Hanif Mahboobi - Profile on Academia.edu (original) (raw)

Papers by Hanif Mahboobi

Research paper thumbnail of Computational Study of Binding Between DDX3 and Hiv-1 MRNA Nucleocytoplasmic Export Complex

Computational Study of Binding Between DDX3 and Hiv-1 MRNA Nucleocytoplasmic Export Complex

Biophysical Journal, 2014

Research paper thumbnail of Robust adaptive backstepping control of uncertain Lorenz system

… Journal of Nonlinear …, Jan 1, 2010

In this paper, a novel robust adaptive control method is proposed for controlling the Lorenz chao... more In this paper, a novel robust adaptive control method is proposed for controlling the Lorenz chaotic attractor. A new backstepping controller for the Lorenz system based on the Lyapunov stability theorem is proposed to overcome the singularity problem that appeared in using the typical backstepping control method. By exploiting the property of the system, the resulting controller is shown to be singularity free and the closed loop system is globally stable. Due to unavailability of system states measurement in practice, the controller is selected such that only one system state is needed.

Research paper thumbnail of Robust adaptive backstepping control of uncertain Lorenz system

Chaos: An Interdisciplinary Journal of Nonlinear Science, 2010

In this paper, a novel robust adaptive control method is proposed for controlling the Lorenz chao... more In this paper, a novel robust adaptive control method is proposed for controlling the Lorenz chaotic attractor. A new backstepping controller for the Lorenz system based on the Lyapunov stability theorem is proposed to overcome the singularity problem that appeared in using the typical backstepping control method. By exploiting the property of the system, the resulting controller is shown to be singularity free and the closed loop system is globally stable. Due to unavailability of system states measurement in practice, the controller is selected such that only one system state is needed.

Research paper thumbnail of Qualitative study of nanocluster positioning process: Planar molecular dynamics simulations

Current Applied Physics, 2009

One of the key factors in the assembly of nanoclusters is the precise positioning of them by a ma... more One of the key factors in the assembly of nanoclusters is the precise positioning of them by a manipulation system. Currently the size of clusters used as building blocks is shrinking down to a few nanometers. In such cases, the particle nature of matter plays an important role in the manipulator/cluster/substrate interactions. Having a deeper insight to the aforementioned nano-scale interactions is crucial for prediction and understanding of the behavior of nanoclusters during the positioning process. In the present research, 2D molecular dynamics simulations have been used to investigate such behaviors. Performing planar simulations can provide a fairly acceptable qualitative tool for our purpose while the computation time is greatly reduced in comparison to 3D simulations. The system consists of a tip, cluster and substrate. The focus of the present research is on ultra-fine metallic nanoclusters. To perform this research, Nose-Hoover dynamics and Sutton-Chen interatomic potential will be used to investigate the behavior of the above system which is made from different transition metals. The effects of material type, tip form and manipulation strategy on the success of the process have been investigated by planar molecular dynamics. Such qualitative simulation studies can evaluate the chance of success of a certain nanopositioning scenario regarding different working conditions before consuming large-scale computation time or high experimental expenses.

Research paper thumbnail of Molecular dynamics study of ‘success evaluation’ for metallic nanoparticles manipulation on gold substrate

Molecular dynamics study of ‘success evaluation’ for metallic nanoparticles manipulation on gold substrate

Micro & Nano Letters, 2010

... 1Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran ... more ... 1Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran 2Center of Excellence in Design, Robotics and Automation, School of Mechanical Engineering, Sharif University of Technology, Tehran, Iran 3Piezoactive Systems Laboratory ...

Research paper thumbnail of TWO-DIMENSIONAL ATOMISTIC SIMULATION OF METALLIC NANOPARTICLES PUSHING

TWO-DIMENSIONAL ATOMISTIC SIMULATION OF METALLIC NANOPARTICLES PUSHING

Modern Physics Letters B, 2009

Nanomanipulation as a new emerging area enables precise manipulation, interaction and control at ... more Nanomanipulation as a new emerging area enables precise manipulation, interaction and control at the nanoscale. Currently, the modeling schemes are based on continuum mechanics approaches. A main consideration in the nanomanipulation process is the fact that ...

