Gene Detection With Carbon Nanotubes

Author(s):  
B. Arash ◽  
Q. Wang ◽  
N. Wu

The potential of carbon nanotubes (CNTs) as nanosensors in detection of genes through a vibration analysis is investigated with molecular dynamics. The carbon nanotube based nanosensor under investigation is wrapped by a gene whose structure includes a single strand deoxyribose nucleic acid (DNA) with a certain number of distinct nucleobases. Different genes are differentiated or detected by identifying a differentiable sensitivity index that is defined to be the shifts of the resonant frequency of the nanotube. Simulation results indicate that the nanosensor is able to differentiate distinct genes, i.e., small proline-rich protein 2 A, small proline-rich protein 2B, small proline-rich protein 2D, and small proline-rich protein 2E, with a recognizable sensitivity. The research provides a rapid, effective, and practical method for detection of genes.

Author(s):  
Behrouz Arash ◽  
Quan Wang ◽  
Vijay K. Varadan

The potential of single-walled carbon nanotubes as nanosensors in detection of noble gases via a vibration analysis is investigated using molecular dynamics simulations. An index based on frequency shifts of the nanotubes in an environment of noble gas atoms is defined and examined to measure the sensitivity of the sensors. The effects of density of gas atoms on the tube sensors, the diameter and length of the tubes, and the type of restrained boundary of the tubes on the sensitivity are studied. The simulation results indicate that the resolution of a sensor made of a (8, 8) carbon nanotube with a length of 4.92 nm can achieve an order of 10−6 fg and the sensitivity can be enhanced by nanotubes with smaller sizes and stiffer boundary conditions.


2013 ◽  
Vol 80 (4) ◽  
Author(s):  
Yuan Cheng ◽  
Nicola Maria Pugno ◽  
Xinghua Shi ◽  
Bin Chen ◽  
Huajian Gao

Molecular dynamics simulations are performed to investigate the effect of surface energy on equilibrium configurations and self-collapse of carbon nanotube bundles. It is shown that large and reversible volumetric deformation of such bundles can be achieved by tuning the surface energy of the system through an applied electric field. The dependence of the bundle volume on surface energy, bundle radius, and nanotube radius is discussed via a dimensional analysis and determined quantitatively using the simulation results. The study demonstrates potential of carbon nanotubes for applications in nanodevices where large, reversible, and controllable volumetric deformations are desired.


2013 ◽  
Vol 479-480 ◽  
pp. 75-79 ◽  
Author(s):  
Bin Hao Chen ◽  
Yi Wu Chao ◽  
Cheng Chi Wang

