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For the first time, molecular dynamics simulation was used to analyse the solubility of five kinds of nanoparticles (SiO2, ZnO, Al2O3, Fe2O3, TiO2), cellulose crystalline region and cellulose molecules in this paper. The results show that the solubility of cellulose nanoparticles is positively related to the number of –OH groups on the surface of nanoparticles. The solubility between nano particles and cellulose molecules is smaller than that between cellulose crystalline region and cellulose molecules, which leads to the direct introduction of nano particles for physical modification reducing the solubility parameters of insulating paper. Through the analysis of mechanical properties, thermal stability and insulation properties, it is concluded that the comprehensive performance of the model with 70% crystalline region ratio is the best. The proportion of crystalline region further increased, the improvement of thermal stability is not obvious; the relative permittivity and the content of crystalline region are in line with the binomial fitting curve, and the constant term in the fitting curve is the relative permittivity of the amorphous region model; increasing the proportion of crystalline region is beneficial to improve the insulation performance of cellulose insulation paper. [ABSTRACT FROM AUTHOR]

To further enhance the performance of nano-silica modified M-phenylene isophthalamide (MPIA) insulation paper, nano-SiO2 particles are modified by 3-aminopropyltriethyloxy silane (APTS) surface into meta-aramid insulation paper to form grafting nano-silica particles (GNP). In order to find the relative best performance of the nanoparticle doping ratio, molecular dynamics simulations were used to study the effect of different GNP volume fractions on the mechanical parameters of the MPIA amorphous region, and the highest mechanical performance was obtained with a volume fraction of 9.4 vol. %. Under this doping condition, the interaction between GNP and MPIA fibers was enhanced by the formation of a large number of hydrogen bonds. The addition of GNP decreased the diffusion of water, acid and gas in MPIA fibers and the influence of these substances on the thermal stability of aramid fibers. All these indicate that the addition of GNP further improves the performance of aramid insulation paper, improves the thermal stability of aramid insulation paper and delays the aging process of oil-immersed aramid insulation paper. This article provides a reference and basis for the preparation of meta-aramid insulation paper with relatively good thermal stability. [ABSTRACT FROM AUTHOR]

In view of the small molecular model established in the field of high voltage insulation, the actual operation of transformer cannot be fully reflected at micro-level. Therefore, this paper aims to improve the performance of computing environment and expand molecular scale. Firstly, two servers were connected through a high-speed communication network as the initial cluster architecture. Secondly, spatial decomposition and load balancing algorithms were used to improve the operation efficiency of cluster. Meanwhile, the oil-paper composite media model of 105 atoms could be established based on this cluster, but it consumed a lot of time. Therefore, we analysed the relationship between operation efficiency and four characteristic quantities such as central processing unit performance, number of cores, simulation time and number of nodes. Then the highest point of cluster operating efficiency was found through continuous optimisation. It can be summarised that the calculating speed of cluster is nearly 10 times faster than that of the large server. Meanwhile, according to the results based on this cluster, it can be concluded that water molecules would migrate towards the oil during heating. When the initial moisture content in paper is high, the high water region would appear at the oil-paper interface. [ABSTRACT FROM AUTHOR]

In operation, the insulation paper used for transformers is subject to electric stress. This paper may deteriorate as a result of the accumulation of mechanical stress and the polarisation of the electric field. The effect of electric fields on insulation paper is typically investigated through macroscopic tests; thus, the microscopic mechanism must be explored further. In this study, single- and multi-chain cellulose models were constructed to simulate the yield behaviour of cellulose under a strong electric field (1010 V m− 1) through molecular dynamics. The cracking process of insulation paper was also examined according to density functional theory. Results indicated that both single- and multi-chain celluloses yield under a strong electric field. This yield behaviour is consistent with that of the electric field, and it eventually breaks the cellulose chains. The energy gap between the lowest unoccupied and the highest occupied molecular orbitals suggested that cellulose molecules may encounter insulation breakdown at an electric field strength of 105 V m− 1. Furthermore, the initial fracture in the molecular chain of cellulose was observed under the weakest glycosidic bond. [ABSTRACT FROM PUBLISHER]

The diffusion behaviour of hydrogen, carbon monoxide, carbon dioxide, methane, acetylene, ethylene and ethane in oil and paper medium was examined using molecular dynamics to reveal the diffusion mechanism of gas molecules in transformer oil–paper insulation system at the microscopic level. These compounds are commonly used in the dissolved gas analysis of power transformers and produced during the ageing process of oil–paper composite insulating material. Two groups of models were constructed using molecular dynamics simulation software to simulate the diffusion behaviour of the aforementioned seven types of small gas molecules in oil and paper. The diffusion coefficients, displacement features, free volume characteristics and interaction energies of the gas molecules were investigated. In particular, the diffusion micro-mechanism of the gas molecules was observed. The differences in diffusion features among the gas molecules were discussed, and the factors influencing the diffusion of the gas molecules were compared. Simulation results indicate that the diffusion coefficients of gas molecules in cellulose is an order of magnitude lower than that in oil, and the diffusion coefficients of these gas molecules in the two types of insulation media have different orders. Free volume of gas molecules is the main factor that influences the diffusion behaviour in oil, whereas intermolecular interaction is the main influencing factor of diffusion behaviour in cellulose. [ABSTRACT FROM PUBLISHER]