Research paper thumbnail of Planar Molecular Dynamics Simulation of Metallic Nanoparticles Manipulation

Planar Molecular Dynamics Simulation of Metallic Nanoparticles Manipulation

2008 8th IEEE Conference on Nanotechnology, 2008

The aim of this research is to conduct atomistic investigations of physical interaction analysis ... more The aim of this research is to conduct atomistic investigations of physical interaction analysis of nanoscale objects manipulation. The system consists of tip, particle and substrate. The manipulation tool moves with a constant speed while pushing the particle in a desired direction. The focus of the research is on ultra-fine metallic nanoparticles. To perform this research, Nose-Hoover dynamics and Sutton-Chen

Research paper thumbnail of Qualitative Study of Nanoassembly Process: 2-D Molecular Dynamics Simulations

Precise positioning of nanoclusters through manipulation in the presence of other clusters is one... more Precise positioning of nanoclusters through manipulation in the presence of other clusters is one of the main challenging tasks in nanoclusters assembly. Currently, the size of clusters which are used as building blocks is decreasing to a few nanometers. As a result, the particle nature of the matter has a crucial role in manipulator/cluster/substrate interactions. In order to understand and predict the behavior of nanoclusters during the positioning process, it is, therefore, essential to have a deep insight into the aforementioned nanoscale interactions. In this research, 2-D molecular dynamics simulations are used to investigate such behaviors. Performing the planar simulations can provide a rather satisfactory qualitative instrument for our aim while the computation time is considerably decreased in comparison with 3-D simulations. The system considered here is made up of a tip, two clusters and a substrate. The main focus here is on metallic nanoclusters. In order to study the behavior of the above system which is made up of di erent transition metals, Nose-Hoover dynamics and Sutton-Chen interatomic potential are used. Furthermore, the e ect of the material characteristics, tip form and manipulation scheme on the success of the process are examined. Such qualitative simulation studies can pave the pathway towards certain nanopositioning scenarios when considering di erent working conditions before consuming largescale computation time or high experimental expenses.

Research paper thumbnail of Precise positioning and assembly of metallic nanoclusters as building blocks of nanostructures: A molecular dynamics study

Molecular dynamics simulations are used to study the manipulation of metallic nanoclusters. These... more Molecular dynamics simulations are used to study the manipulation of metallic nanoclusters. These particles are assumed as potential building blocks for bottom-up manufacturing of nanoscale structures. One of the key factors in the assembly of nanoclusters is the precise positioning of them by a manipulation system. Prediction of the corresponding behavior under the influence of working conditions is of crucial importance for planning of controlled positioning and assembly of nanoclusters. The focus of the present research is on ultra-fine metallic nanoclusters. The effects of material type and manipulation strategy on the success of the process have been investigated by molecular dynamics. Such qualitative simulation studies can evaluate the chance of success of a certain nanopositioning scenario regarding different working conditions before consuming high experimental expenses.

Research paper thumbnail of Planar molecular dynamics simulation of Au clusters in pushing process

International Journal of Nanomanufacturing, 2010

Based on the fact that the manipulation of fine nanoclusters calls for more precise modelling, th... more Based on the fact that the manipulation of fine nanoclusters calls for more precise modelling, the aim of this paper is to conduct an atomistic investigation for interaction analysis of particle-substrate system for pushing and positioning purposes. In the present research, 2D molecular dynamics simulations have been used to investigate such behaviours. Performing the planar simulations can provide a fairly acceptable qualitative tool for our purpose while the computation time is reduced extremely in comparison to 3D simulations. To perform this study, Nose-Hoover dynamics and Sutton-Chen interatomic potential will be used to investigate the behaviour of the aforementioned system. Pushing of Au clusters on Au substrate has been chosen as illustrative examples. Dependency of the aforementioned behaviour on temperature has been investigated. Higher temperature affects the pushing success level considerably. In addition, the simulation was performed for Ag cluster as well to compare the performance to one for Au cluster.