Carbon nanotubes (CNTs) have been proposed as one of the most promising materials for nanoelectro-mechanical system due to high elastic modulus, high failure strength and excellent resilience [1,. Recent development of many-body interaction [3, made possible realistic molecular dynamics (MD) simulations of carbon-made systems. We carried out such studies for carbon nanotubes under generic modes of mechanical load: axial compression, bending, and torsion. A singular behavior of the nanotube energy at certain levels of strain corresponds to abrupt change in morphology. In this letter, we report the torsional instability analysis of single wall carbon nanotube filled with hydrogen via molecular dynamics simulations. The simulations are carried out at a temperature 77K which previous study obtained the hydrogen storage inside CNT at this condition [A. C. Dillo. Here we use atomistic simulations to study a flexible surface narrow carbon nanotube with tube diameters 10.8 Å. According to conventional physisorption principles, the gas-adsorption performance of a porous solid is maximized when the pores are no larger than a few molecular diameters [8]. Under these conditions, the potential fields produced at the wall overlap to produce a stronger interaction force than that observed in adsorption on a simple plane. However, the mechanisms responsible for the adsorption and transportation of hydrogen in nanoporous solids or nanopores are not easily observed using experimental methods. As a result, the use of computational methods such as molecular dynamics (MD) or Monte Carlo (MC) simulations have emerged as the method of choice for examining the nanofluidic properties of liquids and gases within nanoporous materials [9,1. Several groups have performed numerical simulations to study the adsorption of water in CNTs [11-1, while others have investigated the diffusion of pure hydrocarbon gases and their mixtures through various SWNTs with diameters ranging from 2 ~ 8 nm [17-19] or the self-and transport diffusion coefficients of inert gases, hydrogen, and methane in infinitely-long SWNTs [20-21]. In general, the results showed that the transport rates in nanotubes are orders of magnitude higher than those measured experimentally in zeolites or other microporous crystalline solids. In addition, it has been shown that the dynamic flow of helium and argon atoms through SWNTs is highly dependent on the temperature of the nanotube wall surface [22]. Specifically, it was shown that the flow rate of the helium and argon atoms, as quantified in terms of their self-diffusion coefficients, increased with an increasing temperature due to the greater thermal activation effect. Previous MD simulations of the nanofluidic properties of liquids and gases generally assumed the nanoporous material to have a rigid structure. However, if the nanoporous material is not in fact rigid, the simulation results may deviate from the true values by several orders of magnitude. Several researchers have investigated the conditions under which the assumption of a rigid lattice is, or is not, reasonable [23, 24]. In general, the results showed that while the use of a rigid lattice was permissible in modeling the nanofluidic properties of a gas or liquid in an unconfined condition, a flexible lattice assumption was required when simulating the properties of a fluid within a constrained channel. Moreover, in real-world conditions, the thermal fluctuations of the CNT wall atoms impact the diffusive behavior of the adsorbed molecules, and must therefore be taken into account. This study performs a series of MD simulations to investigate the transport properties of hydrogen molecules confined within a narrow CNT with a diameter of 10.8 Å (~ 1 nm) at temperatures ranging from 100 ~ 800 K and particle loadings of 0.01~1 No/Å. To ensure the validity of the simulation results, the MD model assumes the tube to have a flexible wall. Hydrogen molecules are treated as spherical particles. In performing the simulations, the hydrogen molecules are assumed to have a perfectly spherical shape. In addition, the interactions between the molecule and the CNT wall atoms and the interactions between the carbon atoms within the CNT wall are modeled using the Lennard-Jones potential [25,2. The simulations focus on the hydrogen adsorption within the SWNT not adsorption in the interstices or the external surface of nanotube bundles.


2019 ◽  
Vol 33 (23) ◽  
pp. 1950258 ◽  
Author(s):  
Danhui Zhang ◽  
Houbo Yang ◽  
Zhongkui Liu ◽  
Anmin Liu

Polynylon66, as a kind of important engineering plastics, is widely used in various fields. In this work, we studied the interfacial interactions between polynylon66 and single-walled carbon nanotubes (SWCNTs) using molecular dynamics (MD) simulations. The results showed that the polynylon66 could interact with the SWCNTs and the mechanism of interfacial interaction between polynylon66 and SWCNTs was also discussed. Furthermore, the morphology of polynylon66 adsorbed to the surface of SWCNTs was investigated by the radius of gyration. Influence factors such as the initial angle between polynylon66 chain and nanotube axis, SWCNT radius and length of polynylon66 on interfacial adhesion of single-walled carbon nanotube-polymer and the radius of gyration of the polymers were studied. These results will help to better understand the interfacial interaction between polymer and carbon nanotube (CNT) and also guide the fabrication of high performance polymer/carbon nanotube nanocomposites.


1998 ◽  
Vol 13 (9) ◽  
pp. 2357-2362 ◽  
Author(s):  
Madhu Menon ◽  
Deepak Srivastava

Complex three-point junctions of single-walled carbon nanotubes are proposed as building blocks of nanoscale electronic devices. Both T- and Y-junctions, made up of tubes with differing diameters and chiralities, are studied as prototypes. All the proposed complex junctions have been found to be local minima of the total energy on relaxation with a generalized tight-binding molecular dynamics scheme.


2006 ◽  
Vol 17 (02) ◽  
pp. 187-196 ◽  
Author(s):  
OSMAN BARIŞ MALCIOĞLU ◽  
EMRE TAŞCI ◽  
ŞAKİR ERKOÇ

Thermal stability and molecular electronic properties of a single walled, bamboo shaped carbon nanotube has been investigated. Molecular dynamics method is applied to investigate thermal stability, and electronic properties are calculated at the Extended Huckel level. Although bamboo shaped carbon nanotubes observed in experimental literature are multi-walled, it is shown that the suggested structural model in this work, which is single-walled, is also both thermodynamically and energetically stable. Bamboo shape of the model investigated is due to periodical coronene-like spacers. The resultant structure is compartmented, having geometrical aberrations in the vicinity of spacers. There is no degradation in the average coordination number. The geometrical aberrations in the vicinity of spacers is due to curvature induced by the pentagons of the resultant geometry.