The study of nano-scratching under water lubrication is helpful to understand the role of lubrication mechanism in the machining of single crystal γ-TiAl alloy. In this paper, through the comparative analysis of nano-scratching under different thicknesses of water layers, it was found that under a water layer thickness of 1 nm, nano-scratching not only improves the surface quality but also achieves multiple reductions in scratch force, stress, temperature and subsurface structural damage. In order to deeply reveal the internal mechanism of workpiece temperature variation under different thicknesses of water layer lubrication, a fitting formula was innovatively adopted to conduct quantitative analysis. In addition, with the increase of the thickness of the water layer, it was observed that the water film effect was continuously enhanced, and this change caused the matrix stress to gradually increase, which hindered the forward motion of the nanoscratch, ultimately resulting in an increase in the friction coefficient. These findings provide valuable insights into the nanoscratching mechanism of monocrystalline γ-TiAl alloy in the presence of water film, and provide a new perspective for understanding the complex mechanism of nanoscratch behaviour under water lubrication, thus promoting the understanding of nanoscale lubrication effects. [ABSTRACT FROM AUTHOR]

Staphylococcus aureus is a highly virulent nosocomial pathogen producing a wide array of virulence factors to orchestrate a deadly disease. Delafloxacin is a fluoroquinolone antibiotic targeting gyrase to confer its antibacterial properties by stabilising DNA breakage. Due to the presence of certain mutations in gyrase A (GyrA), fluoroquinolone resistance has been reported. In this paper, the computational basis of delafloxacin resistance in S. aureus is studied. Computational techniques including molecular dynamics simulations simulation were applied to observe the effects of delafloxacin binding to gyrase coupled with MM-PBSA-based binding energy calculation and PCA to further ascertain the stability of the complexes. The mutation in gyrase did not cause any significant structural perturbation owing to delafloxacin binding. A significant change in free binding energy was seen in mutant–delafloxacin complexes in contrast to wild-type counterparts. The lowest (most negative) binding free energy obtained in the WT–delafloxacin complex indicated a better affinity and more stable interaction than the mutant complexes. The key residues of GyrA involved in interaction with delafloxacin were identified using their contribution to binding energy through the implementation of per-residue MM-PBSA decomposition. Delafloxacin failed to maintain stable interaction when bound to a mutant binding pocket and trans-located to an alternate site. [ABSTRACT FROM AUTHOR]

In this paper, we introduce our development of both online and desktop graphical user interfaces (GUIs) for the xtb programme to enhance accessibility and user-friendliness. The field of molecular modelling has been profoundly transformed by the advent of modern semiempirical calculations, with the xtb programme from Prof. Stefan Grimme's group emerging as an exceptionally powerful tool in this domain. xtb programme operates through a command prompt interface, necessitating a certain level of technical proficiency from its users. The need to use a command prompt might be repealing for some users, such as beginners or users who are not dedicated to computational techniques. This was the primary motivation to develop GUIs for this programme, considering that experienced molecular modellers would also appreciate a user-friendly GUI application that helps them automate their modelling tasks. The online GUI represents a significant leap forward, allowing users to execute xtb calculations directly from their web browsers. Complementing the online version, our desktop GUI extends the functionalities available to users, harnessing the more extensive capabilities of the xtb programme. As all other tools of atomistica.online project, xtb GUIs are freely available at the project's official website – . [ABSTRACT FROM AUTHOR]

Identifying a means of effectively separating and adsorbing the harmful constituents from flue gas emissions is always crucial for the protection of human health and the environment. All-atom molecular dynamics were employed to analyze the dynamic behaviour of flue gas molecules in Au nanopores. The influences of various system temperatures, gas concentrations, and pore sizes on the adsorption conformation, diffusion coefficient, average adsorption energy, and adsorption probability of the flue gases inside an Au nanopore were examined. Results showed that when the temperature rose to 300∼400 K, the gaseous H2S constituent in the flue gas was swiftly adsorbed to the nanopore walls due to the strong H2S-Au interactions, enabling an effective separation of H2S from the flue gas. In addition, increases in pore size (d ≥ 40 Å) reduced the adsorption probability of CO2 and CO on the nanopore surfaces, which also promoted constituent separations of H2S from the flue gas. When the concentration of flue gas exceeded 6.6 mol/L, hydrogen bonds of H2O clusters and their networks entangled, impeding molecular diffusion and thereby reducing the functionality of nanopore-trapping molecules. The results presented in this paper provide a valuable reference for filter material design for flue gas depuration. [ABSTRACT FROM AUTHOR]

