Coarse grained molecular dynamics and theoretical studies of carbon nanotubes entering cell membrane

Motivated by recent experimental observations that carbon nanotubes （CNT） can enter animal cells, here we conduct coarse grained molecular dynamics and theoretical studies of the intrinsic interaction mechanisms between CNT＇s and lipid bilayer. The results indicate that CNT-cell interaction is dominated by van der Waals and hydrophobic forces, and that CNT＇s with sufficiently small radii can directly pierce through cell membrane while larger tubes tend to enter cell via a wrapping mechanism. Theoretical models are proposed to explain the observed size effect in transition of entry mechanisms.

Torsional Characteristics of Single Walled Carbon Nanotube with Water Interactions by Using Molecular Dynamics Simulation

The torsional characteristics of single walled carbon nanotube(SWCNT) with water interactions are studied in this work using molecular dynamics simulation method. The torsional properties of carbon nanotubes(CNTs) in a hydrodynamic environment such as water are critical for its key role in determining the lifetime and stability of CNT based nano-fluidic devices. The effect of chirality, defects and the density of water encapsulation is studied by subjecting the SWCNT to torsion. The findings show that the torsional strength of SWCNT decreases due to interaction of water molecules and presence of defects in the SWCNT. Additionally,for the case of water molecules encapsulated inside SWCNT, the torsional response depends on the density of packing of water molecules. Our findings and conclusions obtained from this paper is expected to further compliment the potential applications of CNTs as promising candidates for applications in nano-biological and nano-fluidic devices.

Size dependency and potential field influence on deriving mechanical properties of carbon nanotubes using molecular dynamics

A thorough understanding on the mechanical properties of carbon nanotube （CNT） is essential in extending the advanced applications of CNT based systems. However, conducting experiments to estimate mechanical properties at this scale is extremely challenging. Therefore, development of mechanistic models to estimate the mechanical properties of CNTs along with the integration of existing continuum mechanics concepts is critically important. This paper presents a comprehensive molecular dynamics simulation study on the size dependency and potential function influence of mechanical properties of CNT. Commonly used reactive bond order （REBO） and adaptive intermolecular reactive bond order （A1REBO） potential functions were considered in this regard. Young＇s modulus and shear modulus of CNTs are derived by integrating classical continuum mechanics concepts with molecular dynamics simulations. The results indicate that the potential function has a significant influence on the estimated mechanical properties of CNTs, and the influence of potential field is much higher when studying the torsional behaviour of CNTs than the tensile behaviour.

Effect of hydrophobicity on the water flow in carbon nanotube-A molecular dynamics study

This work focuses on the study of the effect of hydrophobicity on the water flow in carbon nanotubes(CNTs)using a molecular dynamics(MD)approach for a wide range of potential applications such as water purification and high efficiency of nanofluid energy absorption systems(NEAS).The hydrophobicity between liquid water and surface of CNTs was characterized by interaction-energy-coefficient(IEC)—a parameter describing the energy interaction strength between water molecules and carbon atoms.It is shown that the static contact angles between water and carbon surface decrease from 155° to 44°when the values of IEC increase from 0.042 kJ/mol to 2.196 kJ/mol.In addition,the pressure drops in CNT became independent of IEC when the IEC value was higher than 1.192 kJ/mol for a given flow rate.It was found that the hydrophobicity of CNT surface has a significant impact on the pressure drop of water flow in the CNTs and MD method provides a quantitative evaluation of the impact.

Thermal conductivity of carbon nanoring linked graphene sheets:A molecular dynamics investigation

Improving the thermal conduction across graphene sheets is of great importance for their applications in thermal management. In this paper, thermal transport across a hybrid structure lbrmed by two graphene nanoribbons and carbon nanorings （CNRs） was investigated by molecular dynamics simulations. The effects of linker diameter, number, and height on thermal conductivity of the CNRs-graphene hybrid structures were studied respectively, and the CNRs were found effective in transmitting the phonon modes of GNRs. The hybrid structure with 2 linkers showed the highest thermal conductivity of 68.8 W·m^-1·K^-1. Our work presents important insight into fundamental principles governing the thermal conduction across CNR junctions and provides useful guideline for designing CNR-graphene structure with superior thermal conductivity.

