Paraquat, one of the most widely utilized herbicides globally, causes a significant environmental challenge due to its poor degradation rate and tendency to adsorb into clay interlayers. Several remediation methods have been proposed but their effectiveness remains suboptimal. The primary reason for this is the lack of microscopic understanding of paraquat–montmorillonite interactions. In this work molecular dynamics simulations were applied to study the interlayer structures and mobility of paraquat intercalated montmorillonite. Two stable hydration states were identified from the calculated immersion energy curve, which corresponded to a water content of 185 mgwater/gclay and 278 mgwater/gclay (the most stable). Paraquats remained in direct contact with the clay surface in both the anhydrous and hydrated states. At the water content of 185 mgwater/gclay, paraquats formed π-π stacking while at 278 mgwater/gclay, they were separated by a layer of water. Paraquat showed very small self-diffusion coefficients in the interlayer space of montmorillonite, indicating rather limited motions. The results in this work provide a basis for a better understanding of the interaction of paraquat with clay minerals.

Dodecyl dimethyl benzyl ammonium (DDBA) is a novel cation surfactant used to modify clay minerals. DDBA-intercalated montmorillonite is formed by the ion exchange between DDBA cations in the solution and cations in the montmorillonite interlayers. By using molecular dynamics simulations, we investigated the basal spacings, interlayer structures and dynamics of DDBA-montmorillonites. The results showed that the calculated basal spacings agreed well with experimental values and that the layering behaviours of DDBA had been revealed. The ammonium groups of DDBA ions preferred staying close to the centre of Si–O six-member rings. The benzyl group and lauryl group were oriented in parallel in the monolayer state, whereas they were tilted in other states. DDBA ions have very low mobility in the interlayer region, indicating that the negatively charged montmorillonite surfaces can effectively fix this positively charged surfactant. The microscopic structures and dynamics obtained in the present study provide atomic-scale insights into the properties of DDBA-intercalated clay minerals.

Interlayer swelling of hydrated montmorillonite is an important issue in clay mineralogy. Although the swelling behavior of montmorillonite under ambient conditions has been investigated comprehensively, the effects of basin conditions on the hydration and swelling behaviors of montmorillonite have not been characterized thoroughly. In the present study, molecular dynamics simulations were employed to reveal the swelling behavior and changes in the interlayer structure of Na-montmorillonite under the high temperatures and pressures of basin conditions. According to the calculation of the immersion energy, the monolayer hydrate becomes more stable than the bilayer hydrate at a burial depth of 7 km (at a temperature of 518 K and a lithostatic pressure of 1.04 kbar). With increasing burial depth, the basal spacings of the monolayer and bilayer hydrates change to varying degrees. The density-distribution profiles of interlayer species exhibit variation in the hydrate structures due to temperature and pressure change, especially in the structures of bilayer hydrate. With increasing depth, more Na+ ions prefer to distribute closer to the clay layers. The mobility of interlayer water and ions increases with increasing temperature, while increasing pressure caused the mobility of these ions to decrease.

Fe is a common substituent in palygorskites (Plg), but its effect on the microscopic properties is unclear. In the current study, molecular dynamics (MD) simulations were carried out to investigate the effect of Fe on the properties of the nano-pores in Plg. The structures and dynamics of water and Na+ ions in the pores were computed by analyzing the MD trajectories. The results revealed that for both Fe-containing and ordinary Plg, zeolitic water molecules can diffuse into the pores with very low mobility whereas Mg-coordinated water fails to escape. Na+ ions show no obvious diffusivity because they are fixed above the Si–Osix-membered rings. Detailed comparison indicates that Fe-substitution has no significant influence on the pore properties of Plg.

The swelling properties of smectite-type clay particles (including montmorillonite) are of interest in various industries. A fundamental understanding of the surface properties of smectite particles at the sub-micron level would facilitate investigation of the effect of distributed properties such as charge and elemental composition. Swelling and delamination of SWy-2 Na-montmorillonite (Na-Mnt) nano-clay particles were studied here using size distributions obtained by sedimentation field-flow fractionation (SdFFF). Fractions were examined by electron microscopy and inductively-coupled optical emission spectroscopy (ICP-OES). Two distinct populations were observed in the size distribution of SWy-2 Na-Mnt particles (bimodal size distribution), with mean equivalent spherical diameters of ~60 nm and 250 nm, respectively. In contrast, the size distribution of STx-1 Ca-montmorillonite (Ca-Mnt) particles showed only one peak with a mean equivalent spherical diameter of ~410 nm, which changed to 440 nm after 4 days of hydration. Analyses of the fractions by ICP-OES obtained along the size distribution of Na-Mnt showed an abundance of Ca and Mg in the fractions below 250 nm, and confirmed the presence of Fe and Mg as isomorphous substituents. Electron micrographs of the fractions obtained from Na-Mnt size distributions were used to calculate the thickness of the clay particles. Bridging forces between pure orMgsubstituted montmorillonite and either Ca2+ or Na+ were calculated using semi-empirical methods. The results demonstrated that swelling and delamination of Na-Mnt clay particles are dictated by properties such as elemental composition and surface charge which are distributed along the size distribution.

