property of the system, the resulting controller is singularity free and the closed-loop system is stable globally. Since in practice we have not access to full information of the system states, we set the controller parameters in order to achieve a...

Optimal motion control of three-sphere based low-Reynolds number swimming microrobot

, Article Robotica ; Volume 40, Issue 5 , 2022 , Pages 1257-1273 ; 02635747 (ISSN) Nejat Pishkenari, H ; Mohebalhojeh, M ; Sharif University of Technology

Cambridge University Press 2022

Abstract

Microrobots with their promising applications are attracting a lot of attention currently. A microrobot with a triangular mechanism was previously proposed by scientists to overcome the motion limitations in a low-Reynolds number flow; however, the control of this swimmer for performing desired manoeuvres has not been studied yet. Here, we have proposed some strategies for controlling its position. Considering the constraints on arm lengths, we proposed an optimal controller based on quadratic programming. The simulation results demonstrate that the proposed optimal controller can steer the microrobot along the desired trajectory as well as minimize fluctuations of the actuators length. ©...

Simulation of imaging in tapping-mode atomic-force microscopy: a comparison amongst a variety of approaches

, Article Journal of Physics D: Applied Phyics ; Vol.44, Number 7, p.1-9, 2011 Nejat Pishkenari, H ; Mahboobi, S. H ; Meghdari, A. (Ali) ; Sharif University of Technology

Abstract

Models capable of accurate simulation of microcantilever dynamics coupled with complex tip–sample interactions are essential for interpretation and prediction of the imaging results in amplitude modulation or tapping-mode atomic-force microscopy (AM-AFM or TM-AFM). In this paper, four approaches based on combinations of lumped and finite element methods for modelling of cantilever dynamics, and van der Waals and molecular dynamics for modelling of tip–sample interactions, are used to simulate the precise imaging by AM-AFM. Based on the simulated imaging and force determination, the efficiency of different modelling schemes is evaluated. This comparison is performed considering their...

Vibrational properties of C60: A comparison among different inter-atomic potentials

, Article Computational Materials Science ; Volume 122 , 2016 , Pages 38-45 ; 09270256 (ISSN) Nejat Pishkenari, H ; Ghaf Ghanbari, P ; Sharif University of Technology

Elsevier 2016

Abstract

Using seven bond-order potentials and five force fields, the fundamental natural frequency of C60,Ag(1) (breathing mode), and two other basic modes, namely Hg(1) (squashing mode) and T2g(1) are calculated. The same frequencies are derived through a DFT B3LYP/6-31G(d) calculation. Furthermore, the results are compared with Raman and IR scattering data, and previous quantum mechanics calculations, depicting the strength of each interatomic potential in predicting the vibrational properties of Buckminsterfullerene. AIREBO, which is formulated for analyzing hydrocarbons, shows the highest accuracy among all of the potentials under investigation. In general, bond-order potentials predict a...

Simulations of surface defects characterization using force modulation atomic force microscopy

, Article Proceedings of the ASME International Design Engineering Technical Conferences and Computers and Information in Engineering Conference 2009, DETC2009, 30 August 2009 through 2 September 2009 ; Volume 6 , August–September , 2010 , Pages 681-687 ; 9780791849033 (ISBN) Nejat Pishkenari, H ; Meghdari, A. M ; Sharif University of Technology

2010

Abstract

This paper is devoted to the characterization of the surface defects using a recently developed AFM technique named as 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 including different transition metals, molecular dynamics (MD) simulation with Sutton-Chen (SC) interatomic potential is used. Along this line, an 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...

Simulations of surface defects characterization using force modulation atomic force microscopy

, Article Proceedings of the ASME Design Engineering Technical Conference, 30 August 2009 through 2 September 2009, San Diego, CA ; Volume 6 , 2009 , Pages 681-687 ; 9780791849033 (ISBN) Nejat Pishkenari,H. N ; Meghdari, A ; Sharif University of Technology

2009

Abstract

This paper is devoted to the characterization of the surface defects using a recently developed AFM technique named as 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 including different transition metals, molecular dynamics (MD) simulation with Sutton-Chen (SC) interatomic potential is used. Along this line, an 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...

