Molecular dynamics simulation studies of mechanical properties of different carbon nanotube systems

Various mechanical properties of single-walled carbon nanotubes (SWCNT) and double-walled carbon nanotubes (DWCNT) are evaluated using molecular dynamics (MD) simulations. A tensioning process was first performed on a SWCNT whose interaction is based on the Brenner’s ‘second generation’ potential under varying length–diameter ratios and strain rates, in order to understand the SWCNT’s behaviour under axial tension. The results showed an increase in the SWCNT’s ultimate tensile strength and a decrease in critical strain given the conditions of increasing strain rate and a decreasing length–diameter ratio. Comparison was done with previous studies on axial tensioning of SWCNT to validate the results obtained from the set-up, based on the general stress–strain relationship and key mechanical properties such as the strain at failure and the Young’s modulus. A DWCNT was then constructed, and Lennard-Jones ‘12-6’ potential was used to describe the energy present between the nanotube layers. Extraction of the inner tube in a DWCNT was performed using two inner wall tubings of different diameters to draw comparison to the energies needed to separate fully the outer and inner tubing. Finally, a bending test was performed on two DWCNTs with different intertube separations. Insights into the entire bending process were obtained through analyses of the variations in the strain energy characteristic of the surface atoms near the bending site, as the DWCNT is gradually bent until failure.     

Computational modeling of the effective Young’s modulus values of fullerene molecules: a combined molecular dynamics simulation and continuum shell model

Estimating the Young’s modulus of a structure in the nanometer size range is a difficult task. The reliable determination of this parameter is, however, important in both basic and applied research. In this study, by combining molecular dynamics (MD) simulations and continuum shell theory, we designed a new approach to determining the Young’s modulus values of different spherical fullerenes. The results indicate that the Young’s modulus values of fullerene molecules decrease nonlinearly with increasing molecule size and understandably tend to the Young’s modulus of an ideal flat graphene sheet at large molecular radii. To the best of our knowledge, this is first time that a combined atomistic–continuum method which can predict the Young’s modulus values of fullerene molecules with high precision has been reported.     

Temperature and configurational effects on the Young’s modulus of poly (methyl methacrylate): a molecular dynamics study comparing the DREIDING,AMBER and OPLS force fields

The effects of the configuration and temperature on the Young’s modulus of poly (methyl methacrylate) (PMMA) have been studied using molecular dynamics simulations. For the DREIDING force field under ambient temperatures, increasing the number of monomers significantly increases the modulus of isotactic and syndiotactic PMMA while the isotactic form has a greater modulus. The effects of temperature on the modulus of isotactic PMMA have been simulated using the DREIDING, AMBER, and OPLS force fields. All these force fields predict the effects of temperature on the modulus from 200 to 350 K that are in close agreement with experimental values, while at higher temperatures the moduli are greater than those measured. The glass transition temperature determined by the force fields, based on the variation of the modulus with temperature, is greater than the experimental values, but when obtained from a plot of the volume as a function of the temperature, there is closer agreement. The Young’s moduli calculated in this study are in closer agreement to the experimental data than those reported by previous simulations.     

Improving stress shielding following total hip arthroplasty by using a femoral stem made of β type Ti-33.6Nb-4Sn with a Young’s modulus gradation

Stress shielding-related bone loss occurs after total hip arthroplasty because the stiffness of metallic implants differs from that of the host femur. Although reducing stem stiffness can ameliorate the bone resorption, it increases stress at the bone–implant interface and can inhibit fixation. To overcome this complication, a novel cementless stem with a gradient in Young’s modulus was developed using Ti-33.6Nb-4Sn (TNS) alloy. Local heat treatment applied at the neck region for increasing its strength resulted in a gradual decrease in Young’s modulus from the proximal to the distal end, from 82.1 to 51.0 GPa as calculated by a heat transfer simulation. The Young’s modulus gradient did not induce the excessive interface stress which may cause the surface debonding. The main purpose of this study was to evaluate bone remodeling with the TNS stem using a strain-adaptive bone remodeling simulation based on finite element analysis. Our predictions showed that, for the TNS stem, bone reduction in the calcar region (Gruen zone 7) would be 13.6% at 2 years, 29.0% at 5 years, and 45.8% at 10 years postoperatively. At 10 years, the bone mineral density for the TNS stem would be 42.6% higher than that for the similar Ti-6Al-4V alloy stem. The stress–strength ratio would be lower for the TNS stem than for the Ti-6Al-4V stem. These results suggest that although proximal bone loss cannot be eliminated completely, the TNS stem with a Young’s modulus gradient may have bone-preserving effects and sufficient stem strength, without the excessive interface stress.     