As I noted in the preface to the second special issue, the papers that are included 'represent only a small selection, to some extent arbitrary, of the papers being published in the robust field of free energy simulations'. 25 August 2020 This is the third issue of I Molecular Simulations i devoted to Free Energy Simulations. The paper by Singh and Sharma deals with the adsorption of surfactant micelles at metal-water interfaces; that by Deng and Wang, with -sheet peptide self-assembly morphology; that by Walker et al., with the binding mechanism of ATP:Mg SP 2+ sp and ADP:Mg SP 2+ sp ; and that by Du et al. with compression-induced solid-solid transitions in colloids. [Extracted from the article]

In this work, molecular docking and molecular dynamics (MD) simulation were applied to investigate the ability of natural cyclodextrins (CDs; Alpha, Beta and Gamma Cyclodextrins) and modified CDs (hydroxypropyl, random methyl and amino Beta Cyclodextrins) to form the stable inclusion complexes (ICs) with Crizotinib, the oral small molecule kinase inhibitor as a chemotropic drug. Results of molecular docking and MD simulation studies demonstrated that Crizotinib forms stable ICs with all natural and modified CDs and in the presence of this drug, all six CDs become more rigid. The presence of Crizotinib and the release of water molecules result in a decrease in the number of hydrogen bonds between cyclodextrins (CDs) and solvent molecules within the encapsulated CDs, compared to the hydrogen bonds observed in free CDs. Additionally, HPBCD exhibited the strongest affinity for binding and established the highest quantity of hydrogen bonds with Crizotinib. Finally, all results of this paper demonstrated the potential of using this formulation to improve the bioavailability of the selected drug. [ABSTRACT FROM AUTHOR]

Microtubulin is an important research target for anti-tumour drugs, which can be used to inhibit microtubulin polymerisation and improve the efficacy of tumour therapy. In this paper, 61 microtubule protein inhibitors with anticancer activity are selected as the data set for building a stable and effective QSAR (Topomer CoMFA) model, resulting in a Topomer CoMFA model with validation coefficients of q 2 = 0.737 and r 2 = 0.922. Fifteen new inhibitors with theoretically high activity are designed by screening the zinc database for new fragments with good activity through the contribution descriptors obtained by Topomer CoMFA. After simulating the binding affinity and interaction of the inhibitors with the proteins by molecular docking, all these compounds formed strong interactions such as hydrogen bonds with multiple amino acids in the receptor proteins. Furthermore, molecular dynamics results show that the predicted highly active compounds exhibited stable and favourable binding patterns to the active pocket. In addition, these new compounds exhibit good ADMET properties. The present work establishes a reliable QSAR model for computational simulation screening of microtubulin drug development and provides a basis for further access to novel microtubulin inhibitors. [ABSTRACT FROM AUTHOR]

To explore the mechanical properties and deformation mechanism of twin γ-TiAl alloy under load and impact, based on the special interface structure in polycrystals, twinning at room temperature is established in this paper simulation of nanoindentation response of twin γ-TiAl alloy. Through the load-displacement curve, the hardness and Young's modulus of the workpiece are obtained. By analysing the microstructure evolution behaviour under the action of the indenter, it is found that during the loading process, multiple dislocation rings are generated in the grain and slip to the lower part of the workpiece, resulting in the hardness decreasing with the increase of the indentation depth, which is consistent with the indentation size effect; The dislocation lock generated during the unloading process delayed the annihilation of the defect structure, but the dislocation and stacking fault structure disappeared completely and the stress concentrated at the defect residue; in the stress relaxation stage, the dislocation ring structure in the grain extends and annihilates away from the grain boundary, releasing a large amount of stress to reduce the indentation load, and then the defect structure around the indenter is stable to keep the load stable, with high stress at the defect. [ABSTRACT FROM AUTHOR]

This paper proposes simulation protocols in terms of an auto-calibration strategy for the parameterisation of Gibbs ensemble Monte Carlo simulations for Lennard–Jones fluids. The proposed simulation protocols have been deduced from various approaches proposed in literature and have been tested against pure LJ fluids and their mixtures. These simulation protocols are intended to reduce or avoid time-consuming pre-simulations by adjusting the trial move limits, the number of attempted transfers, or the probability of attempted transfer during the equilibration phase, and can serve as a starting point for simulating more complex molecules, beyond LJ-fluids. This new approach aims to adjust simulation parameters to ensure a sufficient amount of successful trial moves as suggested in literature. It is similar to a previously proposed trial move adjustment and can easily be implemented in existing simulation code. Abbreviations: BWR EoS: Benedict–Webb–Rubin equation of state; CBMC: Configurational-bias Monte Carlo; EoS: Equation of state; GEMC: Gibbs ensemble Monte Carlo; LJ: Lennard–Jones; M1; M2; M3: Abbreviations for the three simulated mixtures; MC: Monte Carlo; PAT: Probability of attempted transfer; TL: Translation within a box (GEMC move); TR: Transfer to the other box (GEMC move); t-PR EoS: Volume-translated Peng-Robinson equation of state [ABSTRACT FROM AUTHOR]

