Non-equilibrium molecular dynamics study on radial thermal conductivity and thermal rectification of graphene

In the present study, the radial thermal rectification and thermal conductivity of the graphene were investigated by non-equilibrium molecular dynamics simulation and then corrected by quantum correction to make it closer to the fact. The Optimised three-body Tersoff potential is employed in order to simulate the interactions between the carbon atoms in the graphene sheet. A circular region in the centre and the one at the graphene edge are selected as hot and cold bath to generate radial temperature gradient. It is observed that the heat current passes through radially inward direction than outward with the same temperature gradient and hence there is a radial thermal rectification in graphene. Also, temperature distribution and heat flux are theoretically introduced as a function of distance from the graphene centre and then it is confirmed by the molecular dynamics simulation data. Finally, the influence of temperature gradient and size of graphene on radial thermal rectification and the impact of size on the radial thermal conductivity is investigated.     

Molecular dynamics simulation of lactate dehydrogenase adsorption onto pristine and carboxylic-functionalized graphene

ABSTRACT

Lactate dehydrogenase (LDH) is a tetrameric enzyme which is composed of two subunits known as LDHA and LDHB, which are encoded by the LDHA and LDHB genes respectively. LDH catalyses the last step in anaerobic glycolysis through the reversible conversion of pyruvate to lactate via coupled oxidation of NADH cofactor. The LDHA plays an important regulatory role in anaerobic glycolysis, by catalysing the final step of the process. Therefore, it is likely that increases in the expression level of LDHA in cancer cells could facilitate the efficiency of anaerobic glycolysis. Measuring the level of serum LDHA is a key step in the diagnosis of many cancer types. In this study, the adsorption, stability, and dynamics of LDHA on the surface of pristine graphene (PG) and carboxylated graphene (COOH-Graphene) were investigated using its molecular dynamics simulation. Variations in root mean square deviation, root mean square fluctuation, solvent accessible surface area and adsorption energy of the LDHA during the simulation were calculated to analyse the effect of PG and COOH-Graphene on the overall conformation of LDHA. Results showed that the adsorption of LDHA on COOH-Graphene is mostly mediated by electrostatic interactions, whereas on the PG, both Van der Waals and π-π interactions are prominent.     

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.     

Molecular dynamics simulations of thermal expansion properties of single layer graphene sheets

The area coefficients of thermal expansion (CTEs) of perfect single layer graphene sheet (SLGS) and SLGS with vacancy defects of different distributions were calculated in this work through molecular dynamics (MD) simulations. The effects of some parameters such as temperature, SLGS size, sample area size, vacancy fraction and vacancy distribution on CTE were investigated extensively. Numerical results clearly revealed that for both perfect and defective SLGSs, the area CTEs are negative and nonlinear with the temperature variation within a wide temperature range. Moreover, the area CTEs tend to be more insensitive to the temperature when temperature is higher than 600 K. The area CTE of a perfect SLGS converges only when the SLGS size and the ratio of the sample size to the SLGS size is above a critical value. When the SLGS size or the sample size is small, the area CTE shows distinct size-dependence. In addition, a set of empirical formulations is proposed for evaluating the area CTEs of perfect SLGSs within a wide temperature range. For the SLGS with vacancy defects, the area CTE decreases with the increase of vacancy fraction within the temperature range considered. Furthermore, compared with a decentralised distribution of vacancy defects, a concentrated distribution leads to a smaller value of area CTE of SLGS, especially for the case of high vacancy fraction.     

Molecular dynamics study of carbon nanotube oscillator on gold surface

We investigated the substrate effect of carbon nanotube (CNT) oscillators using classical molecular dynamics simulations. Double-walled CNT oscillators on {100} gold surface were considered. The nanotube–gold interactions induced the compressive deformations of the outer nanotube and affected the transitional velocity and the energy dissipation of the nanotube oscillator. When the inner nanotube was extruded from the outer nanotube, the central regions of the outer nanotube were compressed by the nanotube–gold interactions and then, these compressive forces pushed out the inner nanotube and finally, the transitional velocity of the inner nanotube was slightly increased at the edges regions. Since the energy dissipation of the nanotube oscillator on gold surface was higher than that in vapor, the decrease of the transitional velocity for the nanotube oscillator on gold surface was greater than that for the nanotube oscillator in vapor.     

