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Graphene-based nanomaterials possess broad applications because of their excellent multi-functional properties. In this work, a facile self-assembling method was presented for preparing one kind of graphene oxide-based paper/hollow microspheres hybrid. It was found that most of the hollow microspheres can strongly anchored on the surface of graphene oxide paper (GOP) by an in-situ scanning electron microscope peeling testing combining with molecular dynamics (MD) simulation. In addition, the uniform distribution of hollow microspheres on the surface of GOP cannot only provide a better surface wettability, but also can effectively improve the interfacial stress-transfer capability between such hybrid and polymer matrix. Our work provides a guidance for the structural designs of graphene-based nanomaterials and broaden their applications.

Highly ordered polymer composites of layered graphene/graphene oxide (GO) sheets, i.e. graphene/GO paper, are attractive candidates for novel structural and functional applications. Here, molecular dynamics simulations are employed to elucidate the structural and mechanical properties of the graphene/GO paper based polymer composites. We find that the large scale properties of these composites are controlled by the conformation and content of polymer molecules within the interlayer galleries. Polymer conformations affect the interlayer spacing, while the polymer content controls the layer–matrix interactions, thereby affecting the elastic modulus of the composites. Additionally, the chemical composition of individual GO sheets also plays a critical role in establishing the mechanical properties of the composites. Specifically, a higher density of oxygen-containing groups leads to the decrease of elastic modulus of individual GO sheets. However, the groups also lead to the increased hydrogen bonds between the GO sheets and polymer molecules, resulting in the corresponding increase in overall stiffness. Our studies suggest the possibility of tuning the properties of graphene/GO paper composites by altering the conformation and content of polymer, as well as the density of functional groups on individual GO sheets.

In this paper we show that, high sensitivity and high selectivity room temperature ammonia (NH3) gas sensors with both visual and electrical response can be made from family of lead halide perovskites with different cations and anions. These sensors, based on papers, act as general platforms for new generation of solid state gas sensors for sensitive detection of NH3 gas by simple color change (∼10 ppm sensitivity) as well as electrical resistance change with sub ppm sensitivity limited by electrical noise only. The sensors with materials like CH3NH3PbI3 (MAPI), CH3NH3PbBr3 (MAPB) and CH(NH2)2PbI3 (FAPI), are grown on paper from solution. MAPB changes color from orange to white and FAPI and MAPI from black to yellow under NH3 gas exposure respectively. For electrical sensor operation, a fixed concentration (20 ppm) of NH3 gas, the sensitivity of MAPI is highest at 96 % followed by MAPB at 82 % and FAPI at 65 %. The sensors with electrical read out could trace NH3 gas well below ppm level with only few nanowatt of power consumption. Based on experiments, a sensing mechanism has been proposed. The proposed mechanism mainly consists of decomposition of the perovskite halides to lead (Pb) halide by preferential adsorption of NH3 gas molecules. The proposed mechanism has also been substantiated by molecular dynamics simulations. These sensors fabricated by simple solution process on paper substrates and operable at ambient temperature, are compatible with very low power (∼ nW) paper electronics.

Transformer faults frequently occur because of a deterioration of the insulation performance caused by corrosive sulfides. By studying the distribution and diffusion of different sulfides in oil paper, the mechanism of sulfur corrosion can be further investigated. Here, the diffusion of macromolecular sulfides (represented by DBDS and n-hexadecanethiol) and small molecular sulfides (represented by hydrogen sulfide) in oil-paper insulation systems were studied based on molecular dynamics simulation methods. The simulation results showed that cellulose had a strong interaction with hydrogen sulfide, while oil had a strong interaction with DBDS and n-hexadecathiol. This makes the trajectory and relative concentration of the various sulfides in the oil-Paper system different: DBDS was mainly distributed in oil, n-hexadecathiol was distributed at the oil-paper interface, and hydrogen sulfide was mainly distributed in cellulose. In addition, the diffusibility of DBDS and n-hexadecathiol in oil and cellulose were negatively correlated with the interaction energy: a larger interaction energy resulted in lower diffusion. The diffusion of hydrogen sulfide in oil paper was determined by the free volume fraction. A larger free volume fraction resulted in more intense molecular diffusion. The results of this work can provide a reference for prevention of sulfur corrosion.

It is important to study the diffusion of acids because acids can accelerate the aging of oil-paper insulation systems. In the paper, the diffusion of acids is weakened by adding nano-SiO2 in oil. The results of relative concentration, centroid trajectory and density field distribution by molecular dynamics simulation show that there are more acids in the oil of nano-SiO2 oil-cellulose paper system (Nano-O-P model) than that of pure mineral oil-cellulose paper system (Pure-O-P model). This is primarily attributed to the hydrogen bonding of nano-SiO2 to acids and the adsorption energy of oil to acids was increased in the Nano-O-P model. The number of hydrogen bonds between formic acids and cellulose in the Nano-O-P model was reduced by 32.5% compared with that in the Pure-O-P model, protecting the intermolecular hydrogen bonding structure of the cellulose paper and reducing the promotional effect of acids on the aging of oil-paper insulating systems.

Based on fundamental difference in diffusion mechanisms of substitutional and interstitial atoms and using molecular dynamics simulation of hydrogen migration, it is shown that accelerated hydrogen flux in the polycrystalline iron, as observed in the course of cathodic charging, cannot originate from the enhanced hydrogen grain boundary diffusion. A possible role of grain boundary cracking is supposed.

The formation mechanisms of wrinkles in single layer graphene sheets and graphene oxide (GO) papers, as well as their effects on the corresponding Young’s moduli have been studied based on the molecular dynamics simulations. Wrinkling occurs in GO papers in the form of undulation as a consequence of the interactions between the adjacent individual GO sheets. In particular, the edge-to-edge interactions play a dominant role in determining the wrinkled structure, whereas the face-to-face interactions hardly cause wrinkles as they are thermodynamically stable with inherently low potential energies. Both graphene sheets and GO papers with wrinkles show two different modes of deformation in tension. Although wrinkles have only a negligible effect on Young’s modulus of the individual graphene sheets, they reduce the Young’s modulus of GO papers by as much as 60% of the pristine value.