Twin boundary (TB) plays an important role in the deformation process of materials. In this paper, molecular dynamics (MD) simulation was used to investigate the nanoindentation deformation behaviour of single-crystal FeCoCrNiCu high entropy alloy (SC-HEA) and nano-twinned FeCoCrNiCu high entropy alloy (NT-HEA) with different twin spacings. It is found that the main characteristic of plastic deformation of SC-HEA is the dislocation loop emission. The dislocation movement and distribution of NT-HEA are very different from that of SC-HEA. We found that partial dislocation slip parallel to the twin boundary (PSPTB) and twin partial slip (TPS) can lead to alloy softening. The hindrance of the TB causes the dislocation to slip within a single layer (known as confined layer slip, CLS), which strengthens the material. In the process of nanoindentation, the softening and strengthening mechanisms are constantly competing. When the twin spacing is larger than 1.23 nm, CLS dominates the competition with the hardening mechanism, and the hardness of the material increases with the decrease of the twin spacing. When the twin spacing is less than 1.23 nm, the dominant mechanism of plastic deformation changes to the softening mechanism controlled by TPS, and the hardness thus decreases as twin spacing increases. [ABSTRACT FROM AUTHOR]

In this paper, the CH4 combustion characteristics in CO2/O2/N2 atmosphere subjected to electric field were studied by the molecular dynamics simulation method. Conventional and unique pathways were obtained. The evolution law of reactants and main products and the first reaction time of main intermediates under the influence of different electric field intensities were analysed. Results showed that the addition of external electric fields increased conventional responses and species diversity. The generation of new pathways induced the production of new species, and the further reactions of new species produced other new pathways, thus accelerating the generation of new pathways and species in the electric field. It was noteworthy that, the applied external electric field could advance the reaction start time and reinforce the combustion process, but its effect on the reaction rate was highly nonlinear. The CH4 reaction with CO2 was significantly intensified at E ≥ 105 V/m, while suppressed at E = 104 V/m. Furthermore, electric fields could promote the oxidation degree of CH4, especially at E = 106 V/m. The studies provide theoretical guidance for revealing the mechanism of methane combustion under a high concentration CO2 atmosphere and promoting the efficient capture of CO2. [ABSTRACT FROM AUTHOR]

Thermoelectric compounds have the potential to produce electricity from waste heat, these materials are environmentally-friendly, which can play a key role on sustainable energy solution. This paper reports an investigation of electronic, optical and thermoelectric properties of two Half Heusler compounds TiNiSn and TiPtSn by employing density functional theory (DFT). Both compounds i.e. TiNiSn and TiPtSn exhibit an overestimated band gap with respective values 0.40 and 0.95 eV obtained by Tran Blaha modified Becke–Johnson functional (TB-mBJ) approximation, while, we found 0.113 and 0.84 eV within GGA + U (U = 6.13 eV) approximation, which are around other theoretical and experimental results. A detailed investigation of the obtained optical properties particularly, dielectric function, absorption, refractive index, and reflectivity of these compounds are given and discussed. Additionally, the transport properties of these compounds have been examined within Boltzmann statistics through BoltzTrap code, as well as certain thermoelectric parameters such as electrical conductivity, Seebeck coefficient and figure of merits are also determined. The obtained results reveal that the studied compounds are quite promising materials for thermoelectric applications. [ABSTRACT FROM AUTHOR]

Heat transfer is an important transmission phenomenon in the nature, and thermal conductivity is a basic thermodynamic data. In the process of chemical production, the reactants and products are mostly mixed liquid systems, but their thermal conductivity data are missing and difficult to define. The mechanism of thermal conductivity of liquid organics is still not sufficiently clarified at present. In this paper, the heat conduction of binary liquid organic mixtures: 3-pentanone + butanol, butanol + decane and heptane + n-undecane was simulated by nonequilibrium molecular dynamics, and the thermal conductivity at different weight fraction was calculated. The deviation between the calculated value and the experimental value of thermal conductivity is less than 9.3%. The results of heat flux decomposition and atomic heat path analysis show that thermal energy is mainly transferred through Coulomb interaction, kinetic energy and torsion angle. In addition, the molecular structure of the mixture and the weight fraction of each component are significantly correlated with the heat transfer mechanism. This study provides a preliminary insight into the heat transfer mechanism of binary liquid organic mixtures. [ABSTRACT FROM AUTHOR]

Glass transition temperature (Tg) is one of the most significant thermophysical property which is hard to measure experimentally. With the development of machine learning, many molecular presentation methods and prediction algorithms have been proposed for predicting Tg. However, most descriptors of these algorithms are linear, while the values of molecular descriptors obtained from experiments or simulation software may have nonlinear relationships. General nonlinear machine learning methods are difficult to apply for the super high dimensional characteristics of molecular descriptors. In this paper, molecular descriptors are defined in manifold space and manifold learning is used for dimension reduction. Different from other linear algorithms for selecting molecular descriptors, Locally Linear Embedding (LLE) is utilised to reduce dimensionalities by extracting new features from numerous molecular descriptors. The features with dimensionality reduction are fed to the eXtreme Gradient Boosting (XGBoost) model. This ensemble algorithm is suitable for predicting glass transition temperature due to its high adaptability and nonlinear approximation ability. Genetic algorithm (GA) is adopted for optimising the parameters of XGBoost. The combinatorial approach consists of dimensionality reduction, prediction and optimisation. Experimental results show that the proposed machine learning approach LLE-XGBoost-GA has higher accuracy in Tg prediction of polymers. [ABSTRACT FROM AUTHOR]