Interfacial adhesion properties of graphene sheet on nanoscale corrugated surface: a molecular dynamics simulation study

Adhesive contacts between graphene sheet (GS) and corrugated substrates made of an ordered array of atomic pillars with variable geometries were investigated by molecular dynamics simulations. Depending on the height and interval distance of the pillars, GS can conformably coat the surface, partially adhere, or remain flat on top of the pillars. The relationship between the geometries of the pillar and the final adhesion configurations of GS was partially established. A critical adsorption energy was determined to achieve stable adsorption configuration of GS on corrugated substrates made of ordered pillar arrays. Besides the geometries of pillars, the effects of initial coating angle of GS were also considered as an important factor that affects the final adsorption configuration. We observed two interesting morphologies of GS, ‘I shape’ and ‘L shape’, which were determined by the initial coating angles.     

Molecular dynamics simulation of dispersion improvement of graphene sheets in nanofluids by steric hindrance resulting from functional groups

Nanofluids are candidate materials for thermal management of heat transfer equipment. Practical applications of thermally enhanced nanofluids contribute to the reduction of weight of systems, leading to improved energy efficiency. Microsize particles sink into the systems because of gravity, therefore rendering the addition meaningless in terms of improving thermal properties. However, nanoparticles can be buoyant, leading to Brownian motion in the fluid, when they do not aggregate with each other. The most important factor in nanofluids is long-term stability of the dispersion in the fluid. Numerous studies have reported the dispersion stability; functional groups attached to nanoparticles play a role in causing steric hindrance and have an affinity for the surrounding fluid, resulting in preserving the dispersion. We investigate the structural effects on dispersion by molecular dynamics simulations of nanofluid containing graphene sheets with functional groups of varying lengths at the surface. The results demonstrate that short functional groups were too short to cause significant steric hindrance, while relatively longer functional groups tended to stack onto the graphene sheets, leading to trapping due to strong van der Waals interactions. Additionally, we discuss the minimum number of functional groups necessary for maintaining dispersion through calculations of the area of a single functional group.     

Molecular dynamics simulation of liquid water under the influence of an external electric field

Molecular dynamics simulations of liquid water were performed at 258K and a density of 1.0?g/cm³ under various applied external electric field, ranging 0～10¹⁰?V/m. The influence of external field on structural and dynamical properties of water was investigated. The simple point charge (SPC) model is used for water molecules. An enhancement of the water hydrogen bond structure with increasing strength of the electric field has been deduced from the radial distribution functions and the analysis of hydrogen bonds structure. With increasing field strength, water system has a more perfect structure, which is similar to ice structure. However, the electrofreezing phenomenon of liquid water has not been detected since the self-diffusion coefficient was very large. The self-diffusion coefficient decreases remarkably with increasing strength of electric field and the self-diffusion coefficient is anisotropic.     

Molecular simulation of permeation behaviour of ethanol/water molecules with single-layer graphene oxide membranes

Graphene oxide (GO)-based materials have shown promise as water-permeating membranes in pervaporation separation. However, the feed permeation and surface affinity of single-layer nanoporous GO sheet for liquid mixtures remain unresolved. Here, the pressure-driven molecular transport of pure ethanol and pure water, as well ethanol-water mixtures, crossing through single-layer nanoporous GO sheet was studied by non-equilibrium molecular dynamics simulations. We show that single-layer GO sheet with controlled pore sizes can effectively reject ethanol and allow water permeation with high permeability. This means that porous GO sheets could act as an effective dehydration membrane, therefore providing the initial barrier for ethanol passage in GO-based membrane. The pore size effect was considered as the separation mechanism. Both ethanol and water molecules in the mixture show comparable affinity with GO surfaces. The hydrogen-bonding coupling interaction between mixture and surface functional groups provide addition influence on the molecular transport through GO pores.     

Molecular dynamics simulation of primary detonation process of TATB crystal under shock loading

Molecular dynamics simulations were performed to gain fundamental insights into the mechanisms for the primary detonation process of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) under shock wave loading using self-consistent charge density-functional tight binding(SCC-DFTB) calculations combined with the multiscale shock technique (MSST). The primary process starts with shock loading and ends with the formation of dynamically stable heterocyclic clusters, which could inhibit the reactivity of TATB. The results show that the initial step of shocked TATB decomposition is the N–O bond cleavage; then carbon rings aggregate and connect by N atoms to form clusters; after the carbon rings open, heterocyclic clusters with nitrogen are formed, and persist throughout the simulation. This is a new mechanism for the primary processes of shocked TATB and this initiation mechanism is independent of the initial shock speeds.     

