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nanomechanics
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Mechanical differences between ATP and ADP actin states: A molecular dynamics study
, Article Journal of Theoretical Biology ; Volume 448 , 2018 , Pages 94-103 ; 00225193 (ISSN) ; Shamloo, A ; Sharif University of Technology
Academic Press
2018
Abstract
This paper aims to give a comprehensive atomistic modeling of the nanomechanical behavior of actin monomer. Actin is a ubiquitous and essential component of cytoskeleton which forms many different cellular structures. Despite for several years great effort has been devoted to the investigation of mechanical properties of the actin filament, studies on the nanomechanical behavior of actin monomer are still lacking. These scales are, however, important for a complete understanding of the role of actin as an important component in the cytoskeleton structure. Based on the accuracy of atomistic modeling methods such as molecular dynamics simulations, steered molecular dynamics method is performed...
Nanomechanics of actin filament: a molecular dynamics simulation
, Article Cytoskeleton ; Volume 75, Issue 3 , March , 2018 , Pages 118-130 ; 19493584 (ISSN) ; Mehrafrooz, B ; Sharif University of Technology
John Wiley and Sons Inc
2018
Abstract
Actin is known as the most abundant essentially protein in eukaryotic cells. Actin plays a crucial role in many cellular processes involving mechanical forces such as cell motility, adhesion, muscle contraction, and intracellular transport. However, little is known about the mechanical properties of this protein when subjected to mechanical forces in cellular processes. In this article, a series of large-scale molecular dynamics simulations are carried out to elucidate nanomechanical behavior such as elastic and viscoelastic properties of a single actin filament. Here, we used two individual methods namely, all-atoms and coarse-grained molecular dynamics, to evaluate elastic properties of a...
Fabrication mechanism of nanostructured HA/TNTs biomedical coatings: an improvement in nanomechanical and in vitro biological responses
, Article Journal of Materials Science: Materials in Medicine ; Volume 27, Issue 10 , 2016 ; 09574530 (ISSN) ; Riahi, Z ; Eslami, A ; Sadrnezhaad, S. K ; Sharif University of Technology
Springer New York LLC
2016
Abstract
In this paper, a mechanism for fabrication of nanostructured hydroxyapatite coating on TiO2 nanotubes is presented. Also, the physical, biological, and nanomechanical properties of the anodized Ti6Al4V alloy consisting TiO2 nanotubes, electrodeposited hydroxyapatite, and the hydroxyapatite/TiO2 nanotubes double layer coating on Ti6Al4V alloy implants are compared. Mean cell viability of the samples being 84.63 % for uncoated plate, 91.53 % for electrodeposited hydroxyapatite, and 94.98 % for hydroxyapatite/TiO2 nanotubes coated sample were in the acceptable range. Merely anodized prototype had the highest biocompatibility of 110 % with respect to the control sample. Bonding strength of...
Nanomechanical properties of lipid bilayer: Asymmetric modulation of lateral pressure and surface tension due to protein insertion in one leaflet of a bilayer
, Article Journal of Chemical Physics ; Volume 138, Issue 6 , 2013 ; 00219606 (ISSN) ; Amininasab, M ; Ejtehadi, M. R ; Kowsari, F ; Dastvan, R ; Sharif University of Technology
2013
Abstract
The lipid membranes of living cells form an integral part of biological systems, and the mechanical properties of these membranes play an important role in biophysical investigations. One interesting problem to be evaluated is the effect of protein insertion in one leaflet of a bilayer on the physical properties of lipid membrane. In the present study, an all atom (fine-grained) molecular dynamics simulation is used to investigate the binding of cytotoxin A3 (CTX A3), a cytotoxin from snake venom, to a phosphatidylcholine lipid bilayer. Then, a 5 ms coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment...
A molecular dynamics simulation study of nanomechanical properties of asymmetric lipid bilayer
, Article Journal of Membrane Biology ; Volume 246, Issue 1 , 2013 , Pages 67-73 ; 00222631 (ISSN) ; Amininasab, M ; Vali, M ; Ejtehadi, M ; Kowsari, F ; Sharif University of Technology
2013
Abstract
A very important part of the living cells of biological systems is the lipid membrane. The mechanical properties of this membrane play an important role in biophysical studies. Investigation as to how the insertion of additional phospholipids in one leaflet of a bilayer affects the physical properties of the obtained asymmetric lipid membrane is of recent practical interest. In this work a coarse-grained molecular dynamics simulation was carried out in order to compute the pressure tensor, the lateral pressure, the surface tension and the first moment of lateral pressure in each leaflet of such a bilayer. Our simulations indicate that adding more phospholipids into one monolayer results in...