Surface wettability plays an essential role in bubble nucleation. This paper investigates the phase transition behaviour of argon films placed on inhomogeneous wettability substrates using molecular dynamics simulations. The location of bubble nucleation and initial nucleation time is investigated to reflect the effect of hydrophobic area fraction of inhomogeneous wettability surfaces on bubble nucleation. The results show that the bubbles appear first on the hydrophobic part of the inhomogeneous wettability surface. The relationship between hydrophobic area fraction and initial nucleation time is nonlinear. The initial nucleation time first decreases and then increases as the area of the hydrophobic region increases. In addition, the bubble nucleation process is restricted when the hydrophobic occupation is relatively large on inhomogeneous wettability surfaces. At last, the mechanism of bubble nucleation on inhomogeneous wettability surfaces is discussed in combination with the restrictive relationship between heat absorption and solid–liquid interaction energy. The amount of heat absorption does not directly determine the bubble nucleation. Bubble nucleation can arise in the location with a lower surface energy barrier once the heat absorption can overcome the solid–liquid interaction energy. [ABSTRACT FROM AUTHOR]

It has been proved that the incorporation of graphene oxide (GO) can improve the mechanical and durability performance of cementitious matrix to varying degrees. However, it is unclear how defects, functional group content, and composition, as well as other factors, affect the enhancing effect of GO on the mechanical characteristics of calcium-silicate-hydrate (C–S–H). In this paper, molecular dynamics (MD) simulation is employed to engineer the mechanical properties of the GO/C–S–H composite. The effects of defect type and size, functional group content and composition on the mechanical properties of GO/C–S–H composite are investigated. The results show that (i) GO sheets with quadrilateral and hexagonal defects can effectively strengthen GO/C–S–H composites, but GO sheets with triangular defects cannot be enhanced. And the enhancement effect grows with the increase in defect sizes; The tensile strength of both perfect GO/C–S–H composites and defective GO/C–S–H composites increases significantly with increasing strain rate; (ii) increasing the functional group content of GO can improve the tensile strength of GO/C–S–H; (iii) the mechanical properties of GO/C–S–H composites can be tuned by changing the ratio of hydroxyl and epoxy groups. These findings inspire the optimal design of GO/C–S–H composites using nanotechnology. [ABSTRACT FROM AUTHOR]

Graphene-based materials have been considered as reinforcement for cement-based materials due to its excellent properties. In this paper, the effects of graphene oxide (GO) and graphene nanoplatelets (GNPs) on the mechanical properties and microstructure of cement-based composites are investigated. The results reveal that the incorporation of 0.02 wt% GO and GNPs can enhance the flexural strength by 16.3% and 11.6%, respectively. In addition, GO and GNPs can fill the cracks and form a compacted microstructure in cement mortars. Furthermore, the enhanced mechanism of calcium silicate hydrate composite (C–S–H), which is the main production of cement hydration, is studied by reaction molecular dynamics. The results from simulation show that Young's modulus and tensile strength of C–S–H are enhanced by 32.1% and 23.8% with the incorporation of GO, because the hydrogen-bonds (H-bonds) linkages and Ca2+ near the interface surface play an important role to improve the interface adhesion and transfer more loads between GO and C–S–H. Comparatively, the graphene nanosheet unremarkable enhances the mechanical behaviour of C–S–H composite due to poor binding in the interlayer region. [ABSTRACT FROM AUTHOR]

The modelling of semi-conductor elements in molecular electronics as an emerging technological field requires further development. Using circuit elements, a typical model is presented in this paper. Taking the advantage of this model, a pyridine derivative molecular diode is modelled and the theory behind the components of the molecule model is explained. Subsequently, the physical properties of the proposed pyridine derivative molecular diode, including the electric potential drop along the molecule, rectification ratio, diode current, power consumption, transmission spectrum, and electron density along the molecular diode, are investigated. Then, using the molecular diode model, the basic logic gates including AND, OR, NOT, and XOR gates are modelled and using the basic gate model, the modelling of basic reversible molecular logic gates including Feynman, Toffoli, BVF, and Peres gates are implemented. Moreover, a full adder is modelled using the two Peres gate model. [ABSTRACT FROM AUTHOR]

When performing computations where load balancing is complex, dynamic load balancing is becoming increasingly necessary. In this paper, we examine one of these methods, Task-Based Parallelism. Many libraries implement Task-Based Parallelism, however, in this paper we examine the OpenMP standard and implementations, and apply it to the Classical Molecular Dynamics code, DL_POLY_4, focusing on the two body force calculations that make up a large percentage of the compute in many simulation runs. Our results show reasonable performance using OpenMP tasks, however, some of the extensions available in other libraries such as OmpSs or StarPU may help with performance for problems similar to Molecular Dynamics, where avoiding race conditions between tasks can have a substantial scheduling overhead. [ABSTRACT FROM AUTHOR]