Adamantane/beta-cyclodextrin affinity biosensors based on single-walled carbon nanotubes

One challenging goal for the development of biosensors is the conception of three-dimensional biostructures on electrode surfaces. With the aim to develop 3D architectures based on single-walled carbon nanotubes (SWCNTs) frameworks a novel adamantane-pyrrole monomer was synthesized. After electrochemical polymerization at 0.95V in acetonitrile, the resulting polypyrrole film provided affinity interactions with beta-cyclodextrin. SWCNT coatings were thus functionalized with poly(adamantane-pyrrole) and applied to the anchoring of glucose oxidase (GOX), modified with beta-cyclodextrin. By using this affinity system adamantine-cyclodextrin, beta-cyclodextrin-modified gold nanoparticles were attached onto the functionalized SWCNT deposit as intermediate layer. This allows the immobilization of adamantane-tagged GOX. The responses of these biosensors to glucose were measured by potentiostating the modified electrodes at 0.7V versus saturated calomel electrode (SCE) in order to oxidize the enzymatically generated hydrogen peroxide in the presence of glucose and oxygen. The highest sensitivity and maximum current density were recorded for the configuration based on beta-cyclodextrin-modified gold particles as intermediate layer between adamantine-functionalized SWCNTs and GOX (31.02 mAM(-1)cm(-2) and 350 microAcm(-2), respectively). The similar configuration without SWCNTs exhibits a sensitivity and J(max) of 0.98 mAM(-1)cm(-2) and 75 microAcm(-2), respectively. The resulting supramolecular assemblies were characterized by scanning electron microscopy (SEM). Advantages and disadvantages of the different preparation methods and the performance of each affinity sensor setup are discussed in detail.     

First-principles study of the structural,elastic and electronic properties of SbXI (X=S,Se, Te) crystals

The structural, elastic, elastic anisotropy and electronic properties of ferroelectric SbSI and paraelectric SbSI, SbSeI and SbTeI crystals were computed using the local density approximation with first-principle calculations, based on density functional theory. The independent elastic constants of SbXI compounds were computed and the results reveal that they are mechanically stable. Some polycrystalline quantities such as bulk modulus, shear modulus, acoustic velocities, Young’s modulus, Poisson’s ratio, elastic anisotropy and elastic Debye temperatures of these compounds were derived from computed elastic constants. Energy band structures show that these compounds have an indirect band gap. The electronic charge distribution and partial density of states of SbXI compounds indicate that the Sb-X bond is typically covalent with a strong hybridization as well as Sb-I compounds that have strong ionic character. The results obtained were compared with experimentally measured values and other theoretical data.     

Density functional investigation of hydrogen gas adsorption on Fe?doped pristine and Stone?Wales defected single?walled carbon nanotubes

The adsorptions of hydrogen molecule of the Fe?-?doped pristine and Stone?-?Wales defected armchair (5,5) single?-?walled carbon nanotubes (SWCNTs) compared with the pristine SWCNT were investigated by using the density functional theory at the B3LYP/LanL2DZ level. The doping of Fe atom into SWCNTs occurring via an exothermic process was found. The adsorptions of hydrogen molecule on the Fe?-?doped structures of either perfect or SW defected SWCNTs are stronger than on their corresponding undoped structures. The structural and electronic properties of the pristine and SW defected SWCNTs, their Fe?-?doped structures and their hydrogen molecule adsorptions are reported.     

Structural stability and buckling analysis of a series of carbon nanotorus using molecular dynamics simulations

Based on molecular dynamics (MD) simulations, the buckling analysis of a perfect carbon nanotorus is presented herein. First of all, the minimum length of single-walled carbon nanotubes (SWCNTs) with different radii is determined at which perfect toroidal CNTs can be formed without any ripple at the inner side of the rings. According to the results, by increasing the radius of SWCNT (r), the radius of its corresponding perfect nanotorus (R) increases. Also, for SWCNTs with various lengths, it is found that the buckling force and strain of related carbon nanotoruses increase by increasing R/r. In addition, as the perfect toroidal CNTs are arranged vertically in a column form in accordance with two different schemes, the effects of increasing the radius (R) and the number of carbon nanotoruses (the height of the column made by nanotoruses) on the buckling force and strain are investigated. Based on the results, as a fixed number of carbon nanotoruses with the same radius are arranged vertically in the column form, the buckling force and strain increase by increasing R/r. By contrast, increasing the height of the column made by carbon nanotoruses with similar radius leads to the reduction of buckling force and strain.     