Numerical distortion and effects of thermostat in molecular dynamics simulations of single-walled carbon nanotubes

In this paper, single-walled carbon nanotubes （SWCNTs） are studied through molecular dynamics （MD） simulation. The simulations are performed at temperatures of 1 and 300K separately, with atomic interactions characterized by the second Reactive Empirical Bond Order （REBO） potential, and temperature controlled by a certain thermostat, i.e. by separately using the velocity scaling, the Berendsen scheme, the Nose-Hoover scheme, and the generalized Langevin scheme. Results for a （5,5） SWCNT with a length of 24.5 nm show apparent distortions in nanotube configuration, which can further enter into periodic vibrations, except in simulations using the generalized Langevin thermostat, which is ascribed to periodic boundary conditions used in simulation. The periodic boundary conditions may implicitly be applied in the form of an inconsistent constraint along the axis of the nanotube. The combination of the inconsistent constraint with the cumulative errors in calculation causes the distortions of nanotubes. When the generalized Langevin thermostat is applied, inconsistently distributed errors are dispersed by the random forces, and so the distortions and vibrations disappear. This speculation is confirmed by simulation in the case without periodic boundary conditions, where no apparent distortion and vibration occur. It is also revealed that numerically induced distortions and vibrations occur only in simulation of nanotubes with a small diameter and a large length-to-diameter ratio. When MD simulation is applied to a system with a particular geometry, attention should be paid to avoiding the numerical distortion and the result infidelity.

Mechanical properties and thermal conductivity of pristine and functionalized carbon nanotube reinforced metallic glass composites:A molecular dynamics approach

This work uses the molecular dynamics approach to study the effects of functionalization of carbon nanotubes(CNTs)on the mechanical properties of Cu64Zr36 metallic glass(MG).Three types of functional groups,carboxylic,vinyl and ester were used.The effect of CNT volume fraction(Vf)and the number of functional groups attached to CNT,on the mechanical properties and thermal conductivity of CNT-MG composites was analysed using Biovia Materials Studio.At lower values of Vf(from 0 to 5%),the percentage increase in Young’s modulus was approximately 66%.As the value of Vf was increased further(from 5 to 12%),the rate of increase in Young’s modulus was reduced to 16%.The thermal conductivity was found to increase from 1.52 W/mK at Vf?0%to 5.88 W/mK at Vf?12%,thus giving an increase of approximately 286%.Functionalization of SWCNT reduced the thermal conductivity of the SWCNT-MG composites.

Investigation of Mechanical Behavior of Defective Carbon Nanotubes Using Molecular Dynamics Simulation

Carbon nanotubes （CNTs） having pristine structure （i.e., structure without any defect） hold very high mechanical properties. However, CNTs suffer from defects ＇which can appear at production stage, purification stage or be deliberately introduced by irradiation with energetic particles or by chemical treatment. In this article, mechanical properties of single-walled nanotubes with defects are studied under both compressive and tensile loads using molecular dynamics （MD） simulations. Two types of defectStone-Wales and vacancy defects with different defect densities are considered for present investigation. Molecular simulations are carried out using the classical MD method. The Brenner potential is used for carbon-carbon interaction in the CNT. Temperature of the system is controlled by velocity scaling. Simulation results show that the defects have negligible effect on the modulus of elasticity of nanotubes. However, they have significant effect on the failure stress and strain of the nanotubes.

The Hardness of Amorphous Si-DLC Films by Molecular Dynamics Simulations

Silicon-doped diamond-like carbon （Si-DLC） films possess the potential to improve wear performance of DLC films in humid atmospheres and at higher temperatures. But many experimental results of Si-DLC films show that their structure and mechanical properties have changed greatly with the increasing silicon content. Therefore, molecular dynamics （MD） simulations were used to generate hydrogen-free Si-DLC films and study their nano-indentation process under the interaction of a diamond indenter. The results show that sp3/sp2（C） （only carbon atoms） always decreases with the increasing silicon content. But sp3/sp2（C＋Si） ratio increases firstly and reaches a maximum at the silicon content of 0.2, and then decreases with the further increase of the silicon content. Bulk modulus and hardness of the Si-DLC films both decrease with the increasing of the silicon content, which has the same trend with Papakonstantinou and Ikeyama＇s results. It is concluded that the hardness of the Si-DLC films is dependent on sp3/sp2（C）, not sp3/sp2（C＋Si）.

Role of atomic transverse migration in growth of diamond-like carbon films

The growth of diamond-like carbon （DLC） films is studied using molecular dynamics simulations. The effect of impact angle on film structure is carefully studied, which shows that the transverse migration of the incident atoms is the main channel of film relaxation. A transverse-migration-induced film relaxation model is presented to elucidate the process of film relaxation which advances the original model of subplantation. The process of DLC film growth on a rough surface is also investigated, as well as the evolution of microstructure and surface morphology of the film. A preferential-to-homogeneous growth mode and a smoothing of the film are observed, which are due to the transverse migration of the incident atoms.