The nanoscale elastic properties of moist clay minerals are not sufficiently understood. The aim of the present study was to understand the fundamental mechanism for the effects of water and pore size on clay mineral (K+-smectite) elastic properties using the General Utility Lattice Program (GULP) with the minimum energy configurations obtained from molecular dynamics (MD) simulations. The simulation results were compared to an ideal configuration with transversely isotropic symmetry and were found to be reasonably close. The pressures computed from the MD simulations indicated that the changes due to water in comparison to the dry state varied with the water content and pore size. For pore sizes of around 0.8–1.0 nm, the system goes through a process where the normal pressure is decreased and reaches a minimum as the water content is increased. The minimum normal pressure occurs at water contents of 8 wt.% and 15 wt.% for pore sizes of around 0.8 nm and 1 nm, respectively. Further analyses of the interaction energies between water and K+-smectite and between water and water revealed that the minimum normal pressure corresponded to the maximum rate of slope change of the interaction energies (the second derivative of the interaction energies with respect to the water content). The results indicated that in the presence of water the in-plane stiffness parameters were more correlated to the pressure change that resulted from the interplay between the interactions of water with K+-smectite and the interactions of water with water rather than the water content. The in-plane stiffness parameters were much higher than the out-of-plane parameters. Elastic wave velocities for the P and S waves (VP and VS) in the dry K+-smectite with a pore size of ~1 nm were calculated to be 7.5 and 4.1 km/s, respectively. The P and S wave velocity ratio is key in the interpretation of seismic behavior and revealed that VP/VS = 1.64–1.83, which were values in favorable agreement with the experimental data. The results might offer insight into seismic research to predict the mechanical properties of minerals that are difficult to obtain experimentally and can provide complimentary information to interpret seismic surveys that can assist gas and oil exploration.

To investigate the influence of clay mineral microstructures on mechanical properties across varying hydration levels, this study employed molecular dynamics simulations to conduct uniaxial tensile strength tests in three orthogonal directions (x, y, z) using illite, montmorillonite and kaolinite. The moisture content was varied from 0% to 10% in 1% increments and from 0% to 50% in 10% increments. The observations highlight the role of water molecules in disrupting the inherent microscopic atomic structure of clay minerals, leading to diminished stability and a decline in tensile strength. As moisture content increased, there was a pronounced increase in the layer spacing of all three clay minerals, indicative of their hydration expansion behaviour. Concurrently, discernible reductions in both the tensile strength and Young's modulus of the clay minerals were observed.

This paper aims to explore the influence of solvent effects on the crystal habit of venlafaxine hydrochloride using the modified attachment energy (MAE) model by molecular dynamics (MD) simulation. Solvent effects were investigated based on the different morphologies of venlafaxine hydrochloride acquired by simulation and experimental technology from the solvents of isopropanol, dimethyl sulfoxide, and acetonitrile. Firstly, morphologically dominant crystal faces were obtained through the prediction of crystal habit in vacuum by the attachment energy (AE) model. Subsequently, the MAEs were calculated by the MD simulation to modify the crystal shapes in a real solvent environment, and the simulation results were in agreement with the experimental ones. Meanwhile, in order to have a better understanding of the solvent effects, the surface structure was introduced to analyze the solvent adsorption behaviors. The results show that the crystal habits of venlafaxine hydrochloride are affected by the combination of the AE and surface structures. Finally, the flowability of the obtained crystal powders from different solvents was investigated by measurement and analysis of the angle of repose and compressibility. The above results verify that the physical properties are closely related to the morphologies of the crystals.