DFT studies of COOH tip-functionalized zigzag and armchair single wall carbon nanotubes

Structure and energy calculations of pristine and COOH-modified model single wall carbon nanotubes (SWCNTs) of different length were performed at B3LYP/6-31G* level of theory. From 1 to 9 COOH groups were added at the end of the nanotube. The differences in structure and energetics of partially and fully functionalized SWCNTs at one end of the nanotube are observed. Up to nine COOH groups could be added at one end of (9,0) zigzag SWCNT in case of full functionalization. However, for (5,5) armchair SWCNT, the full functionalization was impossible due to steric crowding and rim deformation. The dependence of substituent attachment energy on the number of substituents at the carbon nanotube rim was observed.     

Induction of programmed cell death in Arabidopsis and rice by single-wall carbon nanotubes

? Premise of the study: Single-walled carbon nanotubes (SWCNTs) have many unique structural and mechanical properties. Their potential applications, especially in biomedical engineering and medical chemistry, have been increasing in recent years, but the toxicological impact of nanoparticles has rarely been studied in plants. ? Methods: We exposed Arabidopsis and rice leaf protoplasts to SWCNTs and examined cell viability, DNA damage, reactive oxygen species generation, and related gene expression. We also tested the effects of nanoparticles on Arabidopsis leaves after injecting a SWCNT solution. EM-TUNEL (electron-microscopic terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling) and a cerium chloride staining method were used. ? Key results: SWCNTs caused adverse cellular responses including cell aggregation, chromatin condensation along with a TUNEL-positive reaction, plasma membrane deposition, and H(2)O(2) accumulation. The effect of SWCNTs on the survival of cells was dose dependent, with 25 μg/mL inducing 25% cell death in 6 h. In contrast, activated carbon, which is not a nano-sized carbon particle, did not induce cell death even 24 h after treatments. The data indicated that the nano-size of the particle is a critical factor for toxicity. Moreover, endocytosis-like structures with cerium chloride deposits formed after SWCNT treatment, suggesting a possible pathway for nanoparticles to traverse the cell membrane. ? Conclusions: Consequently, SWCNTs have an adverse effect on protoplasts and leaves through oxidative stress, leading to a certain amount of programmed cell death. Although nanomaterials have great advantages in many respects, the benefits and side effects still need to be assessed carefully.     

Simple benzene derivatives adsorption on defective single-walled carbon nanotubes: a first-principles van der Waals density functional study

We have investigated the interaction between open-ended zig-zag single-walled carbon nanotube (SWCNT) and a few benzene derivatives using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such sp ²-like materials are typically investigated using conventional DFT methods, which significantly underestimate non-local dispersion forces (vdW interactions), therefore affecting interactions between respected molecules. Here, we considered the vdW forces for the interacting molecules that originate from the interacting π electrons of the two systems. The ?0.54 eV adsorption energy reveals that the interaction of benzene with the side wall of the SWCNT is typical of the strong physisorption and comparable with the experimental value for benzene adsorption onto the graphene sheet. It was found that aromatics are physisorbed on the sidewall of perfect SWCNTs, as well as at the edge site of the defective nanotube. Analysis of the electronic structures shows that no orbital hybridization between aromatics and nanotubes occurs in the adsorption process. The results are relevant in order to identify the potential applications of noncovalent functionalized systems.

Carbon nanotube prevents the secondary structure formation of amyloid-β trimers: an all-atom molecular dynamics study

Abstract

Increasing evidence shows that the formation of misfolded aggregates amyloid-β (Aβ) peptide is associated with the Alzheimer’s disease (AD). Recent experiments reveal a significant correlation of the amount of trimer species bound to neurons with increasing neuro-toxicity. Our previous computational study demonstrated that carbon nanotubes (CNT) can inhibit effectively the formation of β-sheet-rich oligomers of Aβ(16-22) – a hydrophobic peptide essential for Aβ fibrillization. However, the influence of CNT on the oligomers formed by full-length Aβ remains elusive. In this study, we have investigated the conformational dynamics of Aβ(1-42) trimer, built from an NMR structure of α-helical monomer, in the absence and presence of a single-walled carbon nanotube (SWCNT). Our simulations demonstrate that SWCNT can significantly hinder the trimerisation and prevents the secondary structure formation of Aβ(1-42) peptide. Hydrophobic and aromatic stacking interactions between SWCNT and Aβ play important roles in the secondary structure formation of the Aβ trimer. This study reveals a complete picture of the detailed preventable mechanism of full-length Aβ(1-42) by SWCNT, providing theoretical insights into the development of drug candidates of AD.     