Vibrational analysis of the fullerene family using tersoff potential

, Article Current Applied Physics ; Volume 17, Issue 1 , 2017 , Pages 72-77 ; 15671739 (ISSN) Nejat Pishkenari, H ; Ghaf Ghanbari, P ; Sharif University of Technology

2017

Abstract

Using Tersoff bond order potential, a vibrational analysis of the spherical fullerene family, namely C60, C80, C180, C240, C260, C320, C500, and C720 was performed. To evaluate the validity of our results, we have compared our simulation results with available experimental data and also with DFT B3LYP/6-31G(d) calculations. In general, molecular stiffness tends to decrease with increasing size, but its variation is limited in cases where mostly the tension-compression interaction sites are active such as the breathing mode. Furthermore, the bond length of each molecule is derived and compared with experimental and theoretical values calculated for graphene. Finally, vibrational frequencies...

Molecular Dynamics Simulation of the Dynamic Behavior of Nanoresonators

, M.Sc. Thesis Sharif University of Technology Afsharmanesh, Bahram (Author) ; Nejat Pishkenari, Hossein (Supervisor)

Abstract

In this project, the equilibrium structure of clamped-free silicon nano-beams is investigated using molecular dynamics (MD) simulations. Four main interatomic potentials for silicon nanostructures, i.e. Tersoff, MEAM, Stillinger-Weber and EDIP, are implemented in the current study. Using aforementioned potentials, the structural stability of Si nano-beams are studied and effects of thickness, width, length, size, lattice direction, facets of cross section, and temperature on the equilibrium structure of nano-beams are investigated. The conducted simulations demonstrate that equilibrium structure of nano-beam is completely dependent on the type of atomic potential used for modeling....

Modeling of Force Interactions between Tip of Atomic Force Microscopy in Trolling Mode and Environment

, M.Sc. Thesis Sharif University of Technology Falsafi, Ali (Author) ; Nejat Pishkenari, Hossein (Supervisor)

Abstract

Submerging of the Micro-beam of the AFM is indispensible in case of imaging bio-samples. (Bio-samples are unstable in non-aquos environment.), so hydrodynamical interaction of liquid and beam (viscous and meniscus forces) will result into quality factor decrease. This will cause image resolution decrement as well as damage to the sample because of large tip-sample forces during imaging of the bio-samples. The proposed method “Trolling mode AFM” keeps the micro-beam of the AFM out of the liquid, by adding a nano-needle to the end of the AFM tip. This would lead to resolve the aforementioned problems. Modeling of a part of the operation of this mechanism was done in this thesis, in order to...

A Fabrication Method of Neutrally-buoyant Magnetic Micro-robot to Improve Its Motion Control

, M.Sc. Thesis Sharif University of Technology Pedram, Alireza (Author) ; Nejat Pishkenari, Hossein (Supervisor)

Abstract

Micro-robotics is one of the currently emerging technologies which has attracted attentions for its probable applications in different fields including biotechnology, diagnosis and treatment in medical engineering as well as general studies in micro-scale science and engineering. Magnetic micro-robotics is considered as the most promising group, primarily due to the biocompatibility of magnetic fields and advances in electronic circuits to produce and control such fields. One critical point in utilizing these robots is their high density in comparison with the working fluid and their tendency to sink. In this thesis, a method to fabricate buoyant magnetic robots has been proposed based on...

Completion of Electromagnetic System and Design of Robust Controller to Control the Movement of Micro-robots in Three-Dimensional Space

, M.Sc. Thesis Sharif University of Technology Feyzi, Ramin (Author) ; Nejat Pishkenari, Hossein (Supervisor)

Abstract

Today, the need to access very small environments is felt in various medical, industrial, biological and military fields. Due to their small size, microrobots have the ability to perform tasks that would be very difficult to do on a larger scale, but this ability of microrobots makes feeding and controlling them challenging. There are several methods for providing power and control of microrobots, which include their internal or external stimulation, among which the magnetic stimulation method is used in this research, which does not cause damage to body tissues.In this thesis, an electromagnetic system with nine cylindrical coils is used to control the three-dimensional movement of magnetic...