Electrodeposition and characterization of Ni-Co/SiC nanocomposite coatings
, Article Journal of Alloys and Compounds ; Volume 509, Issue 39 , 2011 , Pages 9406-9412 ; 09258388 (ISSN) ; Dolati, A ; Ahmadi, M. R ; Sharif University of Technology
2011
Abstract
Ni-Co/SiC nanocomposite coatings were electrodeposited in a modified watt type of Ni-Co bath containing 20 nm SiC particles to be codeposited. Potentiodynamic polarization tests were conducted to study the effect of the SiC particulates on the electrodeposition of Ni and Co. Scanning electron microscopy was used to assess the morphology of the Ni-Co alloy and Ni-Co/SiC nanocomposite coatings. The distribution of the particulates in the matrix was considered by means of transmission electron microscopy. Applying nanomechanical testing instruments coupled to atomic force microscopy, mechanical properties of the alloy and composite coatings were studied and compared. The presence of 11 vol.%...
Nanomechanical properties of TiO2 granular thin films
, Article ACS Applied Materials and Interfaces ; Volume 2, Issue 9 , 2010 , Pages 2629-2636 ; 19448244 (ISSN) ; Taghavinia, N ; Keshavarz Alamdari, E ; Volinsky, A.A ; Sharif University of Technology
2010
Abstract
Post-deposition annealing effects on nanomechanical properties of granular TiO2 films on soda-lime glass substrates were studied. In particular, the effects of Na diffusion on the films' mechanical properties were examined. TiO2 photocatalyst films, 330 nm thick, were prepared by dip-coating using a TiO2 sol, and were annealed between 100 °C and 500 °C. Film's morphology, physical and nanomechanical properties were characterized by atomic force microscopy, X-ray photoelectron spectroscopy, X-ray diffraction, differential thermo-gravimetric analysis, and nanoindentation. Contrary to expectations, the maximum film hardness was achieved for 300°C annealing, with a value of 0.69 ± 0.05 GPa....
Nanomechanical properties of functionally graded composite coatings: Electrodeposited nickel dispersions containing silicon micro- and nanoparticles
, Article Materials Chemistry and Physics ; Volume 121, Issue 3 , June , 2010 , Pages 497-505 ; 02540584 (ISSN) ; Dolati, A ; Ghorbani, M ; Monfared, A ; Stroeve, P ; Sharif University of Technology
2010
Abstract
Functionally graded composite coatings constitute a class of materials which are mostly used for mechanical and tribological applications. Among these materials, nickel metal deposits with incorporation of SiC particles have excellent mechanical properties due to nickel metal and good tribological properties due to the SiC particles. In this work, nickel coatings containing different sizes of SiC particles, nanoparticles and microparticles (10 nm to 5 μm), were electrodeposited from an additive-free sulfate bath containing nickel ions and SiC particles. The material properties of the coatings were compared to nickel coatings containing microparticles (5 μm). The effect of current density,...
Introducing structural approximation method for modeling nanostructures
, Article Journal of Computational and Theoretical Nanoscience ; Volume 7, Issue 2 , February , 2010 , Pages 423-428 ; 15461955 (ISSN) ; Alasty, A ; Sharif University of Technology
2010
Abstract
In this work a new method for analyzing nanostructured materials has been proposed to accelerate the simulations for solid crystalline materials. The proposed Structural Approximation Method (SAM) is based on Molecular Dynamics (MD) and the accuracy of the results can also be improved in a systematic manner by sacrificing the simulation speed. In this method a virtual material is used instead of the real one, which has less number of atoms and therefore fewer degrees of freedom, compared to the real material. The number of differential equations that must be integrated in order to specify the state of the system will decrease significantly, and the simulation speed increases. To generalize...