Mean Residence Time of CO2 Molecules in Flexible ZIF-8 Cages Explored by Molecular Dynamics Simulations

The adsorption sites and diffusion mechanism of CO2 molecules in the flexible Zn（MeIM）2 （MeIM=2-methylimidazole） （ZIF-8） have been investigated by grand canonical Monte Carlo and molecular dynamics simulations. A reasonable time correlation function is for the first time constructed to explore the mean residence time of CO2 molecules in the ZIF-8 cages, suggesting that C02 molecules can remain in the same cage for up to several tens of picoseconds. Furthermore, we find that the mean residence time almost linearly increases with the increasing pressure （or loading） at 273 and 298 K.

β-Diketones at Water/Supercritical CO2 Interface： A Molecular Dynamics Simulation

The structural and dynamical properties of hexafluoroacetylacetone(HFA) and acetylacetone(AA) at the water/supercritical CO2(Sc-CO2) interface at 20 MPa and 318.15 K are investigated by molecular dynamics simulations.The TIP3P potential is used for water and the EPM2 model is for CO2.The water phase and SC-CO2 phase form a distinct immiscible liquid-liquid interface.The two chelating molecules show interfacial preference.Comparatively,the AA molecules show somewhat more preference for interfacial region,whereas the HFA molecules are preferably near the Sc-CO2 phase.The orientational distribution of the β-diketone molecules and the radial distribution functions between β-diketones and solvents are obtained in order to study the microscopic structural properties of the β-diketones at the water-SC-CO2 interface.It is found that the translational diffusion and rotational diffusion of HFA and AA are obviously anisotropic and decrease as the β-diketone molecules approach the interface.The anisotropic dynamic behavior for the solute molecules is related to the corresponding structural properties.

Simulations on Various Lubrication Boundaries between Diamond-like Carbon Films

Molecular dynamics （MD） simulations were used to study a sliding friction process between DLC films on various boundary conditions. The experimental results revealed that, in the absence of a lubricant, a transfer film between the DLC films was formed. In contrast, when the oil or water lubricants were added to lubricate between the DLC films, a boundary lubrication layer was found. The friction forces on the water and oil lubrication were almost the same, but the friction force in the absence of a lubricant was larger than those on the water and oil lubrication. The conclusions were in good agreement with the experiments.

Surface vitrification of carbon by laser treatment: Insights of glass formation from molecular dynamics

Microstructural modification of carbon materials,such as carbon fibers(Cf)and pyrolytically deposited carbon,is important for engineering applications.However,the regulation of these materials is not an effortless task.To understand the impacts of thermal spikes from pulsed laser processing on the structural adaptation of amorphous carbon(a-C),we performed melt quenching by molecular dynamics(MD)simulations.Our results confirm that the vitrification behavior of carbon can be tuned by adjusting the cooling rate(R),which is controlled by the thermal spikes of laser processing.Moreover,we set up a two-step way to locate the critical cooling rate(R_(c))of monoatomic carbon,which is refined by the sharp change in the environmental similarity parameter.Using this novel technique,we demonstrate that the ordering degree and the local atomic motif can be largely modified by going across a bar of 100 K/ps,which is extracted as the critical cooling rate to ensure the complete amorphization of carbon.This approach provides a criterion for both experimentally processing and theoretically simulating a-C structures.Therefore,this work provides guidelines on how to tune the amorphous carbon structures of engineering materials and provides an outlook for the wonderland of amorphous carbon materials.

Directional mechanical and thermal properties of single-layer black phosphorus by classical molecular dynamics

Black phosphorus （BP） has received attention due to its own higher carrier mobility and layer dependent electronic properties, such as direct band gap. Interestingly, the single layer black phosphorus （SLBP） has had large popularity in applications related to thermoelectric, optoelectronic, and electronic devices. Here, we investigate the phonon spectrum, thermal conductivities, and stress strain effects. Robust anisotropy was mainly observed in the thermal conductivities together with the alongside zigzag （ZZ） direction value, compared to the armchair （AC） directions. We also investigated the attitude of stress that was anisotropic in both directions, and the stress effects were two times greater across the ZZ path than those in the AC direction at a low temperature. We obtained a ~oung＇s modulus of 63.77 and 20.74 GPa in the AC and ZZ directions, respectively, for a strain range of 0.01. These results had good agreement with first principle calculations. Our study here is useful and significant for the thermal tuning of phosphorus-based nanoelectronics and thermalelectric applications of phosphorus.