Moisture is an important factor that influences the safe operation of transformers. In this study, molecular dynamics was employed to investigate the diffusion behavior of water molecules in the oil–paper insulation materials of transformers. Two oil–cellulose models were built. In the first model, water molecules were initially distributed in oil, and in the second model, water molecules were distributed in cellulose. The non-bonding energies of interaction between water molecules and oil, and between water molecules and cellulose, were calculated by the Dreiding force field. The interaction energy was found to play a dominant role in influencing the equilibrium distribution of water molecules. The radial direction functions of water molecules toward oil and cellulose indicate that the hydrogen bonds between water molecules and cellulose are sufficiently strong to withstand the operating temperature of the transformer. Mean-square displacement analysis of water molecules diffusion suggests that water molecules initially distributed in oil showed anisotropic diffusion; they tended to diffuse toward cellulose. Water molecules initially distributed in cellulose diffused isotropically. This study provides a theoretical contribution for improvements in online monitoring of water in transformers, and for subsequent research on new insulation materials.

Dipeptidyl peptidase I (DPPI) inhibitors have potential use in the treatment of neutrophil inflammatory diseases, such as chronic obstructive pulmonary disease. The three-dimensional quantitative structure-activity relationship (3D-QSAR) model was established in this paper based on the computational biology method for 32 DPPI inhibitor compounds. Good predictability was obtained based on the application of the comparative molecular field analyses (CoMFA q2 = 0.582; r2 = 0.994; rpred2 = 0.661) and the comparative molecular similarity index analyses (CoMSIA q2 = 0.757; r2 = 0.964; rpred2 = 0.518). Contour maps illustrated possible areas affecting activity. Molecular docking results showed the interaction between DPPI inhibitors and protein (PDB: 4CDE ). Reliability was demonstrated further by the molecular dynamics simulation. These results can help gain insight into the mechanism of action of DPPI inhibitors and can provide a new direction for future design of more effective DPPI inhibitors.

This work aimed at studying the potentiality of interactions between kaolinite surfaces and a protein-fragment (350–370 amino acid units) extracted from the glycoprotein E1 in the transmembrane domain (TMD) of hepatitis C virus capsid. A computational work was performed for locating the potential electrostatic interaction sites between kaolinite aluminol and siloxane surfaces and the residues of this protein-fragment ligand, monitoring the possible conformational changes. This hydrated neutralized kaolinite/protein-fragment system was simulated by means of molecular modeling based on atomistic force fields based on empirical interatomic potentials and molecular dynamic (MD) simulations. The MD calculations indicated that the studied protein-fragment interacted with the kaolinite surfaces with an exothermic process and structural distortions were observed, particularly with the hydrophilic aluminol surface by favorable adsorption energy. The viral units isolation or trapping by the adsorption on the kaolinite nanoparticles producing structural distortion of the peptide ligands could lead to the blockage of the entry on the receptor and hence a lack of viral activity would be produced. Therefore, these findings with the proposed insights could be an useful information for the next experimental and development studies in the area of discovering inhibitors of the global challenged hepatitis and other pathogenic viruses based on the phyllosilicate surface activity. These MD studies can be extended to other viruses like the COVID-19 interacting with silicate minerals surfaces., Graphical abstract Unlabelled Image, Highlights • A protein of the Hepatitis C virus is adsorbed favorably on kaolinite surfaces. • Adsorption on kaolinite provokes changes of Hepatitis C virus. • Molecular dynamics are useful for exploring virus adsorption on mineral surfaces.

Graphical abstract, One of the promising drug targets against COVID-19 is an RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. The tertiary structures of the SARS-CoV-2 and SARS-CoV RdRps are almost the same. However, the RNA-synthesizing activity of the SARS-CoV RdRp is higher than that of the SARS-CoV-2 RdRp. We performed molecular dynamics simulations and found differences in their dynamic properties. In the SARS-CoV RdRp, motifs A–G, which form the active site, are up to 63% closer to each other. We also observed cooperative domain motion in the SARS-CoV RdRp. Such dynamic differences may cause the activity differences between the two RdRps.

Graphical abstract, In this study, density functional theory (DFT) and docking calculations were systematically performed to study the non-competitive interaction between Hydroxychloroquine (HCQ) and azithromycin (AZTH). The calculated changes in Gibbs free energy and enthalpy (at 310 K) were positive, indicating the non-spontaneous formation of HCQ-AZTH specifically in water media. Docking calculation confirmed the obtained DFT result as evident from the different binding sites of both drugs to the SARS-CoV-2 main protease and human angiotensin-converting enzyme 2 (ACE2) proteins. The HCQ-AZTH structure revealed enhanced electrochemical properties, suggesting the synergy between HCQ and AZTH without affecting their therapeutic efficacy against SARS-CoV-2.

The present study reports a comprehensive molecular dynamics simulation of the effect of a) temperature (300–1073 K at intervals of every 100 K) and b) point defect on the mechanical behaviour of single (armchair and zigzag direction) and bilayer layer graphene (AA and AB stacking). Adaptive intermolecular reactive bond order (AIREBO) potential function was used to describe the many-body short-range interatomic interactions for the single layer graphene sheet. Moreover, Lennard Jones model was considered for bilayer graphene to incorporate the van der Waals interactions among the interlayers of graphene. The effect of temperature on the strain energy of single layer and bilayer graphene was studied in order to understand the difference in mechanical behaviour of the two systems. The strength of the pristine single layer graphene was found to be higher as compared to bilayer AA stacked graphene at all temperatures. It was observed at 1073 K and in the presence of vacancy defect the strength for single layer armchair sheet falls by 30% and for bilayer armchair sheet by 33% as compared to the pristine sheets at 300 K. The AB stacked graphene sheet was found to have a two-step rupture process. The strength of pristine AB sheet was found to decrease by 22% on increase of temperature from 300 K to 1073 K.

The mechanical properties of the SiC/graphene composites under tensile are studied via molecular dynamics (MD) methods. In our study, the SiC/graphene composites with monolayer graphene and multilayer graphene are built and compared. As a result, the composites with different interface structures present different tensile behaviors. The single graphene sheet in contact with Si-terminated SiC(1 1 1) surface brings the higher failure strain and strength. It is also found that the elastic modulus of the composites increase with the increasing graphene volume fraction. As for the composites fabricated with the multilayers graphene, the failure strain of the whole systems would decrease with the increasing graphene layers in the case that graphene serves as single layer. By contrast, when the graphene sheets serve as continuous layers, the failure strain does not change significantly and the strength would increase monotonically with the increasing number of graphene layers.