Probing the Diameter Limit of Single Walled Carbon Nanotubes in SWCNT: Fullerene Solar Cells

In this work, for the first time, the diameter limit of surfactant wrapped single walled carbon nanotubes (SWCNTs) in SWCNT:C₆₀ solar cells is determined through preparation of monochiral small and large diameter nanotube devices as well as those from polychiral mixtures. Through assignment of the different nanotube chiralities by photoluminescence and optical density measurements a diameter limit yielding 0% internal quantum efficiency (IQE) is determined. This work provides insights into the required net driving energy for SWCNT exciton dissociation onto C₆₀ and establishes a family of (n,m) species which can efficiently be utilized in polymer‐free SWCNT:C₆₀ solar cells. Using this approach the largest diameter nanotube with an IQE > 0% is found to be (8,6) with a diameter of 0.95 nm. Possible strategies to extend this diameter limit are then discussed.     

In vitro selection of peptide aptamers with affinity to single-wall carbon nanotubes using a ribosome display

A ribosome display from a diverse random library was applied for selecting peptide aptamers with high binding affinity to single-wall carbon nanotubes (SWCNTs). The selected peptide aptamer bound to and solubilized SWCNTs more strongly than did the peptide aptamer selected by a phage display method reported previously, and more strongly than other commonly used organic surfactants. The fluorescence spectrum of this aptamer showed a red shift upon interaction with SWCNTs but circular dichroism spectroscopy did not show any significant difference between the presence or absence of SWCNT binding.     

Modeling the interaction between anti-cancer drug penicillamine and pristine and functionalized carbon nanotubes for medical applications: density functional theory investigation and a molecular dynamics simulation

Abstract

The present study focuses on the prediction and investigation of binding properties of penicillamine with pure (5,5) single-walled carbon nanotube (SWCNT) and functionalized SWCNT (f-SWCNT) through the B3LYP and M06-2X functionals using the 6-31G** basis set. The electronic and structural properties, adsorption energy and frontier molecular orbitals of various configurations are examined. Our theoretical results indicated that the interaction of the nanotubes with penicillamine molecule is weak so that the drug adsorption process is typically physisorption. Also, results of theoretical calculations show that the adsorption of the drug molecule on f-SWCNT is stronger with shorter intermolecular distances in comparison to pure SWCNT. The natural bond orbital (NBO) analysis of studied systems demonstrates that the charge is transferred from penicillamine molecule to the nanotubes. Furthermore, molecular dynamics (MD) simulation is employed to evaluate the dynamic and diffusion behavior of drug molecule on SWCNT and f-SWCNT. Energy results show that drug molecule spontaneously moves toward the carriers, and the van der Waals energy contributions in drug adsorption are more than electrostatic interaction. The obtained results from MD simulation confirm that the functionalization of SWCNT leads to increase in the solubility of the carrier in aqueous solution.

Communicated by Ramaswamy H. Sarma     

On the elastic properties of single-walled carbon nanotubes/poly(ethylene oxide) nanocomposites using molecular dynamics simulations

Molecular dynamics simulations are used to study the physical and mechanical properties of single-walled carbon nanotubes/poly(ethylene oxide) nanocomposites. The effects of nanotube atomic structure, diameter, and volume fraction on the polymer density distribution, polymer atom distribution, stress–strain curves of nanocomposites and Young’s, and shear moduli of single-walled carbon nanotubes/poly(ethylene oxide) nanocomposites are explored. It is shown that the density of polymer, surrounding the nanotube surface, has a peak near the nanotube surface. However, increasing distance leads to dropping it to the value near the density of pure polymer. It is seen that for armchair nanotubes, the average polymer atoms distances from the single-walled carbon nanotubes are larger than the polymer atom distance from zigzag nanotubes. It further is shown that zigzag nanotubes are better candidates to reinforce poly (ethylene oxide) than their armchair counterparts.     

Inhibitory effects of single-walled carbon nanotubes on biofilm formation from Bacillus anthracis spores

This study reports the inhibitory effect of single walled carbon nanotubes (SWCNTs) on biofilm formation from Bacillus anthracis spores. Although the presence of 50 to 100 μg ml^?1 of SWCNTs in the suspension increased spore attachment in the wells of 96-well plates, the presence of 200 μg ml^?1 of SWCNTs in the germination solution decreased the germination percentage of the attached spores by 93.14%, completely inhibiting subsequent biofilm formation. The inhibition kinetics of 50 μg ml^?1 SWCNTs on biofilm formation showed that this concentration inhibited biofilm formation by 81.2% after incubation for 48 h. SWCNT treatment in the earlier stages of biofilm formation was more effective compared to treatment at later stages. Mature biofilms were highly resistant to SWCNT treatment.     