Research paper thumbnail of Precise positioning and assembly of metallic nanoclusters as building blocks of nanostructures: A molecular dynamics study

Physica E: Low-dimensional Systems and Nanostructures, 2009

Molecular dynamics simulations are used to study the manipulation of metallic nanoclusters. These... more Molecular dynamics simulations are used to study the manipulation of metallic nanoclusters. These particles are assumed as potential building blocks for bottom-up manufacturing of nanoscale structures. One of the key factors in the assembly of nanoclusters is the precise positioning of them by a manipulation system. Prediction of the corresponding behavior under the influence of working conditions is of crucial importance for planning of controlled positioning and assembly of nanoclusters. The focus of the present research is on ultra-fine metallic nanoclusters. The effects of material type and manipulation strategy on the success of the process have been investigated by molecular dynamics. Such qualitative simulation studies can evaluate the chance of success of a certain nanopositioning scenario regarding different working conditions before consuming high experimental expenses.

Research paper thumbnail of On the optimum design of fuzzy logic controller for trajectory tracking using evolutionary algorithms

Differential Evolution (DE) and Genetic Algorithms (GA) are population based search algorithms th... more Differential Evolution (DE) and Genetic Algorithms (GA) are population based search algorithms that come under the category of evolutionary optimization techniques. In the present study, these evolutionary methods have been utilized to conduct the optimum design of the fuzzy controller for mobile robot trajectory tracking. Comparison between their performances has also been conducted. In this paper we will present a fuzzy controller to the problem of mobile robot path tracking for the CEDRA rescue robot with a complicated kinematical model. After designing the fuzzy tracking controller, the membership functions will be optimized by evolutionary algorithms in order to obtain more acceptable results.

Research paper thumbnail of Actin Reorganization through Dynamic Interactions with Single-Wall Carbon Nanotubes

ACS Nano, 2014

Single-wall carbon nanotubes (SWCNTs) have been widely used for biological applications in recent... more Single-wall carbon nanotubes (SWCNTs) have been widely used for biological applications in recent years, and thus, it is critical to understand how these inert nanomaterials influence cell behavior. Recently, it has been observed that cellular phenotypes such as proliferation, force generation and growth change upon SWCNT treatment, and SWCNTs directly affect the organization and redistribution of the actin cytoskeleton. However, the interactions between SWCNTs and actin at the molecular level or how this interaction changes actin structure remain largely unknown. Here, we investigated direct interaction of actin with SWCNT using all-atom molecular dynamics simulations and NIR spectroscopy of actin-dispersed SWCNTs. Actin can stably bind to the SWCNT surfaces via hydrophobic interactions but still allows nanotubes to slide and rotate on the actin surface. Our results establish several nanoscale conformational changes for the actinÀSWCNT complexes, and we suggest these changes likely induce reorganization of actin filaments observed at larger scales.

Research paper thumbnail of Adaptive regulation and set-point tracking of the Lorenz attractor

Adaptive regulation and set-point tracking of the Lorenz attractor

Chaos Solitons & Fractals, 2007

In this paper, an approach is proposed for controlling the uncertain Lorenz system. Based on an i... more In this paper, an approach is proposed for controlling the uncertain Lorenz system. Based on an identification technique, a controller is designed that guarantees the regulation of all states in the presence of system uncertainty. Since in some applications the challenging problem of output tracking is desired, we have proposed several effective set-point tracking control techniques. The control schemes that

Research paper thumbnail of Precise positioning and assembly of metallic nanoclusters as building blocks of nanostructures: A molecular dynamics study

Physica E-low-dimensional Systems & Nanostructures, 2009

Molecular dynamics simulations are used to study the manipulation of metallic nanoclusters. These... more Molecular dynamics simulations are used to study the manipulation of metallic nanoclusters. These particles are assumed as potential building blocks for bottom-up manufacturing of nanoscale structures. One of the key factors in the assembly of nanoclusters is the precise positioning of them by a manipulation system. Prediction of the corresponding behavior under the influence of working conditions is of crucial importance for planning of controlled positioning and assembly of nanoclusters. The focus of the present research is on ultra-fine metallic nanoclusters. The effects of material type and manipulation strategy on the success of the process have been investigated by molecular dynamics. Such qualitative simulation studies can evaluate the chance of success of a certain nanopositioning scenario regarding different working conditions before consuming high experimental expenses.