Peptides mediate up to 40% of protein interactions, their high specificity and ability to bind in places where small molecules cannot make them potential drug candidates. However, predicting peptide–protein complexes remains more challenging than protein–protein or protein–small molecule interactions, in part due to the high flexibility peptides have. In this review, we look at the advances in docking, molecular simulations and machine learning to tackle problems related to peptides such as predicting structures, binding affinities or even kinetics. We specifically focus on explaining the number of docking programmes and force fields used in molecular simulations, so a prospective user can have an educated guess as to why choose one modelling tool or another to address their scientific questions.

Nano-nozzles are an essential part of the nano electromechanical systems (NEMS). Cross-sectional geometry of nano-nozzles has a significant role on the fluid flow inside them. So, main purpose of the present study is related to the effects of different symmetrical cross-sections on the fluid flow behavior inside of nano-nozzles. To this accomplishment, five different cross-sectional geometries (equilateral triangle, square, regular hexagon, elliptical and circular) are investigated by using molecular dynamics (MD) simulation. In addition, TIP4P is used for atomistic water model. In order to evaluate the fluid flow behavior, non-dimensional physical parameters such as Fanning friction factor, velocity profile and density number are analyzed. Obtained results are shown that the flow behavior characteristics appreciably depend on the geometry of nano-nozzle's cross-section. Velocity profile and density number for five different cross sections of nano-nozzle at three various measurement gauges are presented and discussed.

Crack propagation behaviors in a precracked single crystal Ag under mode I loading at different temperatures are studied by molecular dynamics simulation. The simulation results show that the crack propagation behaviors are sensitive to external temperature. At 0 K, the crack propagates in a brittle manner. Crack tip blunting and void generation are first observed followed by void growth and linkage with the main crack, which lead to the propagation of the main crack and brittle failure immediately without any microstructure evolution. As the temperature gets higher, more void nucleations and dislocation emissions occur in the crack propagation process. The deformation of the single crystal Ag can be considered as plastic deformation due to dislocation emissions. The crack propagation dynamics characterizing the microstructure evolution of atoms around the crack tip is also shown. Finally, it is shown that the stress of the single crystal Ag changes with the crack length synchronously.

The crystal–melt interfacial free energy is an important quantity governing many kinetic phenomena including solidification and crystal growth. Although general calculation methods are available, it is still difficult to obtain the interfacial energies that differ only slightly due to anisotropy. Here, we report such a calculation of Al crystal–melt interfacial energy based on the general framework of the capillary fluctuation method (CFM). The subtle dependence of both the melting temperature and interfacial free energy at melting temperature on the crystal interface orientation was examined. For Al, the average melting temperature is obtained at 934.79 ± 5 K and the orientationally averaged mean interfacial free energy is 98.35 mJ/m2. In addition, the anisotropy of the interfacial free energy is found weak, nevertheless with the values ranked as γ100 > γ110 > γ111.

The fracture behavior of precracked nanocrystals with grain size gradients is simulated using the molecular dynamics method. A large grain size gradient is found to elevate resistance to crack propagation and transform the fracture mode from intergranular to intragranular when the crack is obstructed by a coarse grain. But the intragranular crack is nipped in its bud due to the difficulty of intragranular fracture. However, intergranular fractures can be always kept in nanocrystals with a small grain size gradient. Both the Schmid factors for the slip systems of grains near the crack tip and the critical stress intensity factors are calculated, and energy partitioning is conducted to analyze the mechanisms behind this phenomenon. The research exhibits the key role of grain size gradient in improving the antifracture ability of nanocrystals.

Single-walled carbon nanotubes (SWCNTs), which have a unique electronic structure, nanoscale diameter, high curvature, and extra-large surface area, are ideal for making a new class of nanocomposites. In this study, under the condensed phase optimized molecular potentials for atomistic simulation studies force field, classical molecular dynamics simulation is used to study the molecular interactions between SWCNTs and the molecules of binaphthyl core-based chiral phenylene dendrimers (G0–G2). The simulation results revealed that both G2 and G1 molecules have obvious attractive interactions with SWCNTs, and theoretically demonstrated the possibility of noncovalent functionalization of SWCNTs with chiral dendrimers. The influence of temperature on composites was also studied, and the results indicate that the interaction decreases strongly for SWCNTs@G1 and SWCNTs@G2 with increasing temperature. The possibility during real-world composite processing would create the desired structure bridges between nanotubes and chiral dendrimers, which can be used to produce nanocomposites such as highly sensitive as well as enantioselective fluorescent sensors.