The damage production induced by swift heavy ion (SHI) irradiations in graphene supported on a SiO2 substrate is investigated using molecular dynamics method. The thermal spike model is used to simulate the energy deposited into the lattice due to electron–phonon coupling. By given energy to both the graphene and substrate, we find that carbon chain structures even nanoholes can be produced, which depends on the deposited energy. The minimum value needed to generate defects in supported graphene is higher than 6.5 keV/nm, which is higher than the threshold value for track formation in SiO2. For a suspended graphene sheet, the value is determined to be 8 keV/nm. Thus our results indicate that the presence of SiO2 substrate decreases the damage threshold of graphene. Our simulation further suggests that the damage of supported graphene is due to the synergic effects from direct collision and indirect impact from the substrate. The defect production in supported graphene is along with the formation of ion tracks in SiO2 substrate and the rupture of graphene is initiated from the track core region. Our results provide an atomistic explanation for the reported modification of graphene with SHIs, which is very important for engineering graphene with SHIs.

Assuming dipole–dipole interaction as the dominant relaxation mechanism of protons of water molecules adsorbed onto macromolecule (biopolymer) surfaces we have been able to model the dependences of relaxation rates on temperature and frequency. For adsorbed water molecules the correlation times are of the order of 10 −5 s, for which the dispersion region of spin–lattice relaxation rates in the rotating frame R 1 ρ = 1/ T 1 ρ appears over a range of easily accessible B 1 values. Measurements of T 1 ρ at constant temperature and different B 1 values then give the “dispersion profiles” for biopolymers. Fitting a theoretical relaxation model to these profiles allows for the estimation of correlation times. This way of obtaining the correlation time is easier and faster than approaches involving measurements of the temperature dependence of R 1 = 1/ T 1 . The T 1 ρ dispersion approach, as a tool for molecular dynamics study, has been demonstrated for several hydrated biopolymer systems including crystalline cellulose, starch of different origins (potato, corn, oat, wheat), paper (modern, old) and lyophilized proteins (albumin, lysozyme).

The interfacial force for exfoliating a graphene monolayer from graphite in solvent media was studied by restrained molecular dynamics simulations. Three solvents, N-methylpyrrolidone (NMP), dimethyl sulfoxide (DMSO), and water, were considered. The interfacial structures show that NMP and DMSO have a stronger affinity with graphene surfaces. In the solvent media, there exists an inherent attractive force hindering the exfoliation, which is almost exclusively determined by the interaction between graphene sheets. Along the perpendicular exfoliation direction (relative to the graphene plane), the initial exfoliation is less dependent upon solvent conditions, and the subsequent exfoliation can be facilitated by the solvent-induced interaction. However, along the shift direction parallel to the graphene plane, the organic solvent provides a favorable driving force to assist the exfoliation, whereas water offers obstructing effect. The parallel shift of graphene requires less external power than the perpendicular shift for our simulated systems. The confined solvent molecules between graphene sheets play an important role in exfoliating and stabilizing graphene in solvent media. This result provides a microscopic understanding of the function of solvent-induced interaction in the solvent exfoliation of graphene.

The influence of the chemical functionalization of graphene on the interfacial bonding characteristics between graphene and polymer was investigated using molecular mechanics and molecular dynamics simulations. In this study, three chemical functionalization, (a) phenyl groups, (b) –C6H13 and(c) –C2H4(C2H5)2, which have the same number of carbon atoms, were chosen to investigate the influence of the structure of functionalized groups on the bonding energy and shear stress in the graphene–polyethylene (PE) composites. Our simulations indicated that, the interfacial bonding energy between the graphene modified by –C6H13 groups and PE matrix has the strongest enhancement, but the shear force between the graphene modified by –C2H4(C2H5)2 groups and PE matrix is the strongest in the graphene–polymer composites. Therefore, the suitable structure of chemical groups to the graphene surface may be an effective way to significantly improve the load transfer between the graphene and polymer when graphene is used to produce nanocomposites.

Molecular dynamics simulation method with an improved flexible nitrate model was used in this paper to study the structure and properties of molten LiNO3, NaNO3, and KNO3. Both local structure and physical properties including densities, thermal conductivities, viscosities and heat capacities of the salts were simulated comprehensively. Different simulation methods were used and the results were compared with experimental data. The relationship between the structure and properties of the salts were discussed. Besides, a binary mixture of NaNO3 and KNO3 was also simulated to verify the applicability of the force field and simulation method for salt mixtures. The results indicate that the force field and simulation methods adopted in this paper work well in predicting the properties of both single nitrate salts and their mixtures. This paper did a basis job for further investigation into the simulation of nitrate salt mixtures used in thermal energy storage.

The buckling behavior of a single layer MoS2 (SLMoS2) sheet with defects under uniaxial compression is investigated with molecular simulation in the present paper. Five typical defects are introduced to estimate the instability characteristics of defective MoS2 sheet. The buckling responses, including the critical strain and geometric morphology, influenced by defect type, stain rate, defect density and so on, are comprehensively explored. It is found that different type of defects results in reduction of the bending modulus to some different extent. Compared with the other three post-buckling morphologies, the first typical geometric morphology show the biggest difference between the defect-free and defective SLMoS2 sheets. It seems possible to realize our desired morphology in flexible electronics by proper preparing different kinds of defects. The finding in the present paper should be useful for the promising design of flexible optoelectronic devices and soft bioelectronics.

This paper studies the toughness, strength and interfacial bonding effect of graphene kirigami silicon-based nanocomposite (GKSN) using molecular dynamics (MD) simulation. The GKSN model is proposed based on a hybrid potential. It is found that the toughness and maximum strength of GKSN are related to the number of interior cuts and density of kirigami patterns for graphene kirigami. Mechanical response of GKSN has four typical stages, including initial wrinkling, linear increasing, ratcheting and failure. Locking effect can significantly enhance the toughness and maximum strength of GKSN with some rare expectations. With increasing interfacial bonding strength of GKSN, toughness and maximum strength increase steadily. Finally, two novel nanocomposites based on graphene kirigami can be designed. The obtained results in this paper can provide a fundamental understanding of the maximum strength and an insight for enhancing the toughness of graphene kirigami nanocomposite. The proposed mechanisms may have general significances for the design of the next generation “super-tough” and “super-strong” nanocomposites.