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

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

Journal of Physics D-applied Physics, 2011

Models capable of accurate simulation of microcantilever dynamics coupled with complex tip-sample... more 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 coincidence with the realistic behaviour of AM-AFM in imaging of nanoscale features. In the conducted simulations, a diamond tip is used to scan a C60 molecule absorbed on a graphite substrate. The effects of amplitude set-point, cantilever stiffness and quality factor on the accuracy of different modelling approaches are studied.

Research paper thumbnail of Observer-based control design for three well-known chaotic systems

Observer-based control design for three well-known chaotic systems

Chaos Solitons & Fractals, 2006

In this paper, a singularity-free approach is proposed for controlling three well-known chaotic s... more In this paper, a singularity-free approach is proposed for controlling three well-known chaotic systems namely Lorenz, Chen and Lu. The control design guarantees the regulation of two states and boundedness of the remaining state. The stability of the proposed scheme has been shown using the Lyapunov stability theorem. Implementation of the proposed control technique requires system states, while in most

Research paper thumbnail of Molecular dynamics simulation of manipulation of metallic nanoclusters on stepped surfaces

Central European Journal of Physics, 2011

Molecular dynamics simulations are carried out to investigate the manipulation of metallic cluste... more Molecular dynamics simulations are carried out to investigate the manipulation of metallic clusters on stepped surfaces. Five surface forms are considered in the simulations. The system parts are made of pure transition metals and Sutton-Chen many-body potential is used as interatomic potential. The conditions which are subjected to change in the tests include: materials used for particles and substrate, and surface step conditions. In addition to qualitative observations, two criteria which represent the particle deformation and substrate abrasion are utilized as evaluation tools and are computed for each case. Simulation results show the effect of the aforementioned working conditions on the particle behavior as well as changes in the pushing forces. Obtaining this sort of knowledge is highly beneficial for further experiments in order to be able to plan the conditions and routines which guarantee better success in the manipulation process.

Research paper thumbnail of Observer-based control design for three well-known chaotic systems

Observer-based control design for three well-known chaotic systems

Chaos Solitons & Fractals, 2006

In this paper, a singularity-free approach is proposed for controlling three well-known chaotic s... more In this paper, a singularity-free approach is proposed for controlling three well-known chaotic systems namely Lorenz, Chen and Lu. The control design guarantees the regulation of two states and boundedness of the remaining state. The stability of the proposed scheme has been shown using the Lyapunov stability theorem. Implementation of the proposed control technique requires system states, while in most of practical applications only the system output is available. To overcome this problem, a nonlinear observer is coupled with the controller. Simulation results have illustrated the effectiveness and robustness of the proposed schemes. If the control action is applied to the second system equation, all states will be regulated.

Research paper thumbnail of Qualitative study of nanocluster positioning process: Planar molecular dynamics simulations

Current Applied Physics, 2009

One of the key factors in the assembly of nanoclusters is the precise positioning of them by a ma... more One of the key factors in the assembly of nanoclusters is the precise positioning of them by a manipulation system. Currently the size of clusters used as building blocks is shrinking down to a few nanometers. In such cases, the particle nature of matter plays an important role in the manipulator/cluster/substrate interactions. Having a deeper insight to the aforementioned nano-scale interactions is crucial for prediction and understanding of the behavior of nanoclusters during the positioning process. In the present research, 2D molecular dynamics simulations have been used to investigate such behaviors. Performing planar simulations can provide a fairly acceptable qualitative tool for our purpose while the computation time is greatly reduced in comparison to 3D simulations. The system consists of a tip, cluster and substrate. The focus of the present research is on ultra-fine metallic nanoclusters. To perform this research, Nose–Hoover dynamics and Sutton–Chen interatomic potential will be used to investigate the behavior of the above system which is made from different transition metals. The effects of material type, tip form and manipulation strategy on the success of the process have been investigated by planar molecular dynamics. Such qualitative simulation studies can evaluate the chance of success of a certain nanopositioning scenario regarding different working conditions before consuming large-scale computation time or high experimental expenses.