Molecular dynamics study of methane in water: diffusion and structure

In this study, theoretical analysis on the geometries and electronic properties of various conjugated oligomers based on thiophene (Th) or bicyclic non-classical Th units is reported. The dihedral angle, bond length, bond-length alternation, bond critical point (BCP) properties, nucleus-independent chemical shift (NICS) and Wiberg bond index (WBIs) are analysed and correlated with conduction properties. The changes of bond length, BCP properties, NICS and WBIs all show that the conjugational degree is increased systematically with main chain extension. As a result, the highest occupied molecular orbital–lowest unoccupied molecular orbital energy separation (E _g) is decreased upon chain elongation. The E _g of oligomers based on bicyclic non-classical Th unit is much lower than that of Th-based oligomers due to the narrower E _g of bicyclic non-classical Ths compared to Th, which indicates that the narrow E _g of the bicyclic non-classical Ths can be carried over to their polymers by using them as building blocks for the polymers. The band structures and density of states analysis show that the four polymers all have small band gap ( < 0.9 eV), wide highest occupied bandwidth and relatively small effective mass of hole, which indicate that those proposed polymers may be potential conductors.     

Molecular dynamics study of the thermal conductivity of nanoscale argon films

Non-equilibrium molecular dynamics (MD) simulations were used to study the thermal conductivity of thin argon films. The MD simulations show that the argon film's thermal conductivity is affected by the thickness up to thickness of about 100 nm, which agrees with theoretical estimates. The results show that the MD method is very effective for modeling nanoscale thermal conduction. Besides pure argon films, the effect of vacancies on the argon film's thermal conductivity was also studied. The vacancies greatly reduce the thermal conductivity as a function of the vacancy concentration but not as a function of the vacancy distribution when the film's temperature is constant.     

Wrinkling and thermal conductivity of one graphene sheet under shear

Tersoff-potential - based molecular dynamics method is used to simulate wrinkling deformation of one graphene sheet under shear, and the obtained deformation is compared with analytical solutions of macro-membrane. Furthermore, thermal conductivity of the wrinkled graphene at different temperatures is calculated. It is found that (1) the wrinkling deformation of graphene sheet under shear is close to the analytical solutions of macro-membrane under shear, which implies that the solutions of macro-membrane are applicable to predict the wrinkling deformation of graphene sheets under shear; (2) the more serious the wrinkling of the graphene under shear is, the stronger the phonon scattering is and, therefore, the lower the thermal conductivity of the wrinkled graphene is; (3) within the temperature range of 400–700 K, the thermal conductivity of graphene sheet decreases with increase in temperature.     

Molecular dynamics simulation of crack growth in pure titanium under uniaxial tension

The analysis of crack growth in titanium was performed using molecular dynamics simulation with Embedded Atom Method potentials. The effect of temperature and strain rate on the mechanism of crack growth and the change of microstructure were discussed. After setting an initial crack, the specimen was subjected to uniaxial tension strain up to the total strain level of 0.2 with a constant strain rate. During the period, the shape and the microstructure of crack tip as well as the stress–strain curves were monitored. In the simulation, the gather of voids and stress concentration leading to the crack growth occurred, which are in agreement with experimental results observed by transmission electron microscopy. The transformation from HCP to BCC also occurred at crack tip. The remarkable effect of temperature and strain rate on the growth direction and rate of stacking fault of crack tip was observed. Moreover, initial crack greatly lowered the tension yield point of pure titanium. In the stage of deformation, simulation results showed that loading strain rate and temperature strongly influenced peak stress point, which was increased by the low temperature and high strain, whereas the initial slope of the stress strain curve was independent of loading strain rate.     

Molecular dynamics study of deformation mechanisms of poly(vinyl alcohol) hydrogel

Molecular dynamics (MD) simulations have been performed on the physically crosslinking poly(vinyl alcohol) (PVA) hydrogel to study the deformation mechanisms under uniaxial tensile conditions. The distributions of hydroxyl oxygens and dihedral angle and the number of hydrogen bonds have been analysed to study the structure of the hydrogel. The water content and temperature dependency of mechanical properties have been investigated. The energy contributions from the partially united atom potential have been calculated as a function of strain. It is found that the stress–strain curve comprises toe region, linear region and yield and failure region which is close to most biomaterials. In the toe and yield region, all the contributions to the internal energy change a little. However, in the linear region, the bond stretching and angle bending energy increase rapidly and mainly dominate the region, and the energy increases more rapidly with the increasing water content but the decreasing temperature. The degree of crosslinking decreases with the increasing deformation. The polymer chains occur significant torsional activity in the toe region. Hydrogen bonds are stable in the toe and yield region, but the hydrogen bonds between hydroxyl groups and waters decrease in the linear region.     

