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Moisture is an important factor affecting the insulation properties of transformers. Due to the limitations of macroscopic experimental methods, the diffusion of water at oil-paper interface cannot be accurately measured. Therefore, molecular dynamics method was used in this work to establish oil-paper layer model of 105 atoms. Through jointly analysing the aggregation degree, diffusion coefficient, free volume as well as radial distribution function of water molecules, the diffusion mechanism of water molecules at oil-paper interface was studied. The results show that when the initial water content in paper was high, water molecules would accumulate at oil-paper interface to form the local high-water region during heating. The polarisation of the electric field strengthened the hydrogen bonding interaction between water molecules and increased the probability of occurrence of the high-water region. Meanwhile, electric field reduced the free volume and diffusion coefficient of water molecules and rendered its diffusion coefficient anisotropic. What’s more, when the electric field was combined with the temperature field, the electric field played a leading role in the diffusion of water molecules while the temperature field was less affected. Diffusion coefficients of water molecules at different temperatures from molecular dynamics simulations were well consistent with experimental results, which verified the rationality of the model. [ABSTRACT FROM AUTHOR]

A scientific biography serves as an introduction to a collection of papers honoring the significant contributions to the field of Statistical Mechanics by the late Luis Felipe Rull (1949-2022) and José Luis Fernandez Abascal (1952). Both dedicated their careers to the understanding of condensed matter systems, not only making substantial scientific contributions but also pioneering and expanding computer simulation methods in Spain. They were instrumental figures in the Spanish Statistical Mechanics School, which has flourished due to the efforts of a generation, including Luis and José Luis, who transformed Spanish science since 1975 and laid the foundation for our current achievements. [ABSTRACT FROM AUTHOR]

This paper conducts a computational investigation of the phase behaviour of $ \textrm{C}{\textrm{H}_4} $ C H 4 - $ \textrm{C}{\textrm{O}_2} $ C O 2 binary system, utilising the SAFT-VR Mie equation of state alongside molecular dynamics (MD) simulations. Molecular parameters for pure $ \textrm{C}{\textrm{H}_4} $ C H 4 and $ \textrm{C}{\textrm{O}_2} $ C O 2 compounds were obtained by fitting the SAFT-VR Mie EOS to vapour pressure and saturated liquid density experimental data. The research first validates the SAFT-VR Mie EOS on thermodynamic properties and vapour–liquid equilibria for different compositions, pressures, and temperatures of pure $ \textrm{C}{\textrm{H}_4} $ C H 4 , $ \textrm{C}{\textrm{O}_2} $ C O 2 , and $ \textrm{C}{\textrm{H}_4} $ C H 4 - $ \textrm{C}{\textrm{O}_2} $ C O 2 mixtures with the newly extracted parameters. The study confirms the EOS's accurate prediction of coexistence properties, including pressure, density, and phase-equilibrium curve. MD simulations were performed using the LAMMPS software package, with Mie force field parameters derived from this study for non-bonded interactions. Simulations were conducted using three other force fields (OPLS-UA, UFF, and GAFF) to compare their performance with our approach. The simulation results were compared to laboratory data, or REFPROP, in the absence of laboratory data. The results showed a relatively good agreement, indicating that combining SAFT-VR Mie EOS and MD simulations is a reliable predictive tool for designing gas processing and gas storage applications involving $ \textrm{C}{\textrm{H}_4} $ C H 4 - $ \textrm{C}{\textrm{O}_2} $ C O 2 mixtures. This approach also mitigates the need for expensive and hazardous high-pressure laboratory techniques. [ABSTRACT FROM AUTHOR]

Thermo-osmotic flows, generated by applying a thermal gradient along a liquid-solid interface, could be harnessed to convert waste heat into electricity. While this phenomenon has been known for almost a century, there is a crucial need to gain a better understanding of the molecular origins of thermo-osmosis. In this paper, we start by detailing the multiple contributions to thermo-osmosis. We then showcase three approaches to computing the thermo-osmotic coefficient using molecular dynamics; a first method based on the computation of the interfacial enthalpy excess and Derjaguin's theoretical framework, a second approach based on the computation of the interfacial entropy excess using the so-called dry-surface method, and a novel non-equilibrium method to compute the thermo-osmotic coefficient in a periodic channel. We show that the three methods align with each other, in particular for smooth surfaces. In addition, for a polarised graphene-water interface, we observe large variations of thermo-osmotic responses, and multiple changes in flow direction with increasing surface charge. Overall, this study showcases the versatility of osmotic flows and calls for experimental investigation of thermo-osmotic behaviour in the vicinity of charged surfaces. [ABSTRACT FROM AUTHOR]