Understanding the mechanical behaviour of nanostructures is of great importance due to their applications in nanodevices such as in nanomechanical resonators, nanoscale mass sensors, electromechanical nanoactuators and nanogenerators. Due to the difficulties of performing accurate experimental measurements at nanoscales and the high computational costs associated with the molecular dynamics simulations, the continuum modelling of nanostructures has attracted a considerable amount of attention. Since size influences have a crucial role in the mechanics of structures at nanoscale levels, classical continuum-based theories have been modified to incorporate these effects. Among various modified continuum-based theories, the nonlocal elasticity and the nonlocal strain gradient elasticity have been employed to estimate the mechanical behaviour of nanostructures. In this review paper, first these two modified elasticity theories are briefly explained. Then, the nonlocal motion equations for different nanostructures including nanorods, nanorings, nanobeams, nanoplates and nanoshells are derived. Several papers which reported on the size-dependent mechanical behaviour of nanostructures using modified continuum models are reviewed. Furthermore, important results reported on the vibration, bending and buckling of nanostructures as well as the results of size-dependent wave propagation analyses are discussed.

The application of asphalt materials in pavement engineering has been increasingly widespread and sophisticated over the past several decades. Variations in the properties of asphalt binder during mixing, transportation, and paving can affect the performance of asphalt pavement. However, the asphalt material is a non-homogeneous and complex organic substance, consisting of various molecules with widely various molecular weights, elemental compositions, and structures. This complexity leads to difficulties for researchers to clearly and immediately understand the properties of asphalt materials and their variations. The multi-scale research approach combines macroscopic experimental data and microscopic simulation results from a practical engineering perspective. It helps to improve the understanding of asphalt materials. The molecular dynamics (MD) simulation proposes a corresponding molecular model of asphalt material based on experimental data, and the simulation algorithm is able to derive properties similar to those of real asphalt. This paper provides a comprehensive review of the current studies on MD simulation of asphalt materials, including modeling, properties, and multi-scale analysis. As a key part of the computational simulation, this paper discusses the typical asphalt binder and asphalt-aggregate interface models constructed by different groups, and also presents their differences from real samples and their feasibility based on fundamental properties. After the introduction of molecular models, the extensive work made by researchers based on molecular models is categorically reviewed and discussed. The strengths and weaknesses of MD simulation methods in the study of asphalt materials are also summarized in order to provide the reader with a more comprehensive understanding of the relevant contents and to guide subsequent research.

In this paper, the mechanical properties of excess-sulfate phosphogypsum slag cement (PPSC) were studied by experimental data, microscopic tests and molecular dynamics (MD) simulations. Specifically, the properties of PPSC in terms of setting time, compressive and flexural strengths were investigated by experiment. The hydration products of PPSC were tested and observed by X-ray diffraction (XRD) and scanning electron microscopy (SEM). Furtherly, at the atomic scale, the relationship between nanoscale and macroscopic mechanical properties of PPSC was established. The mechanism of the effect of chemical composition on the mechanical properties of PPSC was studied at multiple scales, and the compound synergistic effect between chemical compositions was further studied. The results show that the mechanical properties of PPSC increase with the increase of CaO/SO3, and decrease with the increase of SiO2/Al2O3. CaO and Al2O3 can improve the mechanical properties of PPSC. The high mobility and structural instability lead to CaO/SO3 has greater effect on the mechanical properties of PPSC than that of SiO2/Al2O3. When CaO/SO3 is 1.8 ∼ 2.0 and SiO2/Al2O3 is 3.5 ∼ 3.7, the mechanical properties of PPSC are better. Moreover, when CaO/SO3 is 2.0 and SiO2/Al2O3 is 3.5, the mechanical properties of PPSC are the best. At this time, the compound synergistic effect of alkaline activator and sulphate activation is the best. This paper provides an important reference for the composition design and application of PPSC.

This paper evaluates the reproducibility of an efficient and portable Tersoff potential calculation using LAMMPS, previously presented at the Supercomputing ’16 Conference. The original artifact description was used to reproduce the results on an AMD EPYC 7551, equipped with NVIDIA Volta V100 GPUs. Molecular dynamics simulations, in particular multi-body potential problems, can provide increased accuracy and support scientific discovery in the fields of computational chemistry and materials science. This paper evaluates the reproducibility of the study, in terms of portability and performance.

Many different researches show that stiffness of nanoplates or nanosheets and other nanostructures are decreased by existing or increasing the small scale effect. But few studies that applied other models or approaches to get relationships between stiffness of nano/microstructures and the small scale effect are found results contrary to the results of the above mentioned researches. In this paper, axisymmetric bending behaviour of the annular single-layered graphene sheet resting on an elastic medium is studied by comparing results of the nonlocal elasticity and classical theories. The Pasternak-type foundation model is employed to simulate the interaction between the graphene sheet and the surrounding elastic medium. To get numerical results, the Ritz method is applied. Also, an aspect ratio is defined, and a parametric study is carried out varying the small scale parameter, elastic foundation parameters and the mentioned aspect ratio of the annular graphene sheet. The applied nonlocal elasticity model to analyze annular graphene sheet resting on an elastic medium is an exact nonlocal stress gradient model which have presented correct results in cases of with and without the elastic medium and whose results are in accord with experimental researches, studies based on other continuum approaches and some molecular dynamics simulations. Results of present paper represent that increase of the small scale effect increases the stiffness of nanostructures. For the first time, it is also shown that the mentioned result is in agreement with experimental researches, other continuum approaches, and some molecular dynamics simulations studies. Also, the simultaneous effects of all the mentioned parameters on the stiffness of nanostructures are investigated.