In this paper, the molecular dynamics simulation method was used to establish the MD model for diamond cutting iron. The cutting process was simulated, and the change rules of temperature, cutting stress and radial distribution function with timestep were analysed. The results show that: As the cutting progresses, the temperature will increase gradually, the cutting stress fluctuates around 50,000 bars, and the wear mechanism of tool is analysed form a microscopic perspective; By adjusting the posture of the tool, the rake angle and the flank angle are changed, and the size of the thermostat layer and boundary layer are adjusted at the same time, which reduces the impact of non-Newton atoms on the workpiece; The change rules of temperature and cutting stress under different rake angle and flank angle conditions are analysed, and the minimum cutting stress is obtained when the rake angle is 15 degrees; By prefabricating a crack on the flank face, the change rule of the crack edge stress is studied. It is found that due to the occurrence of crack, the contact area between the tool and the workpiece is reduced, and there is obvious stress concentration at the edge of the crack. [ABSTRACT FROM AUTHOR]

Reactive molecular dynamics simulations are employed to explore the structural characteristics and tensile properties of calcium silicate hydrate (C–S–H) subjected to temperatures from 50 K to 700 K and strain rates from 0.008ps−1 to 0.8ps−1. The rising temperatures destroy the H-bond network, leading to obvious enlargement along the interlayer direction and the layered structural characteristics convert into staggered characteristics. The mechanical properties linearly decrease with an increase in temperatures and show a nonlinearly decrease with the higher strain rates. Furthermore, the strain rate has a stronger influence on the tensile strength at a higher temperature than that at a lower temperature. The effect of strain rates at various temperatures have the same pattern, which is consistent with the experiment results. The results in this paper provide the molecular-level views about the structure evolutions and mechanical behaviours of cement-based materials at low temperatures to high temperatures environments and different strain rates. [ABSTRACT FROM AUTHOR]

An unmodified polypropylene (PP) model and a modified model with 2% nano-silicon dioxide content were built initially, and then the mechanical parameters of the two models were compared by molecular dynamics simulation. The results show that the modulus of the modified model are larger than those of the unmodified model, and the ductility of both models is stable. The yield point of the modified model was increased by 8.5% at 25°C and 14.2% at 100°C compared with that of the unmodified model, respectively. Its Young's modulus is also increased. The main mechanism is that the addition of nanoparticles results in the decrease in the free volume of PP molecules, and the interaction between the strong polar –OH groups and the H atoms in a large number of –CH3 groups in PP molecules increases the intermolecular force in the whole model, which leads to the improvement of mechanical properties. Higher temperature leads to the intensification of molecular motion, which increases the distance between molecules, decreases the cohesive energy and reduces the mechanical properties of the model. The results of this paper can provide some reference for further research on the improvement of mechanical properties of nano-doped modified materials. [ABSTRACT FROM AUTHOR]

In this paper, molecular dynamics (MD) simulations are used to construct atomistic models of crosslinked epoxy networks. An improved algorithm, which considers both the cutoff distance criterion and the orientation criterion, has been developed to construct the realistic, well-equilibrated crosslinked epoxy networks. Epoxy networks containing diglycidyl ether bisphenol-A (DGEBA) as epoxy resin and tricarballylic acid as crosslinking agent are obtained using this algorithm. The results show that this algorithm can effectively decrease the molecular configurations that have unrealistic newly formed bond angles. Some important properties such as glass transition temperature (Tg), coefficient of thermal expansion (CTE) and Young's modulus are calculated from the equilibrated structures, which are in good agreement with existing experimental and simulated results. [ABSTRACT FROM AUTHOR]

The many-body dissipative particle dynamics (MDPD) is a promising mesoscopic method for solving various interfacial issues. However, an accurate mapping between simulation parameters and corresponding fluid properties is still ambiguous in MDPD due to its additional many-body interaction. In the present paper, we adopt the back-propagation Neural Network (BPNN) model with high-fidelity database as a rigorous calibration approach for MDPD. The relations between three main, simulation parameters (i.e. attractive and repulsive coefficient A,B and cut-off radius of repulsive force r d ) and four real-fluid static and dynamic properties (i.e. density, viscosity, self-diffusion coefficient and surface tension) are achieved accurately with the frame of BPNN. The influences of hyperparameters and training sets on mean squared errors (MSE) are also provided. Moreover, in order to improve the training efficiency of the model, we put forward three data selection methods: random data selection, extreme value data selection and the orthogonal experiment data selection. We compare three sampling methods for training data, and the orthogonal experiment design data selection is proved to be the most effective way to reduce MSE. The BPNN model is the potential to be a powerful tool for determining the simulation parameters within given fluid properties accurately and efficiently in the MDPD system. [ABSTRACT FROM AUTHOR]