As a metalloid with unique properties, single crystal germanium is widely used in semiconductors, infrared optics, and other fields. To ensure the processing accuracy of single-crystal germanium, it is necessary to optimise the selection of parameters during processing. This paper uses molecular dynamics methods to study the cutting process of single-crystal germanium with the cutting depth and cutting speed as parameters and uses nanoindentation method to test the mechanical properties of the processed single-crystal germanium surface. The study found that with the increase of cutting depth, the cutting force and cutting heat increased significantly, the depth of the deformed layer increased significantly, and the stiffness of single-crystal germanium decreased significantly; with the increase of cutting speed, there was no built-up edge Influence, the cutting force is reduced, and more cutting heat is generated, and the depth of the deformation layer is higher, and the HCP structure increases, but the cutting speed has no obvious relationship with the mechanical properties of the machined surface. [ABSTRACT FROM AUTHOR]

This paper examines the satisfaction of the principle of corresponding states (PCS) on thepressure–density–temperature relation and the binary diffusion coefficient of hydrogen/oxygen mixture modelled as binary Lennard–Jones (LJ) fluid especially in a supercritical region. The hydrogen/oxygen mixture properties were computed by molecular dynamics simulation and compared with simulation results for a nitrogen/oxygen mixture as well as while using the Peng–Robinson (PR) equation of state (EOS) for both mixture types and a mono-component LJ-EOS. The Fuller–Schettler–Giddings model with the PR-EOS and Takahashi's EOS were used for binary diffusion coefficient comparison. The pseudocritical point concept of a fluid mixture was applied for PCS reduction and PCS satisfaction was conducted over a wide temperature range above the pseudocritical pressure with changing hydrogen molar fraction. PCS satisfaction for hydrogen/oxygen mixture properties was confirmed at reduced temperature of 1.5 or above. At reduced temperature of 1.0 or below, the hydrogen/oxygen mixture properties disagree with those of the comparison mixture because phase separation occurs. We conclude that the properties of hydrogen/oxygen mixtures can be estimated using the pseudocritical point concept and the investigated EOSs based on the PCS in the supercritical region at reduced temperature of1.5 or above. [ABSTRACT FROM AUTHOR]

This paper reviews some of the graph theory-based methods that were recently developed in our group for post-processing molecular dynamics trajectories. We show that the use of algorithmic graph theory not only provides a direct and fast methodology to identify conformers that are sampled over time, but it also allows to follow in time the interconversions between the conformers through graphs of transitions, also provides statistical characterisations, that would otherwise be hard to obtain. Examples for a gas phase peptide and for the more complex inhomogeneous charged air–liquid water interface are presented in order to demonstrate the power of topological 2D-graphs and their versatility and transferability. [ABSTRACT FROM AUTHOR]

In this paper, we test the ability of a recently proposed effective frequency theory, viz. the generalised Feynman–Kleinert effective frequency theory (GFK), for calculating the Wigner transform of the thermalised flux operator needed in reaction rate computations based on the classical Wigner model. We consider one-dimensional symmetric and asymmetric barriers at both high and low temperatures. The reaction rates obtained from the GFK theory are found to be close to the results obtained using the accurate Wigner function. The reaction rates obtained from the classical Wigner model are approximate since they are based on classical trajectories. We therefore also present a new version of the so-called effective quantum force method, that improves the classical Wigner rates. This new implementation utilises as input matrix elements of the thermalised flux operator obtained from the GFK theory. We find a significant improvement compared to the classical Wigner reaction rates. Possible extensions to multi-dimensional systems are discussed. [ABSTRACT FROM AUTHOR]

In a recent paper, Díaz-Herrera et al. [Mol. Phys. 122, e1989071 (2022)] have studied the condensation transition of spherical droplets in finite closed systems using large-scale Molecular Dynamics simulations. The authors find that the loci of discontinuities in the observed pressure–density isotherms do not converge to the bulk orthobaric curve, apparently at odds with results obtained previously using Monte Carlo simulations. The purpose of this comment is to point out that the Monte Carlo and Molecular Dynamics simulation results are actually mutually consistent, and the apparent differences are not related to the different sizes studied, but to the way each method implements sampling of configuration space. [ABSTRACT FROM AUTHOR]