At meso-scale, Calcium Silicate Hydrate (C-S-H) can be considered as randomly packed globules (about 4.2 nm), which forms the basic unit cell, with water molecules and voids. In this paper, the nanostructures for the globules are developed based on some plausible atomic structures of C-S-H. The mechanical properties for the C-S-H globules are determined through molecular dynamics simulation. Interfaces between the C-S-H globules are also simulated with different amount of water molecules. Key material parameters, e.g., Young’s modulus, strength and fracture energy, are obtained. It has been found that longer mean chain length of silicate tends to increase the strength of C-S-H and change the fracture behavior from brittle to ductile failure, in the chain length direction. In the other direction, however, silicate chains do not play an important role while interlayer structure matters. Moreover, pores in the C-S-H nanostructures can considerably reduce the strength of the globule structures in the normal direction to silicate chain but the weakening effect becomes substantially less in silicate chain direction. Further, it has been found that for all types of the interfaces between C-S-H globules, the interface with no extra water molecules has the greatest tensile/shear strength. The mechanical properties obtained in this paper for C-S-H nanostructures and interfaces could be necessary inputs to the meso-scale modelling of C-S-H via either granular mechanics, i.e., DEM, or continuum mechanics, i.e., FEM.

The quartz crystal microbalance (QCM) is frequently used to measure the adsorption of molecules from a liquid bulk phase onto surfaces. However, determining the true mass adsorbed onto the surface from the raw frequency shift values often involves various correction factors. In this paper, we highlight yet another correction factor that arises from correcting for the bulk, Kanazawa–Gordon-like solvent contribution to the total frequency shift. This correction factor depends on the cross-sectional size of the solute and solvent molecules on the surface, and shows that the apparent mass adsorbed reported by the QCM can significantly differ from the true mass. By performing molecular dynamics simulations of adsorption from a liquid phase, we are able to accurately estimate the molecular sizes of the solvent and solute. Using stearic acid in heptane solutions, and iron oxide surfaces, we quantify the magnitude of the correction factor by comparing the uncorrected and corrected QCM data. This paper emphasizes the importance of accounting for deviations from widely used models in analyzing measured frequency shifts in QCM experiments, to accurately obtain the true adsorbed mass.

Diffusion-selective N 2 /O 2 separation and competitive adsorption by nanoporous Li-LSX zeolite, as the best commercially available adsorbent, is a scientifically interesting phenomenon with important technological applications. In a recent paper ( J. Phys. Chem. C 121, 2017, 1770–1780), we reported the first molecular dynamics (MD) study of the adsorption of the binary N 2 /O 2 mixtures within this zeolite. In the present paper, the microscopic structure and intracrystalline self-diffusion coefficient of N 2 and O 2 as single-component guest species in Li-LSX zeolite are determined at different temperatures and practical loadings. The simulation results are found to be in very good complementary agreement with experimental adsorption findings as well as with the recent predictions based on the binary air mixture simulations. The influences of the internal surface dynamics of extra-framework Li + cation in site III (Li-III) on the guest static and dynamic processes within the zeolite are determined. O 2 has no significant association with Li-III, while all structural analyses prove remarkable adsorption and hence localization of N 2 around the Li-III in the supercages. The degree of localization and the residence time of N 2 on Li-III in particular increases with decreasing temperature and also with fixing of Li-III cations during the simulation. As a guide for future design of N 2 /O 2 separation by zeolite frameworks at ambient temperature, an excellent adsorption selectivity ratio can be achieved if it is practically possible to reduce the dynamics of accessible Li-III sorption sites up to extremely fixed situations. The calculated Arrhenius activation energy for N 2 diffusion process through Li-LSX zeolite is several times higher than that of O 2 . These results are due to the larger quadrupole moment of N 2 and stronger Coulombic attraction between N 2 and Li-III that causes the translational motion of N 2 to be significantly hindered. Overall, the intracrystalline self-diffusion coefficients of both N 2 and O 2 slightly decrease with loading. Current simulations also correctly approve that the Li + cations in sites I′ and II are inaccessible to interact with guest molecules.

Supercritical water gasification technology is an efficient and clean way to use the coal. This technology can convert carbon and hydrogen elements of coal into the mixtures of H2O/H2/CO2 that can be used for electricity generation. The acquisition of PVT properties of H2O/H2/CO2 mixtures is one of the most critical issues in realizing the design and operation of thermal power generation system using this technology. However, no experimental, theoretical and simulation studies exist regarding the PVT properties of H2O/H2/CO2 in the near-critical and supercritical regions of water. In this paper, the molecular dynamics simulations of the PVT properties of H2O/CO2 mixtures are carried out and the theoretical calculations are conducted based on the equation of state, and the results are compared with the experimental values. Moreover, the PVT properties for H2O/H2 mixtures and H2O/H2/CO2 mixtures in the near-critical and supercritical regions of water are predicted using molecular dynamics simulation and compared with the calculation results of the equation of state. The results of this paper are of great significance to the development of supercritical water gasification of coal, and could offer the reference for the application of H2O/H2/CO2 mixtures in practical production.

MAP kinase interacting serine/threonine kinase 1 (MNK1) can promote the development of tumors through over-activation of MNK and phosphorylation of p-eIF4E, which is an important potential target for cancer therapy. A three-dimensional quantitative structure-activity relationship (3D-QSAR) is applied to investigate the relationship between activities and structures in this paper. Herein, a set of 73 4-aniline-thieno[2,3-d] pyrimidine derivatives were selected, and a 3D-QSAR study was performed by using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) model in this paper. The experimental results shown that CoMFA (n = 10; q2 = 0.765; r2 = 0.979), CoMSIA (n = 10; q2 = 0.711; r2 = 0.967) had good stability and predictability. The relationship between the activity and structure of the compound was analyzed by counter maps of the steric, electrostatic and hydrophobic fields. Subsequently, molecular docking was applied to explore key amino acids and docking modes at the active site. Based on the results, 10 new 4-aniline-thieno[2,3-d] pyrimidine derivatives were designed and their activities were predicted. Afterwards, these molecules were submitted to further ADME studies, in which the ADME properties of the 10 designed molecules were found to be within a reasonable range. Molecular Dynamics (MD) simulation analysis confirmed that the residues Leu55, Val63, Lys126, Leu127, Gly130, Ser131, Leu177, Phe192 play a vital role in the active site. In addition, these compounds mainly to bind to MNK1 through lipophilic interactions and hydrogen bonding. These results provided important reference to the discovery and design of new MNK1 inhibitors.