Indentation tests are used to determine the hardness of a material, e.g., Rockwell, Vickers, or Knoop. The indentation process is empirically observed in the laboratory during these tests; the mechanics of indentation is insufficiently understood. We have performed first molecular dynamics computer simulations of indentation resistance of polymers with a chain structure similar to that of high density polyethylene (HDPE). A coarse grain model of HDPE is used to simulate how the interconnected segments respond to an external force imposed by an indenter. Results include the time-dependent measurement of penetration depth, recovery depth, and recovery percentage, with respect to indenter force, indenter size, and indentation time parameters. The simulations provide results that are inaccessible experimentally, including continuous evolution of the pertinent tribological parameters during the entire indentation process.

We propose a mathematically rigorous method to measure the spontaneous curvature of a bilayer membrane by molecular dynamics (MD) simulation, which provides description of the molecular mechanisms that cause the spontaneous curvature. As a main result, for the membrane setup investigated, the spontaneous curvature is proved to be a constant plus twice the mean curvature of the membrane in its tensionless ground state. The spontaneous curvature due to the built-in transbilayer asymmetry of the membrane in terms of lipid shape is studied by the proposed method. A linear dependence of the spontaneous curvature with respect to the head-bead diameter difference and the lipid mixing ratio is discovered. The consistency with the theoretical results provides evidence supporting the validity of our method.

We investigate the hydrodynamic interactions of spherical colloidal nano particles and nano tetrahedra near a planar wall by means of molecular dynamics (MD) simulations of rigid particles within an all-atom solvent. For both spherical and nano-tetrahedral particles, we find that the parallel and perpendicular components of the local diffusion coefficient and viscosity, show good agreement with hydrodynamic theory of Faxén and Brenner. This provides further evidence that low perturbations from sphericality of a nanoparticle’s shape has little influence on its local diffusive behaviour, and that for this particular case, the continuum theory fluid dynamics is valid even down to molecular scales.

Under the COMPASS (condensed-phase optimized molecular potentials for atomistic simulation studies) force field, the molecular dynamics (MD) simulation was applied to first-to-third generation nanosize amine-based and butanediamine-based graphite/dendrimers composites. In this paper, we briefly introduced the constructive process of the composite system by means of MD simulation. The stability and mechanism of six intercalation composites were studied with microcosmic figure and variational energy under the invariable NVT ensemble. The energy variety was analyzed using the radial distribution function. The results indicate that the bulk of the dendrimer is small, the graphite layer is easy to bend and its systematic total energy is higher, which lead to the instability of the composite system. Therefore, the 3G dendrimer is the most stable system.

In this study, the mechanical properties of graphene and single walled carbon nanotubes (SWCNTs) were investigated based on molecular dynamics (MD) simulation. During the characterization of the mechanical properties, the atomistic interactions of the carbon atoms were described using the bonded and non-bonded energies. The bonded energy consists of four different interactions: Bond stretching, bond angle bending, dihedral angle torsion, and inversion. On the other hand, the non-bonded interaction between the carbon atoms within the cut-off ranges was regarded as the van der Waals (vdW) force. The effect of vdW force on the mechanical properties of graphene and SWCNTs would be mainly of concern. Simulation results indicated that the Young's modulus of the graphene with vdW force included is 15% higher than that without considering any vdW interaction. The same tendency also was observed in the armchair and zig-zag SWCNTs. Furthermore, it was revealed that the increment of moduli caused by the vdW force could be primarily attributed to the 1-4 vdW interaction. The influence of the vdW interactions on the mechanical properties of graphene and SWCNTs was then elucidated using the parallel spring concept.

The objective of the present study is to explore pressure-driven flows with the presence of electric double layer (EDL) in nanochannels of various wall lattice planes. Three face-centered cubic (fcc) lattice planes, i.e. fcc(111), fcc(100), and fcc(110), of the channel wall are considered. The structure of diffuse EDL and electrokinetic flow characteristics are dealt with in an atomistic view. Fluid and charge density layering phenomena and their influences on the Stern layer are investigated with the molecular dynamic simulation results. In most of the simulations, a monatomic molecule, W, is used as the solvent model and the charged particles W+ and W− of the same size as the ions. To examine behaviors of the dissimilar particles, a simulation with the aqueous model W for fluid, Na+ for cation and Cl− for anion is also performed. Effects of ion concentrations, wall-fluid interaction energy, and surface charge density on the electro-hydrodynamics are studied. In addition, based on the continuum theory, two analytic expressions for zeta potential with the presence of fluid slippage are derived and analyzed. The present results disclose interesting physics about the influences of wall lattice-fluid interactions, which are significant in further understanding and applications of the nanoscale electrokinetic flows.