Copolymer inhibitor with multifunctional groups has a good effect on inhibiting the secondary reaction in the clinker leaching process for alumina production, but the inhibition mechanism of the copolymer is not clear yet. In this paper, molecular dynamics simulation was used to study the adsorption process of the copolymer inhibitor with multifunctional groups, such as acrylic acid-vinyl alcohol copolymer (PAV) and acrylic acid-hydroxypropyl acrylate copolymer (PAH), on the β-dicalcium silicate (C2S) crystal surface, and reveal its inhibiting mechanism. Meanwhile, the polyacrylic acid (PAA) with only the carboxyl group also is simulated for comparing the inhibition effect with copolymer inhibitors. The results show that the binding energy between copolymer (PAV, PAH) and β-C2S is greater than that of PAA with a single functional group. The order of binding energy is as follows: PAH > PAV > PAA. In aqueous solution, the water molecule can restrict the degree of deformation of polymers, increase the distance between polymers and β-C2S and then lead to weakening of the adsorption of polymers on the crystal surface. The comprehensive and coordination effect of carboxyl and hydroxyl functional groups in PAV and PAH can strengthen the adsorption of copolymers on the β-C2S surface. The different spatial distribution of multifunctional groups in the molecular structure has a different influence on the adsorption of the copolymer. The results can provide a theoretical basis for researching new and highly effective copolymer inhibitors with multifunctional groups. Compared the adsorption state: The comprehensive and coordinate action of carboxyl and hydroxyl groups of the inhibitor with multifunctional groups make the inhibitor have a stronger adsorption ability on the surface of β-C2S than that with a single functional group. The results obtained in this paper can provide a theoretical basis for the research and development of new and highly effective polymeric inhibitors with multifunctional groups. Highlights The interaction between copolymer and β-C2S was investigated by MD simulation. The binding energy order between polymers and β-C2S is PAH > PAV > PAA. The presence of water molecules can weaken the adsorption of the copolymer on the surface of β-C2S. The comprehensive and coordinate action of carboxyl and hydroxyl groups of the inhibitor with multifunctional groups make the inhibitor have a stronger adsorption ability on the surface of β-C2S than that with a single functional group. [ABSTRACT FROM AUTHOR]

Extended phase-space isokinetic methods in their deterministic [Minary et al., Phys. Rev. Lett. 93, 150201 (2004)] and stochastic forms [Leimkuhler et al., Mol. Phys. 111, 3579 (2013)] have proved tremendously successful in allowing multiple time-scale molecular dynamics simulations to be performed with very large time steps. These methods work by coupling the physical degrees of freedom to a set of Nosé-Hoover chain or Nosé-Hoover Langevin thermostats via an isokinetic constraint, which has the effect of avoiding resonance artifacts that plague multiple time-step algorithms. In this paper, we introduce a new resonance-free approach that achieves the same gains in time step but without the imposition of isokinetic constraints or the introduction of extended phase-space variables. Rather, we modify the physical Hamiltonian that effects the same regulation of resonances achieved by the isokinetic constraints. In so doing, we show that sampling errors can be controlled and performance improvements are possible within a simpler Hamiltonian framework. The method is demonstrated in simulations of the structure of liquid water and, in conjunction with enhanced sampling, in generation of the Ramachandran free-energy surface of the solvated alanine dipeptide. [ABSTRACT FROM AUTHOR]

Interfacial thermal resistance between adjacent parts is important in the design of electronics and MEMS/NEMS devices as well as packaging. In this paper, the two-temperature model (TTM) along with non-equilibrium molecular dynamics (TTM-MD) is used to investigate the interfacial thermal resistance between carbon nanotube (CNT) and aluminium substrate. Factors including the direction of heat flow, temperature dependence and CNT engagement as well as the Al crystal orientation on the resultant interfacial thermal resistance are investigated. Thermal rectification can be observed due to the change of heat flow. Internal Al nanowire filling ratio and the crystal structures of Al substrate are found all significantly affecting the resultant interfacial thermal resistance. [ABSTRACT FROM AUTHOR]