Pull-in parameters of cantilever type nanomechanical switches in presence of Casimir force
, Article Nonlinear Analysis: Hybrid Systems ; Volume 1, Issue 3 , 2007 , Pages 364-382 ; 1751570X (ISSN) ; Alasty, A ; Akbari, J ; Sharif University of Technology
2007
Abstract
In this paper, the effect of the Casimir force on pull-in parameters of cantilever type nanomechanical switches is investigated by using a distributed parameter model. In modeling of the electrostatic force, the fringing field effect is taken into account. The model is nonlinear due to the inherent nonlinearity of the Casimir and electrostatic forces. The nonlinear differential equation of the model is transformed into the integral form by using the Green's function of the cantilever beam. The integral equation is solved analytically by assuming an appropriate shape function for the beam deflection. The pull-in parameters of the switch are computed in three cases including nanoactuators...
Closed-form solutions of the pull-in instability in nano-cantilevers under electrostatic and intermolecular surface forces
, Article International Journal of Solids and Structures ; Volume 44, Issue 14-15 , 2007 , Pages 4925-4941 ; 00207683 (ISSN) ; Alasty, A ; Akbari, J ; Sharif University of Technology
2007
Abstract
In this paper, a distributed parameter model is used to study the pull-in instability of cantilever type nanomechanical switches subjected to intermolecular and electrostatic forces. In modeling of the electrostatic force, the fringing field effect is taken into account. The model is nonlinear due to the inherent nonlinearity of the intermolecular and electrostatic forces. The nonlinear differential equation of the model is transformed into the integral form by using the Green's function of the cantilever beam. Closed-form solutions are obtained by assuming an appropriate shape function for the beam deflection to evaluate the integrals. The pull-in parameters of the switch are computed under...
Influence of van der Waals force on the pull-in parameters of cantilever type nanoscale electrostatic actuators
, Article Microsystem Technologies ; Volume 12, Issue 12 , 2006 , Pages 1153-1161 ; 09467076 (ISSN) ; Alasty, A ; Akbari, J ; Sharif University of Technology
2006
Abstract
In this paper, the influence of the van der Waals force on two main parameters describing an instability point of cantilever type nanomechanical switches, which are the pull-in voltage and deflection are investigated by using a distributed parameter model. The fringing field effect is also taken into account. The nonlinear differential equation of the model is transformed into the integral form by using the Green's function of the cantilever beam. The integral equation is solved analytically by assuming an appropriate shape function for the beam deflection. The detachment length and the minimum initial gap of the cantilever type switches are given, which are the basic design parameters for...
An analytical approach to determination of bending modulus of a multi-layered graphene sheet
, Article Thin Solid Films ; Volume 496, Issue 2 , 2006 , Pages 475-480 ; 00406090 (ISSN) ; Seifi, P ; Naghdabadi, R ; Ghanbari, J ; Sharif University of Technology
2006
Abstract
In this paper, the bending modulus of a multi-layered graphene sheet is investigated using a geometrically based analytical approach. For this purpose, a bending potential energy is derived, based on the van der Waals interactions of atoms belonging to the two neighboring sheets of a double-layered graphene sheet. The inter-atomic spacing between the adjacent layers is determined along the line of action of the applied bending moments. The bending potential of the double-layered sheet is calculated by summing up the potentials at discrete hexagons over the length and width of the sheet. A multi-layered graphene sheet is considered as consisting of many stacking double-layers. It is observed...
Influence of van der Waals force on the pull-in parameters of cantilever type nanoscale electrostatic actuators
, Article 8th Biennial ASME Conference on Engineering Systems Design and Analysis, ESDA2006, Torino, 4 July 2006 through 7 July 2006 ; Volume 2006 , 2006 ; 0791837793 (ISBN); 9780791837795 (ISBN) ; Akbari, J ; Alasty, A ; Sharif University of Technology
2006
Abstract
In this paper, the influence of the van der Waals force on two main parameters describing an instability point of cantilever type nanomechanical switches, which are the pull-in voltage and deflection are investigated by using a distributed parameter beam model. The nonlinear differential equation of the model is transformed into the integral form by using the Green's function of the cantilever beam. The integral equation is solved analytically by assuming an appropriate shape function for the beam deflection. The detachment length and the minimum initial gap of the cantilever type switches are given, which are the basic design parameters for NEMS switches. The pull-in parameters of...