Molecular dynamics study of enhanced autophosphorylation by S904F mutation of the RET kinase domain

The aberrant kinase activity of RET (rearranged during transfection), a transmembrane tyrosine kinase, is associated with human cancer. A point mutation caused by the replacement of solvent-front hydrophilic S904, located on the activation loop (A-loop), with a bulky hydrophobic phenylalanine residue can induce resistance to the type I kinase inhibitor vandetanib. A possible mechanism of this drug resistance is the release of a cis-autoinhibited conformation of RET for autophosphorylation, which activates RET kinase. Because the association between S904F mutation and enhanced autophosphorylation is unclear, we conducted molecular modeling analysis to compare unphosphorylated apo wild-type and S904F mutant structures. The structural compactness of the A-loop promoted ATP binding. When the A-loop is extended, the αC helix moves toward the glycine-rich loop, resulting in the protrusion of F735. The extruded F735 connects with E734 and R912 and constrains the ATP pocket entrance. Contrarily, a contracted A-loop pulls the αC helix away from the glycine-rich loop, burying F734 and making the ATP pocket accessible. The mutated F904 stabilizes the contracted A-loop and releases the autoinhibited conformation of RET, thereby facilitating autophosphorylation. We also simulated two ATP-bound systems. The binding free energies of ATP, estimated through the molecular mechanics with a generalized Born and surface area solvation approach, revealed that the S904F mutant was bound more tightly than was the wild type with the ATP. The findings support the premise of autophosphorylation promotion in the S904F mutant.     

Molecular dynamics simulation of tensile strain-altered hydrogen behaviour and its effects on local plasticity

Using molecular dynamics simulation, local plasticity of bcc Fe (0 0 1) is studied at different density of Fe–H cluster. H-induced softening and hardening of Fe substrate are observed along with the tensile elongation at low and high density, respectively. The two contradictory phenomena are ascribed to H behaviours-related plastic deformation. At high H partial pressure, initial H aggregation would lead to the formation of many H-enriched clusters similar to hydride. Tensile strain-induced dislocations (TSID) prefer to be generated and grow at the weakening interface of clusters and iron substrate. At low H partial pressure, TSIDs are uniformly distributed in the whole substrate. Owing to the affinity between H and dislocations, the diffusion of H appears to be distinct under different spatial distribution of TSIDs. H aggregation and dispersion can be enhanced and produce nonuniform and uniform plastic deformation during the continuous tensile process at high and low Fe–H cluster density, respectively. The former can stimulate local failures and accelerate the degradation of mechanical property. The results are helpful for better understanding of Fe–H cluster-related hardening and softening considering external strain-altered H behaviours except for the mechanism of H-dislocation interaction.     

Atomistic uniaxial tension tests: investigating various many-body potentials for their ability to produce accurate stress strain curves using molecular dynamics simulations

Molecular dynamics simulations, which take place on the atomistic scale, are now being used to predict the influence of atomistic processes on macro-scale mechanical properties. However, there is a lack of clear understanding on which potential should be used when attempting to obtain these properties. Moreover, many MD studies that do test mechanical properties do not actually simulate the macro-scale laboratory tension tests used to obtain them. As such, the purpose of the current study was to evaluate the various types of potentials for their accuracy in predicting the mechanical properties of iron from an atomistic uniaxial tension test at room temperature. Results demonstrated that while EAM and MEAM potentials all under predicted the elastic modulus at room temperature, the Tersoff and ReaxFF potentials were significantly more accurate. Unlike EAM and MEAM, both the Tersoff and ReaxFF potentials are bond order based. Therefore, these results demonstrate the importance of considering bonding between atoms when modelling tensile tests. In addition, the ReaxFF potential also accurately predicted the Poisson's ratio, allowing for complete characterisation of the material's behaviour. Overall, these findings highlight the need to understand the capabilities and limitations of each potential before application to a problem outside of the initial intended use.     

Molecular dynamics analysis on tensile properties of carbon nanotubes with different cracks

Molecular dynamics simulation is employed for the axial tension of single-walled carbon nanotubes (SWCNTs) with different cracks. The cracks of SWCNTs in this study actually are the crack-like defects. AIREBO potential is used to simulate the interactions among carbon atoms. The effects of the crack length, temperature, strain rate and tube diameter on the mechanical properties of SWCNTs are studied. It is found that the failure stress and failure strain decrease with the increase of crack length. And the results show that the failure stress and failure strain are related to the applied strain rate and affected by temperature especially by lower temperature. It is also revealed that the failure stress increases with the increase in tube diameter. The deformation behaviours of SWCNTs are also obtained.