2012 ◽  
Vol 583 ◽  
pp. 22-26 ◽  
Author(s):  
Cui Cui Ling ◽  
Qing Zhong Xue ◽  
Xiao Yan Zhou

The effects of functional groups and degree of functionalization on the young modulus of carbon nanotubes (CNTs) are investigated through molecular dynamics and molecular mechanics simulations. It is found that young’s modulus depends greatly on the functional groups and degree of functionalization. The results show that the fluorine (-F) can replace the hydrogen, and young modulus of sing-walled CNTs (SWNT) modified by -F functional group can inherit the mechanical properties of intrinsic SWNT. The binding energy between functional groups and SWNT, and electrostatic energy among the functional groups are mainly responsible for these findings. These characteristics rival those of SWNT modified by hydrogen allow one to consider SWNT modified by -F functional group for a range of technologies, in particular require better inertness and stability than unachievable for the compound.


2011 ◽  
Vol 133 (2) ◽  
Author(s):  
Tarek Ragab ◽  
Cemal Basaran

The unravelling of (10, 10) and (18, 0) single-walled carbon nanotubes (SWCNTs) is simulated using molecular dynamics simulations at different temperatures. Two different schemes are proposed to simulate the unravelling; completely restraining the last atom in the chain and only restraining it in the axial direction. The forces on the terminal atom in the unravelled chain in the axial and radial directions are reported till the separation of the atomic chain from the carbon nanotube structure. The force-displacement relation for a chain structure at different temperatures is calculated and is compared to the unravelling forces. The axial stresses in the body of the carbon nanotube are calculated and are compared to the failure stresses of that specific nanotube. Results show that the scheme used to unravel the nanotube and the temperature can only effect the duration needed before the separation of some or all of the atomic chain from the nanotube, but does not affect the unravelling forces. The separation of the atomic chain from the nanotube is mainly due to the impulsive excessive stresses in the chain due to the addition of a new atom and rarely due to the steady stresses in the chain. From the simulations, it is clear that the separation of the chain will eventually happen due to the closing structure occurring at the end of the nanotube that would not be possible in multiwalled nanotubes.


2020 ◽  
Vol 34 (31) ◽  
pp. 2050355
Author(s):  
Min Li ◽  
Quan Xie ◽  
Xiangyan Luo ◽  
Zean Tian

The deformation behavior of the nanocomposite structure under tension was studied by molecular dynamics (MDs) simulation. This nanocomposite structure is called as SiNW@CNT, which is a silicon nanowire (SiNW) embedded in carbon nanotube (CNT). The simulation results show that the insertion of the SiNW into CNT increases the tensile strength of zigzag CNT and the maximum tensile strain of the armchair CNT. However, it can greatly reduce the maximum tensile strain of the zigzag CNT and the maximum tensile strength of the armchair CNT. In addition, the maximum tensile strain of the SiNW@CNT has little to do with the diameter of the CNT, but is mainly related to the chirality of the CNT. For both hollow CNT and SiNW@CNT, the tensile strength is related to the diameter and chirality, and smaller diameter but greater tensile strength. This findings suggest that the physical properties of the SiNW@CNT can be tailored to specific applications by controlling the CNT diameter and chirality.


2011 ◽  
Vol 1284 ◽  
Author(s):  
Leonardo D. Machado ◽  
Sergio B. Legoas ◽  
Jaqueline S. Soares ◽  
Nitzan Shadmi ◽  
Ado Jorio ◽  
...  

ABSTRACTIn this work we present preliminary results from molecular dynamics simulations for carbon nanotubes serpentine dynamics formation. These S-like nanostructures consist of a series of parallel and straight nanotube segments connected by alternating U-turn shaped curves. Nanotube serpentines were experimentally synthesized and reported in recent years, but up to now no atomistic simulations have been carried out to address the dynamics of formation of these structures. We have carried out fully atomistic molecular dynamics simulations in the framework of classical mechanics with a standard molecular force field. Multi-million atoms structures formed by stepped substrates with a carbon nanotube (about 1 micron in length) placed on top of them have been considered in our simulations. A force is applied to the upper part of the tube during a short period of time and then turned off and the system set free to evolve in time. Our results showed that these conditions are sufficient to form robust serpentines and validate the general features of the ‘falling spaghetti mechanism’ previously proposed to explain their formation.


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