Research paper thumbnail of Computational Study of Binding Between DDX3 and Hiv-1 MRNA Nucleocytoplasmic Export Complex

Computational Study of Binding Between DDX3 and Hiv-1 MRNA Nucleocytoplasmic Export Complex

Biophysical Journal, 2014

Research paper thumbnail of Robust adaptive backstepping control of uncertain Lorenz system

… Journal of Nonlinear …, Jan 1, 2010

In this paper, a novel robust adaptive control method is proposed for controlling the Lorenz chao... more In this paper, a novel robust adaptive control method is proposed for controlling the Lorenz chaotic attractor. A new backstepping controller for the Lorenz system based on the Lyapunov stability theorem is proposed to overcome the singularity problem that appeared in using the typical backstepping control method. By exploiting the property of the system, the resulting controller is shown to be singularity free and the closed loop system is globally stable. Due to unavailability of system states measurement in practice, the controller is selected such that only one system state is needed.

Research paper thumbnail of Robust adaptive backstepping control of uncertain Lorenz system

Chaos: An Interdisciplinary Journal of Nonlinear Science, 2010

In this paper, a novel robust adaptive control method is proposed for controlling the Lorenz chao... more In this paper, a novel robust adaptive control method is proposed for controlling the Lorenz chaotic attractor. A new backstepping controller for the Lorenz system based on the Lyapunov stability theorem is proposed to overcome the singularity problem that appeared in using the typical backstepping control method. By exploiting the property of the system, the resulting controller is shown to be singularity free and the closed loop system is globally stable. Due to unavailability of system states measurement in practice, the controller is selected such that only one system state is needed.

Research paper thumbnail of Qualitative study of nanocluster positioning process: Planar molecular dynamics simulations

Current Applied Physics, 2009

One of the key factors in the assembly of nanoclusters is the precise positioning of them by a ma... more One of the key factors in the assembly of nanoclusters is the precise positioning of them by a manipulation system. Currently the size of clusters used as building blocks is shrinking down to a few nanometers. In such cases, the particle nature of matter plays an important role in the manipulator/cluster/substrate interactions. Having a deeper insight to the aforementioned nano-scale interactions is crucial for prediction and understanding of the behavior of nanoclusters during the positioning process. In the present research, 2D molecular dynamics simulations have been used to investigate such behaviors. Performing planar simulations can provide a fairly acceptable qualitative tool for our purpose while the computation time is greatly reduced in comparison to 3D simulations. The system consists of a tip, cluster and substrate. The focus of the present research is on ultra-fine metallic nanoclusters. To perform this research, Nose-Hoover dynamics and Sutton-Chen interatomic potential will be used to investigate the behavior of the above system which is made from different transition metals. The effects of material type, tip form and manipulation strategy on the success of the process have been investigated by planar molecular dynamics. Such qualitative simulation studies can evaluate the chance of success of a certain nanopositioning scenario regarding different working conditions before consuming large-scale computation time or high experimental expenses.

Research paper thumbnail of Molecular dynamics study of ‘success evaluation’ for metallic nanoparticles manipulation on gold substrate

Molecular dynamics study of ‘success evaluation’ for metallic nanoparticles manipulation on gold substrate

Micro & Nano Letters, 2010

... 1Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran ... more ... 1Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran 2Center of Excellence in Design, Robotics and Automation, School of Mechanical Engineering, Sharif University of Technology, Tehran, Iran 3Piezoactive Systems Laboratory ...

Research paper thumbnail of TWO-DIMENSIONAL ATOMISTIC SIMULATION OF METALLIC NANOPARTICLES PUSHING

TWO-DIMENSIONAL ATOMISTIC SIMULATION OF METALLIC NANOPARTICLES PUSHING

Modern Physics Letters B, 2009

Nanomanipulation as a new emerging area enables precise manipulation, interaction and control at ... more Nanomanipulation as a new emerging area enables precise manipulation, interaction and control at the nanoscale. Currently, the modeling schemes are based on continuum mechanics approaches. A main consideration in the nanomanipulation process is the fact that ...