Zeta potential and the position of the shear plane are key physical properties characterizing the behavior of clay minerals in the colloidal system, and have been applied in many fields such as electroosmotic consolidation and electro-kinetic decontamination. In the past decades, numerous studies have been conducted on measuring and calculating the zeta potential. Nevertheless, few researchers have been reported to achieve a systematic understanding and predicting the zeta potential and the shear plane's position, especially for clay particles. This paper provided a molecular dynamics (MD)-based method to determine the zeta potential and shear layer thickness simultaneously to fill the gap. In the paper, the structure of the electrical double layer (EDL) was investigated for montmorillonite mesopore containing NaCl electrolyte in the concentration of 0.20–1.30 mol/L. The density profiles of ion species were well predicted by the Stern model, combining the Stern potential's determination. The calculated zeta potential based on the electroosmotic velocity profile in nonequilibrium molecular dynamics (NEMD) simulation was improved by introducing the slip length and was found to be closely comparable to the experimental values. Furthermore, the results confirmed that the shear plane cannot be observed from the electroosmotic velocity profile and self-diffusion coefficient of species in the MD simulation. The position of the zeta potential was determined by the Stern model and triple-layer model (TLM), showing a certain distance from the Stern plane. The zeta position was found that has a linear relationship with the Debye length and linearly depends on the ionic strength in the log scale, in agreement with previous investigations. The findings provided a systematic insight into the electrical double layer structure, zeta potential and shear plane for montmorillonite.

The narrow use and poor mechanical properties of flexible polymers limit its further development. In this paper, the addition of a new type of MOFs material UiO-66 to the flexible polyacrylate polymer not only gives the polymer fluorescence properties but also enhances the mechanical properties of the polymer. This paper mainly studies the effects of different functional groups on the fluorescence properties of UiO-66 and the influence of the interface between UiO-66 and the polymer matrix. The experimental analysis of morphology and chemical structure showed that UiO-66-x and its composite membranes with different functional groups were successfully prepared. A series of comprehensive studies have shown that the fluorescence properties of UiO-66-x with different functional groups are different, which is mainly due to the different conjugated structure of the system. The composite film introduced with UiO-66-x not only has fluorescent properties, but also has excellent mechanical properties, thermal stability and solvent stability. The increase in mechanical properties is mainly attributed to the interaction between nanoparticles and polymers. Finally, molecular dynamics simulations are used to confirm the interaction between nanoparticles and polymers. At the same time, the current work can provide a convenient example for the application of metal organic framework (MOF) in enhancing the fluorescence and mechanical properties of polymers.

The asphaltene stability in crude oil can be disturbed due to changes to thermodynamic conditions during production, raising flow assurance concerns. The addition of chemical inhibitors, such as surfactants, to a crude oil can improve the asphaltene stability. The impact of chemical inhibitors on the asphaltene aggregation intensity and aggregate characteristics, which is needed for design of an efficient inhibitor for a target crude oil, is poorly understood. In this paper, a molecular dynamics simulation tool is employed to simulate the molecular behaviour of the asphaltene and n-octylphenol (OP) at various concentrations of OP (0–15 wt%) and thermodynamic conditions (T = 300–360 K and P = 1–60 bar). To meet the objectives, the average aggregation number of different asphaltenes and asphaltene mixtures is measured besides the aggregate characteristics, including aggregate gyration radius, density, and shape. The results show that the archipelago asphaltenes (A1) do not self-aggregate severely, and the gyration radius distribution of the aggregates is similar after the OP addition. Nevertheless, the average aggregation number and the aggregate density analysis show that the aggregation intensity reduces slightly when the OP concentration is increased. Because the continental asphaltene (A2) can form hydrogen bonds, the addition of OP increases the aggregate dispersity significantly, which is identified with the highest peaks at 28 and 35 A after the addition of 7 and 15 wt% OP, respectively. It is found that OP increases the variations in the aggregate shape and type for A2 aggregates. It is concluded that a high concentration of OP (above 7 wt%) is needed to avoid the asphaltene aggregation. The pressure increase does not change the aggregate shape both with or without the OP. However, adding OP increases the aggregate gyration radius and decreases the aggregate density at 30 bar. Increasing temperature results in a severe aggregation in the system without the inhibitor as the aggregate gyration radius increases, and aggregates become more compact and spherical. However, by adding OP, both the average aggregation number and aggregate gyration radius decrease (especially at 360 K). According to the sensitivity analysis results, integrating GPUs with CPUs can speed up the simulation approximately three times, compared to the system processing with only CPUs. Outcomes from this research work can help for a better understanding of the molecular behaviour of asphaltene and inhibitors at various thermodynamic situations, leading to the improvement of inhibitor design. This paper highlights the competence of molecular dynamics for exploring the optimal inhibitor concentration and the thermodynamic conditions in which the inhibitor has the highest impact on asphaltene aggregation.

The existence of defects such as intrinsic cracks and holes will greatly weaken the excellent mechanical behaviors of graphene sheets. In order to improve the mechanical properties of defective graphene (DG), this paper reports a novel nano-repair strategy that the interlayer cross-linkings are regarded as glue to bond defect-free graphene patch on DG. A systematic computational study on tensile strength of the repaired graphene (RG) has been performed using molecular dynamics (MD) simulations. It was found that, the optimal repair efficiency can reach 1.87. Furthermore, the shape of patch plays an important role on repair efficiency as well. This paper proves the repairability of the tensile strength of graphene with hole defects, and innovatively proposes the strengthening method of DG to optimize mechanical properties.

Temperature is one of the important factors affecting the heat transfer of liquid organic, but the mechanism of the effect of temperature on the thermal conductivity of liquids is not deeply studied. In this paper, the microscopic thermal conduction of heptane, hexanal, 2-hexanone and hexanol at different temperatures were simulated by nonequilibrium molecular dynamics. Based on the simulation results, the relationship between the heat transfer of liquid organics and temperature was analyzed mainly from the molecular structure and the simulated system, and the thermal conductivity at the corresponding temperature was predicted. The results indicate that the Coulomb interaction term, the van der Waals interaction term and the torsion term, which contribute significantly to the total heat flux, all decrease with increasing temperature, which makes the thermal conductivity of the four organics decrease with increasing temperature. This paper speculates that the rise of temperature increases the atomic vibration of the simulated molecules, accelerates the molecular motion, and decreases the mass density of the simulated system, and make the four organic thermal conductivity of the changes described above. In addition, the mean relative deviation of the calculated thermal conductivity from the experimental values is 8.54% and the maximum deviation is 9.23%, the simulation results are basically consistent with the experimental values. The present work provides a preliminary understanding for studying the effect of temperature on the thermal conduction of liquid organics.