Hierarchical Multi-Scale Modeling of Large Plastic Deformation with Application in Powder Compaction
, Ph.D. Dissertation Sharif University of Technology ; Khoei, Amir Reza (Supervisor)
Abstract
The hierarchical multi-scale approach is one of the most powerful techniques that takes the advantage of different scales and succeeds the limitations of each method in a way that the large systems in coarse-scale can be simulated with atomic precision. In this thesis, the hierarchical atomistic-continuum multi-scale method is developed for modeling the phenomena with non-homogenous deformation, large deformation and plastic behavior. In this regard at first, an atomistic-based higher-order continuum model is formulated in the framework of nonlinear finite element method to present the geometrically nonlinear behavior of nano-structures. The efficiency of higher-order Cauchy-Born hypothesis...
A Coupling Atomistic-continuum Approach for Modeling Dislocation in Plastic Behavior of Nano-structures
, M.Sc. Thesis Sharif University of Technology ; Khoei, Amir Reza (Supervisor) ; Jahanshahi, Mohsan (Co-Advisor)
Abstract
In this study, a novel multi-scale hierarchical method has been employed to explore the role of edge dislocation on Nano-plates with hexagonal atomic structure in large deformation. multiscale hierarchical atomistic/molecular dynamics (MD) finite element (FE) coupling methods are proposed to demonstrate the impact of dislocation on mechanical properties of Magnesium in large deformation. The atomic nonlinear elastic parameters are attained via computing first-order derivation of stress with respect to strain of Representative Volume Element (RVE). To associate between atomistic and continuum level, the mechanical characteristics are captured in the atomistic scale and transferred to the...
Multi-scale Modeling of Crack Using Nano-XFEM
, M.Sc. Thesis Sharif University of Technology ; Haddadpour, Hassan (Supervisor)
Abstract
In this thesis a mutliScale model based on the Cauchy-Born hypothesis and via usage of XFEM is proposed for crack modeling. By solving an example, the important of surface effects in the surface stresses region is shown. Considering not being able to model the surface effects with the Cauchy-Born method, the boundary Cauchy-Born method for modeling crack effects is used. Moreover, three Molecular Dynamics method for modeling crack will be proposed. According to the obtained results from these methods, it was deduced that for calculating the correct surface stresses in Molecular Dynamics the mutual interaction of upper and lower atoms of crack should be omitted. Finally, the validation of...
Concurrent Multi-Scale Approach for Modeling Mechanical Behavior of Crystalline Nano-Structures
, M.Sc. Thesis Sharif University of Technology ; Khoei, Amir Reza (Supervisor)
Abstract
Mindboggling advances in nanotechnology have urged researchers to develop state-of-the-art numerical methods to enable them to simulate and to interpret phenomena at this scale. Unfortunately, Classical models have numerous shortcomings which hinder their applications in new contexts. For instance, classical Continuum Mechanics fails to appropriately depict material behavior at small scales, and, on the other hand, Molecular Dynamics simulations are computationally prohibitive. As a consequence, researchers have devised multi-scale methods during the past decade to overcome these obstacles. In fact, in multi-scale methods information is passed from one mathematical description to the other....
Temperature-Dependent Hierarchical Multi-Scale Modeling of Nano-Materials Considering Surface Effect
, M.Sc. Thesis Sharif University of Technology ; Khoei, Amir Reza (Supervisor)
Abstract
In continuum mechanics, the constitutive models are usually based on the Cauchy-Born (CB) hypothesis which seeks the intrinsic characteristics of the material via the atomistic information and it is valid in small deformation. The main purpose of this thesis is to investigate the temperature effect on the stability and size dependency of Cauchy-Born hypothesis and a novel temperature-dependent multi-scale method is developed to investigate the role of temperature on surface effects in the analysis of nano-scale materials. Three-dimensional temperature-related Cauchy-Born formulation are developed for crystalline structure and the stability and size dependency of temperature-related...
Modeling of Carbon Nanotubes with Molecular Dynamics and Application of Parallel Processing
, M.Sc. Thesis Sharif University of Technology ; Khoei, Amir Reza (Supervisor)
Abstract
Nanotechnology is the knowledge of future. Some people Compare the initialization of nanotechnology to the beginning of the industrial revolution. Experimental modeling of nano-materials can be so expensive, but, with the aid of computational nanomechanics, we can perform less experiments and more numerical simulation. In the past decades, applications of nanotubes in medicine, electrical engineering, mechanical engineering, building nano sensors, nano engines and etc caused a pervasive study on the mechanics of carbon nanotubes. In this Thesis, the writer has implemented the Tersoff interatomic potential to perform molecular dynamics simulations of carbon nanotubes. In this work, tensile...