Research paper thumbnail of Planar Molecular Dynamics Simulation of Metallic Nanoparticles Manipulation

Planar Molecular Dynamics Simulation of Metallic Nanoparticles Manipulation

2008 8th IEEE Conference on Nanotechnology, 2008

The aim of this research is to conduct atomistic investigations of physical interaction analysis ... more The aim of this research is to conduct atomistic investigations of physical interaction analysis of nanoscale objects manipulation. The system consists of tip, particle and substrate. The manipulation tool moves with a constant speed while pushing the particle in a desired direction. The focus of the research is on ultra-fine metallic nanoparticles. To perform this research, Nose-Hoover dynamics and Sutton-Chen

Research paper thumbnail of Qualitative Study of Nanoassembly Process: 2-D Molecular Dynamics Simulations

Precise positioning of nanoclusters through manipulation in the presence of other clusters is one... more Precise positioning of nanoclusters through manipulation in the presence of other clusters is one of the main challenging tasks in nanoclusters assembly. Currently, the size of clusters which are used as building blocks is decreasing to a few nanometers. As a result, the particle nature of the matter has a crucial role in manipulator/cluster/substrate interactions. In order to understand and predict the behavior of nanoclusters during the positioning process, it is, therefore, essential to have a deep insight into the aforementioned nanoscale interactions. In this research, 2-D molecular dynamics simulations are used to investigate such behaviors. Performing the planar simulations can provide a rather satisfactory qualitative instrument for our aim while the computation time is considerably decreased in comparison with 3-D simulations. The system considered here is made up of a tip, two clusters and a substrate. The main focus here is on metallic nanoclusters. In order to study the behavior of the above system which is made up of di erent transition metals, Nose-Hoover dynamics and Sutton-Chen interatomic potential are used. Furthermore, the e ect of the material characteristics, tip form and manipulation scheme on the success of the process are examined. Such qualitative simulation studies can pave the pathway towards certain nanopositioning scenarios when considering di erent working conditions before consuming largescale computation time or high experimental expenses.

Research paper thumbnail of Precise positioning and assembly of metallic nanoclusters as building blocks of nanostructures: A molecular dynamics study

Molecular dynamics simulations are used to study the manipulation of metallic nanoclusters. These... more Molecular dynamics simulations are used to study the manipulation of metallic nanoclusters. These particles are assumed as potential building blocks for bottom-up manufacturing of nanoscale structures. One of the key factors in the assembly of nanoclusters is the precise positioning of them by a manipulation system. Prediction of the corresponding behavior under the influence of working conditions is of crucial importance for planning of controlled positioning and assembly of nanoclusters. The focus of the present research is on ultra-fine metallic nanoclusters. The effects of material type and manipulation strategy on the success of the process have been investigated by molecular dynamics. Such qualitative simulation studies can evaluate the chance of success of a certain nanopositioning scenario regarding different working conditions before consuming high experimental expenses.

Research paper thumbnail of Planar molecular dynamics simulation of Au clusters in pushing process

International Journal of Nanomanufacturing, 2010

Based on the fact that the manipulation of fine nanoclusters calls for more precise modelling, th... more Based on the fact that the manipulation of fine nanoclusters calls for more precise modelling, the aim of this paper is to conduct an atomistic investigation for interaction analysis of particle-substrate system for pushing and positioning purposes. In the present research, 2D molecular dynamics simulations have been used to investigate such behaviours. Performing the planar simulations can provide a fairly acceptable qualitative tool for our purpose while the computation time is reduced extremely in comparison to 3D simulations. To perform this study, Nose-Hoover dynamics and Sutton-Chen interatomic potential will be used to investigate the behaviour of the aforementioned system. Pushing of Au clusters on Au substrate has been chosen as illustrative examples. Dependency of the aforementioned behaviour on temperature has been investigated. Higher temperature affects the pushing success level considerably. In addition, the simulation was performed for Ag cluster as well to compare the performance to one for Au cluster.