The present paper is devoted to the study of diffusion of carbon nanotubes in water by molecular dynamics method. Two nanotube models were used, namely, 1D rigid rod and 3D (6, 6) armchair. The nanotube diameter was 0.818 nm, and their length ranged from 5.25 to 32.2 nm. Both translational and rotational diffusion coefficients were calculated. Besides, longitudinal and transverse diffusion was studied, and the corresponding diffusion coefficients were determined. The first of them was much larger than the second, and the difference reached two times. The average diffusion coefficients are relatively well described by the analytical dependences for rigid cylinders. The diffusion coefficients were calculated using Green–Kubo formula and Einstein relation. Relaxation of autocorrelation functions of nanotube velocity and angular velocity was systematically discussed for all cases. It is shown that this relaxation has two stages and the first stage is an exponential. The corresponding relaxation times were estimated. [ABSTRACT FROM AUTHOR]

Vibrating nanochannels are gaining interest in the fields of bio nano electromechanical systems (bio-NEMS) owing to their acoustic streaming ability (as a tail of nano-swimmers) and drug transportation mechanism. However, it is challenging to articulate such a mechanism experimentally. In this paper, molecular dynamic simulations are carried out to study the effect of the wall vibrations on the forced transportation of a water nanodroplet through a vibrating nanochannel. Here, the motion of water molecules was governed by modified Lennard–Jones (LJ) potential with an initial hydrophobic solid–liquid interface between the walls of nanochannel and water molecules. The density distribution of water molecules was spread towards the nanochannel walls for high vibration (2 (Å) amplitude and 60 GHz frequencies). The average resistance force increased 95.2% for high configuration wall vibrations, showing an increase of 13.96 pN, compared to 7.15 pN for low configuration wall vibrations (0.5 (Å) amplitude and 15 GHz frequency). This work may have significant implications for the application in the fields such as targeted drug delivery, enhanced oil recovery, nanofluidics and inkjet printing. [ABSTRACT FROM AUTHOR]

A model potential has been developed for magnesium nitride (Mg3N2) by fitting the parameters to an experimental lattice constant and bulk modulus. The mechanical properties have been calculated at 0 K. The potential was tested by molecular dynamics simulation at constant number, volume and energy ensemble at 300 K. The structural, ion transport and thermodynamic properties were investigated at a constant number and pressure–temperature ensemble between 300 and 2500 K. The simulated XRD diffractogram at 300 K shows that the crystalline peaks with corresponding (hkl) planes are correctly reproduced. A solid–liquid transition occurs at about 1800 K with a marked variation in all calculated physical properties. The potential successfully models the interactions in Mg3N2 at the solid and liquid phases. The results presented in this paper fill the gap of theoretical study in literature and extend our knowledge further, which could be useful to pave the way for the search of functional materials. [ABSTRACT FROM AUTHOR]

The history of the Monte Carlo for complex chemical systems Towhee open source Monte Carlo molecular simulation tool is discussed. A proof is given that the Widom insertion method for computing the chemical potential is formally correct even when combined with the most general version of arbitrary trial distribution configurational-bias Monte Carlo. A simulation strategy for computing single component vapour–liquid phase coexistence curves is presented as a guide for inexperienced practitioners of Monte Carlo simulations. A review of papers that cite the Towhee code is presented. The paper concludes with a discussion about releasing and sustaining a simulation package that uses an open source software license. [ABSTRACT FROM PUBLISHER]

Although all present papers have used I Materials Studio i to either build models or run simulations, other modelling tools might have also been used in the research studies reported. While there has always been competing demands made for the next direction that I Materials Studio i team should take, none of these have ever been allowed to over-shadow the reason why I Materials Studio i was developed in the first place: Science. The present special issue of I Molecular Simulation i is a collection of papers celebrating the 20th Anniversary of the molecular modelling software: I Materials Studio i ®. [Extracted from the article]

Regarding recent attempts for monitoring dissolved gases in oil transformers, in this paper, novel green phosphorene (GP), a new type of two-dimensional gas sensitive material was modified by transition metal decoration. We applied first-principles calculations based on Density functional theory and investigated the structures and electronic properties of H2, CH4, and C2H2 (dissolved gases) molecules adsorbed on the pristine, and metal decorated (Pt, and Pd) GP monolayer to understand its performance as a sensor. This analysis indicated that Pt-GP could be a satisfying material for C2H2 sensing at specific conditions, while it is unsuitable for detection of CH4, and H2 due to the weak interaction and short recovery time. The adsorption energy (Ead) of C2H2 on Pd-, Pt-GP systems is −1.18, and −1.84 eV, respectively, and 4, and 2 times more electrons were transferred from the C2H2 molecule to the systems, respectively in comparison with the pristine GP. Moreover, Pd-GP has a recovery time of 9.68 s under visible light at 350 K indicating that it is suitable for reusability, and it has a good sensitivity of 65.9% toward C2H2 molecule. Our results showed that the metal-decorated GP sensors are excellent candidates for analyzing dissolved gases in oil-based transformers. [ABSTRACT FROM AUTHOR]