Systems composed of soft matter (e.g. liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in a 'bespoke' fashion, resulting in many published soft matter simulations not being reproducible based on the information provided in the publications. To address the issue of reproducibility and to provide tools for computational screening, we have been developing the open-source Molecular Simulation and Design Framework (MoSDeF) software suite. In this paper, we propose a set of principles to create Transparent, Reproducible, Usable by others, and Extensible (TRUE) molecular simulations. MoSDeF facilitates the publication and dissemination of TRUE simulations by automating many of the critical steps in molecular simulation, thus enhancing their reproducibilitya. We provide several examples of TRUE molecular simulations: All of the steps involved in creating, running and extracting properties from the simulations are distributed on open-source platforms (within MoSDeF and on GitHub), thus meeting the definition of TRUE simulations. [ABSTRACT FROM AUTHOR]

In this paper, Lafuente and Cuesta's cluster density functional theory (CDFT) and lattice mean field approximation (LMFA) are formulated and compared within the framework of lattice density functional theory (LDFT). As a comparison, an LDFT based on our previous work on nonrandom correction to LMFA is also developed, where local density approximation is adopted on the correction. The numerical results of density distributions of an Ising fluid confined in a slit pore obtained from Monte Carlo simulation are used to check these functional approximations. Due to rational treatment on the coupling between site-excluding entropic effect and contact-attracting enthalpic effect by CDFT with Bethe-Peierls approximation (named as BPA-CDFT for short), the improvement of BPA-CDFT beyond LMFA is checked as expected. And it is interesting that our LDFT has a comparative accuracy with BPA-CDFT. Apparent differences between the profiles such as solvation force, excess adsorption quantity and interfacial tension from LMFA and non-LMFAs are found in our calculations. We also discuss some possible theoretical extensions of BPA-CDFT. [ABSTRACT FROM AUTHOR]

Ions significantly alter the water's structure, impacting properties such as the temperature of maximum density and the freezing point. We study structural changes in water upon adding sulfate anions, specifically $ {\rm Na}_2{\rm SO}_4 $ Na 2 SO 4 , $ {\rm K}_2{\rm SO}_4 $ K 2 SO 4 , $ {\rm Li}_2{\rm SO}_4 $ Li 2 SO 4 , and $ {\rm Mg}{\rm SO}_4 $ Mg SO 4 , using computer simulations. We employ the TIP4P/2005 water and the Madrid-2019 force field. By simulating solutions at various concentrations (0.64, 1.30, 1.90, and 3 mol kg $ ^{-1} $ − 1 ) and two temperatures (300 and 240 K), we explore how these electrolytes disrupt water's structure and how they modify the interplay between Low Density Water and High Density Water. Increased salt concentration perturbed water's radial distribution functions (RDFs), particularly up to 240 K. $ {\rm Na}_2{\rm SO}_4 $ Na 2 SO 4 significantly disrupted water structure, reducing RDF peak heights and indicating decreased tetrahedrality, while $ {\rm Mg}{\rm SO}_4 $ Mg SO 4 increased structural order. $ {\rm K}_2{\rm SO}_4 $ K 2 SO 4 displayed anomalous behaviour, minimally affecting water at 1.90 mol kg $ ^{-1} $ − 1 and ambient temperature but causing more ordered structures at 240 K. Orientational order parameter $ q_t $ q t analysis supported these findings. Hydrogen bond network analysis showed notable perturbations at lower temperatures. Diffusion coefficients generally decreased with concentration, with $ {\rm K}_2{\rm SO}_4 $ K 2 SO 4 exhibiting increase at 240 K. These results highlight the complex interactions between sulfate ions and water, enhancing our understanding of electrolyte solutions. [ABSTRACT FROM AUTHOR]

This study evaluates the capabilities of two new ion force fields (Tanaka [Yagasaki et al. JCTC 2020] and Madrid-2019 [Zerón et al. JCP 2019]) in conjunction with the TIP4P/2005 model for water in reproducing the NaCl–water phase diagram using molecular dynamics direct coexistence simulations. The performance of those force-fields is critically compared with the phase diagram recently reported for the Joung Cheatham-TIP4P/2005 force-field [Bianco et al. JCP 2022]. Excellent agreement between the three force-fields and experiments is found for the ice-solution line due to the dominance of the water model in the location of this line. For the NaCl-solution line, the Tanaka and the Madrid-2019 models accurately predict solubility at ambient temperature, but they underestimate somewhat the experimental line as temperature increases. The JC model underestimates NaCl solubility both at ambient and at high temperatures. All models underestimate the stability of the NaCl·2H $ _2 $ 2 O solid, which remains metastable with respect to NaCl. Equilibration of the NaCl·2H $ _2 $ 2 O-solution system is challenging at low temperatures due to the slow diffusion of concentrated NaCl solutions. The phase diagrams obtained serve as a foundation for studying crystal nucleation, and solid-solution interfaces, and provide very valuable information for the development of imporved NaCl–H $ _2 $ 2 O force-fields. [ABSTRACT FROM AUTHOR]