Effects of Hydroxylated Carbon Nanotubes on the Aggregation of Aβ16–22 Peptides: A Combined Simulation and Experimental Study

The pathogenesis of Alzheimer’s disease (AD) is associated with the aggregation of amyloid-β (Aβ) peptides into toxic aggregates with β-sheet character. In a previous computational study, we showed that pristine single-walled carbon nanotubes (SWCNTs) can inhibit the formation of β-sheet-rich oligomers in the central hydrophobic core fragment of Aβ (Aβ_16–22). However, the poor solubility of SWCNTs in water hinders their use in biomedical applications and nanomedicine. Here, we investigate the influence of hydroxylated SWCNT, a water-soluble SWCNT derivative, on the aggregation of Aβ_16–22 peptides using all-atom explicit-water replica exchange molecular dynamics simulations. Our results show that hydroxylated SWCNTs can significantly inhibit β-sheet formation and shift the conformations of Aβ_16–22 oligomers from ordered β-sheet-rich structures toward disordered coil aggregates. Detailed analyses of the SWCNT-Aβ interaction reveal that the inhibition of β-sheet formation by hydroxylated SWCNTs mainly results from strong electrostatic interactions between the hydroxyl groups of SWCNTs and the positively charged residue K16 of Aβ_16–22 and hydrophobic and aromatic stacking interactions between SWCNTs and F19 and F20. In addition, our atomic force microscopy and thioflavin T fluorescence experiments confirm the inhibitory effect of both pristine and hydroxylated SWCNTs on Aβ_16–22 fibrillization, in support of our previous and present replica exchange molecular dynamics simulation results. These results demonstrate that hydroxylated SWCNTs efficiently inhibit the aggregation of Aβ_16–22; in addition, they offer molecular insight into the inhibition mechanism, thus providing new clues for the design of therapeutic drugs against amyloidosis.     

Tensile loading characteristics of hydrogen stored carbon nanotubes in PEM fuel cell operating conditions using molecular dynamics simulation

Mechanical characteristics of hydrogen stored single walled carbon nanotube (SWCNT) in proton exchange membrane fuel cell (PEMFC) operating conditions are analysed in this work using molecular dynamics simulation method. The investigation of mechanical characteristics of hydrogen stored SWCNT is critical in determining the lifetime and stability of SWCNT-based membranes used in PEMFC. The study provides a comprehensive analysis on the effects of geometry, vacancy defects and PEMFC operating temperature on the mechanical properties of hydrogen stored SWCNT. The findings show that the mechanical strength of the hydrogen stored SWCNT can be enhanced by deploying a bigger armchair SWCNT. Furthermore, increase in operating temperature of PEMFC reduces the mechanical resistance of hydrogen stored SWCNT, which however can be overcome by suitably introducing vacancy defects in the SWCNT geometry. This has provided potential way of increasing the hydrogen storage capacity of SWCNT which is very useful for onboard application of PEMFC. It is anticipated that the findings obtained from this paper will have a paramount importance in the field of hydrogen energy fuel cell technology and further compliment the potential applications of SWCNTs as promising candidates for applications in fuel cells and energy storage devices.     

Effect of temperature on elastic properties of CNT-polyethylene nanocomposite and its interface using MD simulations

This paper investigates the effect of temperature on the elastic modulus of carbon nanotube-polyethylene (CNT-PE) nanocomposite and its interface using molecular dynamics (MD) simulations, by utilizing the second-generation polymer consistent force field (PCFF). Two CNTs—armchair and zigzag—were selected as reinforcing nano-fillers, and amorphous PE was used as the polymer matrix. For atomistic modelling of the nanocomposite, the commercially available code Materials Studio 8.0 was used and all other MD simulations were subsequently performed using the open source code Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). To obtain the elastic modulus of the nanocomposite, stress-strain curves were drawn at different temperatures by performing uniaxial deformation tests on the nanocomposite material, whereas the curvatures of the interfacial interaction energy vs. strain curves were utilized to obtain Young’s modulus of the interface. In addition, the glass transition temperatures of the polymer matrix and nanocomposites were also evaluated using density-temperature curves. Based on the results, it is concluded that, irrespective of temperature condition, a nanocomposite reinforced with CNT of larger chirality (i.e., armchair) yields a higher value of Young’s modulus of the nanocomposite and its interface. It was also found that, at the phase transition (from a glassy to a rubbery state) temperature (i.e., glass transition temperature), Young’s moduli of the polymer matrix, nanocomposite, and its interface drop suddenly. The results obtained from MD simulations were verified with results obtained from continuum-based rule-of-mixtures.