It has been difficult to reproduce an arbitrary value of a membrane potential in molecular dynamics (MD) simulations for lipid bilayer systems because the membrane potential is sensitively affected by the net charge difference. The membrane potential and membrane properties depend on the intra- and extracellular ion concentrations. In this paper, we present a simple procedure to reproduce an arbitrary value of the membrane potential by all-atom MD simulations for two POPC bilayers system. The calculated membrane capacitance is consistent with an experimental result for the POPC. We show a correlation between the ion imbalance and the number of lipid molecules per leaflet to reproduce an arbitrary value of the membrane potential in MD simulations. Moreover, we show an asymmetry of lipid head group induced by the electronic polarizability and an asymmetry of lipid tail and water molecules on the membrane surface induced by the ion concentration gradient. [ABSTRACT FROM AUTHOR]

For high-energy single ion events, the relationship between electronic energy loss mechanism and atomic processes is generally described by the inelastic thermal spike model. However, the parameters required for the model are not accurately known and are often estimated from a free electron gas model. To ensure this model is more reliable and predictive, a more accurate calculation for the parameters should be taken. In this paper, the temperature dependence of the electronic heat capacity and electron–phonon coupling factor (e-ph) has been calculated, using density functional theory (DFT). The calculation results demonstrate that the effect of electron thermal excitation on the thermodynamic parameters is sensitive to the bandgap, and these parameters vary immensely with the electron temperature. Besides, to verify the accuracy of obtained parameters, both the swift heavy ions (SHI) irradiation in crystalline 6H-SiC and amorphous 6H-SiC are simulated, using the inelastic thermal spike model. And the results are more consistent with the experiment conclusion, for the obtained parameters by DFT. Hence, the calculated temperature-dependent parameters are more suitable for the inelastic thermal spike model. [ABSTRACT FROM AUTHOR]

The objective of this study was to apply molecular docking and molecular dynamics (MDs) simulation approaches to investigate the host–guest interactions between natural Cyclodextrins (CDs) (Alpha, Beta and Gamma Cyclodextrins) and some modified CDs (hydroxypropyl, sulfobutylether and randomly substituted methyl Beta Cyclodextrins) with Ataluren as a small molecule drug designed for diseases attributable to a nonsense mutation. Molecular docking results presented that randomly substituted methyl beta Cyclodextrin (RMBCD) has the highest binding affinity and Alpha Cyclodextrin (ACD) has the lowest binding affinity to Ataluren. According to the MDs simulation results, ACD and hydroxypropyl Cyclodextrin have not proper cavity for encapsulation of Ataluren. In contrast, Ataluren was totally included into the Beta Cyclodextrin (BCD), Gamma Cyclodextrin, sulfobutylether Beta Cyclodextrin (SBECD) and RMBCD due to appropriate interior capability. Moreover, MDs results showed that SBECD has the most conformational flexibility and BCD has the most conformational stability during simulation time. The results of this paper may open new paths to use this formulation for further researches in the delivery mechanism of hydrophobic pharmaceutical molecules. [ABSTRACT FROM AUTHOR]

In this paper, we characterise the adsorption of ethylene, propanol and hexanal molecules on crystalline ice by grand canonical Monte Carlo simulations performed at 236 K, a temperature which is typical of some Enceladus' environments. We show that at low coverage of the ice surface, the adsorption of propanol and hexanal is driven by the interaction of these molecules with the ice phase and, as a consequence, the adsorbed molecules lie more or less parallel to the ice surface. On the other hand, upon saturation, the adsorbate–adsorbate interactions become more and more important and the molecules tend to become tilted with respect to the surface, the aliphatic chain pointing towards the gas phase, while the polar head of propanol and hexanal molecules always stays attached to the ice surface, irrespective of the coverage. By contrast, the ethylene molecules do not show any strong affinity for the ice surface because of the corresponding weak binding energy. These results are in good agreement with the major features provided by the available experiments on similar systems. [ABSTRACT FROM AUTHOR]

Synthesis of graphene with reduced use of chemical reagents is essential for manufacturing scale-up and to control its structure and properties. In this paper, we report the mechanism for exfoliating graphene from graphite slabs using laser impulse. We set up a molecular dynamics model that accounts for the charge-mediated inter-atomic potential along with the forces from electromagnetic fields of a laser pulse. The role of different laser fluences on the exfoliation process of graphene quantified in terms of the interlayer energy transition, inter-layer displacement jump, and thermal shock propagation in graphene-graphite system. The simulation results confirm the exfoliation of a single layer graphene sheet for the laser power ranging from 100 × 10 − 14 to 2000 × 10 − 14 J/nm2. With an increase of laser fluence from 2000 × 10 − 14 to 4000 × 10 − 14 J/nm2, there is an increase in the graphene yield via the layer-after-layer exfoliation. The bridging bond dynamics between the successive graphene layers govern the exfoliation of the second layer. The results indicate promises for producing chemical-free graphene on a large scale for industrial applications. [ABSTRACT FROM AUTHOR]