Averaged local bond order parameters based on spherical harmonics, also known as Lechner and Dellago order parameters, are routinely used to determine crystal structures in molecular simulations. Among different options, the combination of the $ \bar {q}_{4} $ q ¯ 4 and $ \bar {q}_{6} $ q ¯ 6 parameters is one of the best choices in the literature since distinguishes between solid- and liquid-like particles and between different crystallographic phases, including cubic and hexagonal phases. Recently, Algaba et al. [J. Colloid Interface Sci. 623, 354, (2022)] have used the Lechner and Dellago order parameters to distinguish hydrate- and liquid-like water molecules in the context of determining the carbon dioxide hydrate-water interfacial free energy. According to the results, the preferred combination previously mentioned is not the best option to differentiate between hydrate- and liquid-like water molecules. In this work, we revisit and extend the use of these parameters to deal with systems in which clathrate hydrates phases coexist with liquid phases of water. We consider carbon dioxide, methane, tetrahydrofuran, nitrogen, and hydrogen hydrates that exhibit sI and sII crystallographic structures. We find that the $ \bar {q}_{3} $ q ¯ 3 – $ \bar {q}_{12} $ q ¯ 12 combination is the best option possible between a large number of possible different pairs to distinguish between hydrate- and liquid-like water molecules in all cases. [ABSTRACT FROM AUTHOR]

Supercritical water has attracted much attention from both fundamental and technological perspectives, based largely on its ability to solvate other molecules. Predicting and controlling this requires a deeper understanding of water's polarisation behaviour. Using the computationally efficient Self-Consistent Electrostatic Embedding method, we were able to calculate the water dipole moment over an unprecedented range of thermodynamic conditions, covering gas, liquid and supercritical states, with large simulation systems and a high-level quantum mechanical method. We find a discontinuous change in the dipole moment along subcritical isotherms, corresponding to the sharp transition between the vapour and liquid states, with the latter exhibiting induced dipole moments between 0.5 and 0.9 D, depending on the temperature. In contrast, the dipole moment changes continuously from gas-like to liquid-like behaviour in the supercritical regime, allowing the degree of polarisation to be controlled through manipulating temperature and pressure. The dipole moment was found to be linearly related to the average number of hydrogen-bonded neighbours of water, emphasising the key role of local interactions to the polarisation process. Mean-field approaches based on a dielectric continuum representation of the solvent are unable to predict this behaviour due to the neglect of local interactions. [ABSTRACT FROM AUTHOR]

We study the density correlation function (DCF) of DPPC lipid bilayers. We compare Molecular Dynamics (MD) results with theoretical predictions obtained with a mesoscopic description, in terms of the lipid membrane elasticity. One key objective of our work is the quantification of the lipid membrane elasticity directly from the DCF, both for the membrane undulations and local membrane thickness. Our method does not require the definition of instantaneous surfaces or internal variables defining lipid orientations. Building on our previous work, here we focus on the intralayer correlations, i.e. the DCF of lipids residing on the same monolayer, by tracking only the position of the phosphorus atoms in a lipid head group. We demonstrate the relevance of the intralayer two-dimensional (2D) correlations to the total DCF. We further show that all-atom (AA) and coarse grained (CG) lipid forcefields, feature distintively different DCFs. The CG forcefield predicts results in good agreement with the mesoscopic predictions, for the entire wavevector range; the AA forcefield (CHARMM36) predict strong peristaltic fluctuations at long wavevectors $ q\gtrsim 0.8 $ q ≳ 0.8 nm $ ^{-1} $ − 1 , which are absent in the CG lipid model (MARTINI). [ABSTRACT FROM AUTHOR]

In this paper, we present a molecular dynamics study of the glass transition for a soft-core primitive model for ionic liquids, in which cations are fully flexible chains of tangent soft spherical monomers, being the positively charged monomer at one of the ends of the chain, and anions as charged soft spheres. We have monitored transport coefficients such as the self-diffusion coefficients and the shear viscosity, as well as correlation functions such as the mean-square displacement, the self-intermediate scattering function, and probes of heterogeneous dynamics such as the van Hove distribution function and the four-points susceptibility. The analysis of these properties indicates that, for a given pressure, the glass transition shows a weak temperature dependence on the cation length, occurring first for short-chain than for long-chain ionic liquids. [ABSTRACT FROM AUTHOR]