Research paper thumbnail of Precise positioning and assembly of metallic nanoclusters as building blocks of nanostructures: A molecular dynamics study

Physica E: Low-dimensional Systems and Nanostructures, 2009

Molecular dynamics simulations are used to study the manipulation of metallic nanoclusters. These... more Molecular dynamics simulations are used to study the manipulation of metallic nanoclusters. These particles are assumed as potential building blocks for bottom-up manufacturing of nanoscale structures. One of the key factors in the assembly of nanoclusters is the precise positioning of them by a manipulation system. Prediction of the corresponding behavior under the influence of working conditions is of crucial importance for planning of controlled positioning and assembly of nanoclusters. The focus of the present research is on ultra-fine metallic nanoclusters. The effects of material type and manipulation strategy on the success of the process have been investigated by molecular dynamics. Such qualitative simulation studies can evaluate the chance of success of a certain nanopositioning scenario regarding different working conditions before consuming high experimental expenses.

Research paper thumbnail of On the optimum design of fuzzy logic controller for trajectory tracking using evolutionary algorithms

Differential Evolution (DE) and Genetic Algorithms (GA) are population based search algorithms th... more Differential Evolution (DE) and Genetic Algorithms (GA) are population based search algorithms that come under the category of evolutionary optimization techniques. In the present study, these evolutionary methods have been utilized to conduct the optimum design of the fuzzy controller for mobile robot trajectory tracking. Comparison between their performances has also been conducted. In this paper we will present a fuzzy controller to the problem of mobile robot path tracking for the CEDRA rescue robot with a complicated kinematical model. After designing the fuzzy tracking controller, the membership functions will be optimized by evolutionary algorithms in order to obtain more acceptable results.

Research paper thumbnail of Actin Reorganization through Dynamic Interactions with Single-Wall Carbon Nanotubes

ACS Nano, 2014

Single-wall carbon nanotubes (SWCNTs) have been widely used for biological applications in recent... more Single-wall carbon nanotubes (SWCNTs) have been widely used for biological applications in recent years, and thus, it is critical to understand how these inert nanomaterials influence cell behavior. Recently, it has been observed that cellular phenotypes such as proliferation, force generation and growth change upon SWCNT treatment, and SWCNTs directly affect the organization and redistribution of the actin cytoskeleton. However, the interactions between SWCNTs and actin at the molecular level or how this interaction changes actin structure remain largely unknown. Here, we investigated direct interaction of actin with SWCNT using all-atom molecular dynamics simulations and NIR spectroscopy of actin-dispersed SWCNTs. Actin can stably bind to the SWCNT surfaces via hydrophobic interactions but still allows nanotubes to slide and rotate on the actin surface. Our results establish several nanoscale conformational changes for the actinÀSWCNT complexes, and we suggest these changes likely induce reorganization of actin filaments observed at larger scales.

Research paper thumbnail of Adaptive regulation and set-point tracking of the Lorenz attractor

Adaptive regulation and set-point tracking of the Lorenz attractor

Chaos Solitons & Fractals, 2007

In this paper, an approach is proposed for controlling the uncertain Lorenz system. Based on an i... more In this paper, an approach is proposed for controlling the uncertain Lorenz system. Based on an identification technique, a controller is designed that guarantees the regulation of all states in the presence of system uncertainty. Since in some applications the challenging problem of output tracking is desired, we have proposed several effective set-point tracking control techniques. The control schemes that

Research paper thumbnail of Precise positioning and assembly of metallic nanoclusters as building blocks of nanostructures: A molecular dynamics study

Physica E-low-dimensional Systems & Nanostructures, 2009

Molecular dynamics simulations are used to study the manipulation of metallic nanoclusters. These... more Molecular dynamics simulations are used to study the manipulation of metallic nanoclusters. These particles are assumed as potential building blocks for bottom-up manufacturing of nanoscale structures. One of the key factors in the assembly of nanoclusters is the precise positioning of them by a manipulation system. Prediction of the corresponding behavior under the influence of working conditions is of crucial importance for planning of controlled positioning and assembly of nanoclusters. The focus of the present research is on ultra-fine metallic nanoclusters. The effects of material type and manipulation strategy on the success of the process have been investigated by molecular dynamics. Such qualitative simulation studies can evaluate the chance of success of a certain nanopositioning scenario regarding different working conditions before consuming high experimental expenses.