To improve the efficiency of a machinery component, it is necessary to enhance the quality of lubricants. Lubricants help to reduce the friction and wear between the two surfaces which are in relative motion. The study of friction and wear covers in the field of tribology. Recently tribological behavior has been studied in micro and nanoscale. Nanotribology deals with the study friction, adhesion, wear and lubrication of metal crystal, analyze dynamics and single asperity contacts during sliding, formation and propagation of voids, fracture and nucleation and motion of dislocations properties at atomic level and also study the interfacial properties between the two surfaces. The expensive nanotribological experimental studies and limited availability of experimental facility, motivates researchers to use simulation approach. Molecular Dynamic (MD) simulation facilitate to analysis at molecular level and nanoscale. Present review paper is elucidating the application of MD simulations in the field of Nanotribology. In addition, this study provides utter knowledge about the LAMMPS commands and also confabulate the capabilities of MD simulation in nanotribology area. This review paper is fully dedicated to all those readers who are fascinated to do research in field of nanotribology using molecular dynamics simulation in nanotribology with LAMMPS.

Molecular dynamics (MD) simulation has proved to be a powerful tool in the study of proteins, nucleic acids, lipids, and carbohydrates et al. in fields of health, nutrition, and food science. In particular, MD simulation has been employed in the investigation of various lipid systems such as triglycerides, phospholipid membranes, etc. Due to the continuous updating of computing resources and the development of new MD simulation methods and force field parameters, the simulation's time and size scale of lipids system has increased by several orders of magnitude. However, MD simulation cannot be used for systems invovle chemical reactions. These greatly limit its further application in the field of lipid research. This paper reviews the progress and development of MD simulation, especially for the application of MD simulation in different lipid systems. In this paper, MD simulation and its general workflow was briefly introduced firstly. Subsequently, the application of MD simulation in various lipid systems was reviewed in-depth. Finally, the limitation and future prospects of MD simulation in lipid research were also discussed. This review provided new insights into the investigation of MD simulation, and a novel thought for lipid study. We believe that MD simulation will exhibit more and more great advantages in the investigation of lipids in the future due to the development of novlel methods.

This paper investigates nonlinear vibrations of the nanoplates for a high resolution mass identification. As background, the paper is furnished with a succinct review of the applications of the nanoplates, along with recent studies on nanoplate vibrations. In spite of a number of published works related to vibrations of nanoplates, their nonlinear behaviors have not been fully characterized. Accordingly, we present a mathematical model to examine nonlinear vibrations of nanoplates based on the nonlocal theory postulating nonlinear Winkler foundation. Besides, external force is taken into account to scrutinize nanoplate vibrations. The developed mathematical model consists of the assumption of a tiny mass stuck on the nanoplates. Utilizing the Galerkin’s method considering multiple scales method provides the primary mode of nanoplate oscillations. In view of that, parametric sensitivity analysis depicts that the frequency response of the nanoplates significantly changes by adding minuscule mass. Two different methods are developed for identification of the added mass. The first method works based on the jump phenomenon in nonlinear oscillators due to the added mass. In the second method, an adaptive parameter identifier estimates the added tiny mass based on a parametric dynamic model of the structure and its vibrational response to a periodic applied force. The effectiveness and straightforwardness of both developed methods are illustrated. Furthermore, a comparison with the molecular dynamics simulation is provided to verify the developed nonlocal model of nanoplate vibrations. It is concluded that the developed method can be considered as consequential and potential tools for high resolution mass sensing. The proposed approaches have the potential to be used in virus, enzyme and also humidity sensing.

In this paper, behavior of water flow in single-walled carbon nanotube (SWCNT) under electric charge is investigated using molecular dynamics simulation. It is shown that electric charging of SWCNT causes water flow to exhibit surprising behavior. Among water flow parameters, flow rate or flux of water molecules is of special interest. The two governing phenomena affecting flow rate in a SWCNT are resistance along the nanotube and resistance to flow at its entrance. In present study, effect of electric charging of SWCNT's carbon molecules on these two phenomena is studied in detail in SWCNTs (5, 10) with 3 nm, 5 nm, and 7 nm lengths. Charge magnitudes between zero to 1.0 e/atom are implemented along different lengths of nanotube. Charges are applied either constantly or stepwise. Based on the analysis of numerical results obtained in this paper, it is concluded that electric charging can be used to manipulate these two phenomena and therefore control the rate of water flow in a SWCNT very effectively.

In this paper, large-scale molecular dynamic (MD) simulation is performed to investigate the concentration-dependent vacancy volume relaxation in Al, Cu, and Au, respectively. The vacancy volume relaxation factor is calculated and correlated to the microstructure change based on MD results. It is found that the vacancy volume relaxation factor is nearly a constant at low to mid-vacancy concentration level, i.e., from 10−6 to 10−3 of the lattice concentrations. However, the volume of vacancies will completely collapse at the high vacancy concentration, and the coalescence of vacancies will form massive dislocations. The simulation results are in good agreement with the existing data from both experiments and simulations in the literature. A uniform empirical equation is developed to obtain the vacancy volume relaxation factor as a function of vacancy concentration. Furthermore, the hydrostatic stress is also calculated based on MD simulations. This paper also discusses the relationship between the vacancy volume relaxation and the diffusion-induced strain, such as in the application of electromigration. For a constrained condition, the hydrostatic stresses obtained from MD-based vacancy volume relaxation and a commonly used stress-vacancy equation are compared. An insight on the critical vacancy concentration at which electromigration failure would occur is discussed in detail.