Balanced Fracturing and Cold-welding of Magnesium during Ball Milling Assisted by Carbon Coating:Experimental and Molecular Dynamic Simulation

The lignite-derived carbon from self-protection pyrolysis was employed to balance the fracturing and cold-welding of magnesium during ball milling.Particle size analysis indicates that the introduction of lignite-derived carbon can effectively reduce the particle size of Mg while the introduction of graphite does no help.Besides,the effect of lignite-derived carbon on crystallite size reduction of Mg is also better than graphite.A moderate cold-welding phenomenon was observed after ball-milling Mg with the lignite-derived carbon,suggesting less Mg is wasted on the milling vials and balls.Molecular dynamic simulations reveal that the balanced fracturing and cold-welding of magnesium during ball milling is mainly attributed to the special structure of the lignite-derived carbon:graphitized short-range ordered stacking function as dry lubricant and irregular shape/sharp edge function as milling aid.The preliminary findings in current study are expected to offer implications for designing efficient Mg-based hydrogen storage materials.

Shear Deformation of DLC Based on Molecular Dynamics Simulation and Machine Learning

Shear deformation mechanisms of diamond-like carbon(DLC)are commonly unclear since its thickness of several micrometers limits the detailed analysis of its microstructural evolution and mechanical performance,which further influences the improvement of the friction and wear performance of DLC.This study aims to investigate this issue utilizing molecular dynamics simulation and machine learning(ML)techniques.It is indicated that the changes in the mechanical properties of DLC are mainly due to the expansion and reduction of sp3 networks,causing the stick-slip patterns in shear force.In addition,cluster analysis showed that the sp2-sp3 transitions arise in the stick stage,while the sp3-sp2 transitions occur in the slip stage.In order to analyze the mechanisms governing the bond breaking/re-formation in these transitions,the Random Forest(RF)model in ML identifies that the kinetic energies of sp3 atoms and their velocities along the loading direction have the highest influence.This is because high kinetic energies of atoms can exacerbate the instability of the bonding state and increase the probability of bond breaking/re-formation.Finally,the RF model finds that the shear force of DLC is highly correlated to its potential energy,with less correlation to its content of sp3 atoms.Since the changes in potential energy are caused by the variances in the content of sp3 atoms and localized strains,potential energy is an ideal parameter to evaluate the shear deformation of DLC.The results can enhance the understanding of the shear deformation of DLC and support the improvement of its frictional and wear performance.

Molecular dynamics simulation of the deposition process of hydrogenated diamond-like carbon (DLC) films

The deposition process of hydrogenated diamond-like carbon (DLC) film greatly affects its frictional properties. In this study, CH3 radicals are selected as source species to deposit hydrogenated DLC films for molecular dynamics simulation. The growth and structural properties of hydrogenated DLC films are investigated and elucidated in detail. By comparison and statistical analysis, the authors find that the ratio of carbon to hydrogen in the films generally shows a monotonously increasing trend with the increase of impact energy. Carbon atoms are more reactive during deposition and more liable to bond with substrate atoms than hydrogen atoms. In addition, there exists a peak value of the number of hydrogen atoms deposited in hydrogenated DLC films. The trends of the variation are opposite on the two sides of this peak point, and it becomes stable when impact energy is greater than 80 eV. The average relative density also indicates a rising trend along with the increment of impact energy, while it does not reach the saturation value until impact energy comes to 50 eV. The hydrogen content in source species is a key factor to determine the hydrogen content in hydrogenated DLC films. When the hydrogen content in source species is high, the hydrogen content in hydrogenated DLC films is accordingly high.

Capillary infiltration of liquid silicon in carbon nanotubes:A molecular dynamics simulation

In this work,by simplifying the nanopores of porous C/C preform with single-walled carbon nanotubes(SWCNT)or double-walled carbon nanotubes(DWCNTs),the infiltration of liquid Si in the SWCNTs and DWCNTs was studied by molecular dynamics(MD)simulations.As a result,a quantitative relationship between tube diameter and liquid Si infiltration rate was established,which has been successfully ap-plied to reproduce the available experiment result.The obtained relationship indicates that the capillary infiltration of liquid Si at the nanoscale still conforms to the classic Lucas-Washburn law,however,the liquid Si infiltration quickly stops in small tubes with a diameter of less than 3 nm due to an obvious contraction of the tube wall.This work may provide theoretical guidance for pore structure optimization of porous C/C preform to fabricate high-density C/SiC composites.

Molecular dynamics simulation on mechanical property of carbon nanotube torsional deformation

In this paper torsional deformation of the carbon nanotubes is simulated by molecular dynamics method. The Brenner potential is used to set up the simulation system. Simulation results show that the carbon nanotubes can bear larger torsional deformation, for the armchair type （10,10） single wall carbon nanotubes, with a yielding phenomenon taking place when the torsional angle is up to 63°（1.1rad）. The influence of carbon nanotube helicity in torsional deformation is very small. The shear modulus of single wall carbon nanotubes should be several hundred GPa, not 1 GPa as others reports.