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

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

Journal of Physics D-applied Physics, 2011

Models capable of accurate simulation of microcantilever dynamics coupled with complex tip-sample... more 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 coincidence with the realistic behaviour of AM-AFM in imaging of nanoscale features. In the conducted simulations, a diamond tip is used to scan a C60 molecule absorbed on a graphite substrate. The effects of amplitude set-point, cantilever stiffness and quality factor on the accuracy of different modelling approaches are studied.

Research paper thumbnail of Observer-based control design for three well-known chaotic systems

Observer-based control design for three well-known chaotic systems

Chaos Solitons & Fractals, 2006

In this paper, a singularity-free approach is proposed for controlling three well-known chaotic s... more In this paper, a singularity-free approach is proposed for controlling three well-known chaotic systems namely Lorenz, Chen and Lu. The control design guarantees the regulation of two states and boundedness of the remaining state. The stability of the proposed scheme has been shown using the Lyapunov stability theorem. Implementation of the proposed control technique requires system states, while in most

Research paper thumbnail of Molecular dynamics simulation of manipulation of metallic nanoclusters on stepped surfaces

Central European Journal of Physics, 2011

Molecular dynamics simulations are carried out to investigate the manipulation of metallic cluste... more Molecular dynamics simulations are carried out to investigate the manipulation of metallic clusters on stepped surfaces. Five surface forms are considered in the simulations. The system parts are made of pure transition metals and Sutton-Chen many-body potential is used as interatomic potential. The conditions which are subjected to change in the tests include: materials used for particles and substrate, and surface step conditions. In addition to qualitative observations, two criteria which represent the particle deformation and substrate abrasion are utilized as evaluation tools and are computed for each case. Simulation results show the effect of the aforementioned working conditions on the particle behavior as well as changes in the pushing forces. Obtaining this sort of knowledge is highly beneficial for further experiments in order to be able to plan the conditions and routines which guarantee better success in the manipulation process.

Research paper thumbnail of Observer-based control design for three well-known chaotic systems

Observer-based control design for three well-known chaotic systems

Chaos Solitons & Fractals, 2006

In this paper, a singularity-free approach is proposed for controlling three well-known chaotic s... more In this paper, a singularity-free approach is proposed for controlling three well-known chaotic systems namely Lorenz, Chen and Lu. The control design guarantees the regulation of two states and boundedness of the remaining state. The stability of the proposed scheme has been shown using the Lyapunov stability theorem. Implementation of the proposed control technique requires system states, while in most of practical applications only the system output is available. To overcome this problem, a nonlinear observer is coupled with the controller. Simulation results have illustrated the effectiveness and robustness of the proposed schemes. If the control action is applied to the second system equation, all states will be regulated.

Research paper thumbnail of Qualitative study of nanocluster positioning process: Planar molecular dynamics simulations

Current Applied Physics, 2009

One of the key factors in the assembly of nanoclusters is the precise positioning of them by a ma... more One of the key factors in the assembly of nanoclusters is the precise positioning of them by a manipulation system. Currently the size of clusters used as building blocks is shrinking down to a few nanometers. In such cases, the particle nature of matter plays an important role in the manipulator/cluster/substrate interactions. Having a deeper insight to the aforementioned nano-scale interactions is crucial for prediction and understanding of the behavior of nanoclusters during the positioning process. In the present research, 2D molecular dynamics simulations have been used to investigate such behaviors. Performing planar simulations can provide a fairly acceptable qualitative tool for our purpose while the computation time is greatly reduced in comparison to 3D simulations. The system consists of a tip, cluster and substrate. The focus of the present research is on ultra-fine metallic nanoclusters. To perform this research, Nose–Hoover dynamics and Sutton–Chen interatomic potential will be used to investigate the behavior of the above system which is made from different transition metals. The effects of material type, tip form and manipulation strategy on the success of the process have been investigated by planar molecular dynamics. Such qualitative simulation studies can evaluate the chance of success of a certain nanopositioning scenario regarding different working conditions before consuming large-scale computation time or high experimental expenses.