The mechanism of calcite-organic molecule-water interaction mechanism in oil-wet formation and alteration of carbonates is still ambiguous. This paper combines atomic force microscope (AFM), X-ray photoelectron spectroscopy (XPS) and molecular dynamic (MD) simulation to investigate the regularity and mechanism of calcite-organic molecule-water interaction at the molecular scale. First, the calcite-organic molecule-water interaction regularities, i.e., wettability alteration process, were studied using AFM, XPS and MD. AFM, XPS and MD results all demonstrated that acetic acid adsorbs stably on the calcite surface and can-not be displaced by water molecules, while the resistance to water displacement of the other three organic molecules decreased with decreasing molecular polarity. Subsequently, MD was used to analyze the calcite-organic molecule-water interaction mechanism from three perspectives, including the organic molecule-calcite interaction, the organic molecule-organic/water molecule interaction, and the effect of polar molecules. In the organic molecule-calcite interaction, the adsorption intensity of organic molecules on calcite surface decreases as their molecular polarity decreases. Stronger molecular polarity results in tighter adsorption layer and lower adsorption energy. In the organic molecule-organic/water molecule interaction, the interaction intensity increases as the polarity difference between the two molecules decreases. Larger polarity difference causes stronger miscibility and lower interaction energy. For polar molecules effect, the presence of polar molecules stabilizes the non-polar molecules adsorption and diminishes the displacement efficiency of water molecules. Consequently, this paper proposes the bulk adsorption mechanism to reasonably explain the wettability formation and alteration mechanism of calcite surface, which is of great importance for targeted enhanced oil recovery studies.

The main concern in Molecular Dynamics (MD) simulations is the computational cost, and coarse-graining methods accelerate simulations by reducing the degrees of freedom in the system. Yet, the utilization of these methods should be carefully followed. In this paper, we presented an energy-based coarse-graining method for Tersoff and Stillinger-Weber potential functions. The presented coarse-graining method is based on the domain mapping and modification of potential function. The focus of this paper is on Carbon and Silicon materials; however, this method can be applied to model other materials for which Tersoff and Stillinger-Weber potentials are defined. This method has been validated by demonstrating the consistency of mechanical properties between all-atom and CG models in different case studies. According to the conducted simulations, the precision of the proposed CG technique in the modeling of the bulk behavior is near 100% while it yields completely reasonable results for other simulation setups.

This paper proposes a micromorphic simulation model with novel strain rate relationships between MD simulations and macroscale experiments at the ductile-brittle (DB) transition of glassy polymer and dynamic heterogeneity of deformation. Novelties of this paper are on the strain rate relationship between two different scale regions and investigations on the effects of molecular weight on the relationship. From molecular dynamics model having realistically entangled polymer networks and experiments, the strain rate relationships are derived and then realized through a two-scale multiscale continuum model based on the micromorphic theory. The investigation on the effects of molecular weights on the relationship yields that the relationship is maintained when the molecular weight is higher than the entanglement length. The relationship confirmed that the dynamic heterogeneity alleviates as the polymer enters into the plastic flow above the glass transition temperature and disappears above the melting temperature. These findings will be a basis for developing the constitutive relationship of glassy polymers through a multiscale approach that can incorporate the heterogeneous dynamics of molecules.

This paper presents the fracture toughness of sodium aluminosilicate hydrate (N-A-S-H) gel formed through alkaline activation of fly ash. While the fracture toughness of N-A-S-H is obtained experimentally from nanoindentation experiment implementing the principle of conservation of energy, the numerical investigation is performed via reactive force field molecular dynamics. A statistically significant number of indentations are performed on geopolymer paste yielding frequency distribution of Young’s modulus. Four distinct peaks are observed in the frequency distribution plot from which the peak corresponding to N-A-S-H was separated using statistical deconvolution technique. The young’s modulus of N-A-S-H, thus obtained from statistical deconvolution shows excellent match with the values reported in the literature, thus confirming successful identification of indentations corresponding to N-A-S-H. From the load-penetration depth responses of N-A-S-H, fracture toughness was obtained following the principle of conservation of energy. The experimental fracture toughness shows good correlation with the simulated fracture toughness of N-A-S-H, obtained from reactive force field molecular dynamics. The fracture toughness of N-A-S-H presented in this paper paves the way for multiscale simulation-based design of tougher geopolymer binders.

The paper studies the potential energy surface (PES) of interaction between two rigid diatomic molecules (N2–N2, N2–O2, O2–O2). The dependence of energy on the angles of mutual orientation of the two molecules is carefully described (18000 DFT calculations for each pair) so that the obtained PES would be suitable for detailed simulation of the rotational excitation and relaxation in intermolecular collisions in air. The DFT results were fitted by proposed multi-particle interaction model with good accuracy. Corresponding force field was calculated and tested on two problems (simulation of the equilibrium state and the adiabatic rotational relaxation), its software implementation is attached to the paper and one can use it for molecular dynamics calculations.

Understanding the wetting behavior of the molten iron and graphite is of great significance to guide the gas permeability of the blast furnace. This paper used the molecular dynamics simulation method to analyze the wetting behavior of molten iron on the graphite substrate at the atomic scale. In this paper, it was found that high temperatures can help reduce the time it takes for the wetting process to reach equilibrium. And the graphite basal plane can promote the melting of the iron block at a temperature lower than the melting point. In addition, the graphite basal plane showed good hydrophilicity to the molten iron, and the contact angle can reach 55.65° at 2000 K. The graphite prism plane is hydrophobic to the molten iron. And the results of molecular dynamics simulation showed that high temperature can improve the hydrophilicity of graphite basal plane and reduce the hydrophobicity of graphite prism plane. Therefore, adjusting the temperature and the contact surface between graphite and molten iron can provide theoretical guidance for improving the gas and liquid permeability of blast furnace.

Surfaces with nanostructures can significantly enhance the evaporation heat transfer process. Most previous investigations on the designed surface structures using the empirical way to find better geometries. This paper proposes an optimization method for different types of nanostructured surfaces to seek optimal structures mathematically under the given heat transfer area. In this paper, three defined types of nanostructured surfaces are discussed: concave, convex and concave-convex. Firstly, a positive correlation between the evaporation heat transfer performance and the defined sectional area of the liquid phase is obtained by molecular dynamics simulations of the empirically designed nanostructured surfaces. Then, the optimization of the surface geometry converts to a mathematical problem which to solve the maximum sectional area of the liquid phase. This method is used to optimize the geometries of the concave and convex surfaces. Moreover, the molecular dynamics simulation results indicate that the optimal surfaces conduce to better heat transfer performance than the normal concave, convex and concave-convex ones. Finally, to explain the mechanism, the investigations of the atomic potential energy distributions of liquid atoms, the interaction energy between solid and liquid atoms, the solid-liquid interfacial thermal resistance and the morphology of the liquid-vapor interface are done.