Hierarchical self-assembly underpins much of the diversity of form and function seen in soft systems, yet the pathways by which they achieve their final form are not always straightforward - intermediate steps, kinetic effects and finite sizes of aggregates all influence the self-assembly pathways of these systems. In this paper, we use molecular dynamics simulations of binary mixtures of spheres and ellipsoidal discs to investigate the self-assembly of anisotropic aggregates with internal structures. Through this, the full aggregation pathways of spontaneously chiral, multi-bilayer and multi-layer assemblies have been tracked and characterised via a semi-qualitative analysis. This includes the unambiguous identification of first-, second- and third-generation hierarchical assemblies within a single simulation. Given the significant challenge of tracking full aggregation pathways in experimental systems, our findings strongly support the notion that molecular simulation has much to contribute to improving our understanding of hierarchical self-assembling systems. [ABSTRACT FROM AUTHOR]

The goal of this work is to produce single species of polygons in two dimensions using the self-assembly of a simple patchy molecular model. A molecule is defined as a central soft repulsive Weeks Chandler and Anderson (WCA) atom that is decorated with two or four patches, which describe the two models studied in this work. Model I has two Lennard–Jones (LJ) patches inside of its central atom separated by an angle θ that intends to define the number of polygon sides. The attractive potential of these patches, interacting as pairs, is used to bond molecules together to form polygons. Model II, having two additional soft repulsive WCA patches, tangent on the outside, produces single polygon species configurations. An example of Model I with an angle $ \theta = 120^\circ $ θ = 120 ∘ , forming a mixture of polygons, is included. Model II produces single polygon species with 3-8 sides, depending on the angle θ between the attractive patches. Molecular dynamics simulations in the canonical ensemble are used to calculate thermodynamic properties such as internal energy, percentage of polygons, pressure and contour plots for the percentage of polygons following isochoric processes. Different starting configurations are used to verify the consistency of the equilibrium results. [ABSTRACT FROM AUTHOR]

Thermodynamic and transport properties of particles interacting via the triangular-well potential in the range of $ 1.4 \leq \lambda \leq ~2.6 $ 1.4 ≤ λ ≤ 2.6 have been studied using perturbation theory and Molecular Dynamics simulations. We present thermodynamic properties such as vapour-liquid coexistence, vapour pressures, and density for different values of the attractive range potential. Good agreement is observed between the theoretical approach and computer simulations in a wide range of densities, temperatures, and pressures. Additionally, we show Molecular Dynamic simulation results of transport properties such as the self-diffusion coefficient as a function of both density and temperature. Finally, thermodynamic and transport properties of real fluids like oxygen, methane, hydrogen sulfide, and fluoromethane have been predicted using both approaches. Results of vapour-liquid coexistence, vapour pressures, and critical points were in excellent agreement with experimental data. The coupling of perturbation theory, Molecular Dynamics simulations, and the triangular-well pair potential offers a versatile and efficient method to explore various real fluid systems, which would include associating fluids, complex molecular liquids, and colloidal systems. This approach can advance our understanding of these systems using a simple approach and to contribute the development of more accurate and predictive models. [ABSTRACT FROM AUTHOR]

Using molecular dynamics simulation, the surface tension is calculated and compared with experimental data to provide a microscopic interpretation of the synergistic effect on water surface tension reduction caused by a binary mixture composed of anionic and cationic surfactants. For the anionic and cationic surfactants, the sodium dodecyl sulphate (SDS) and the cetyl trimethylammonium bromide (CTAB) were used, respectively. Besides the electrostatic attraction between the anionic and cationic surfactants, resulting in a synergistic effect, other properties were analysed to study the reduction of the surface tension from a molecular level. For different SDS:CTAB composition of distinct properties of the pseudobinary mixture, such as the hydrogen bonds, order of the tails, and the arrangement of the surfactants at the interface were calculated. Those properties present different behaviours at the maximum and minimum values of the surface tension. The CTAB tails present a higher order than the SDS tails at all SDS:CTAB compositions however, the first ones show a maximum order at the minimum in the surface tension. The excess configurational energy was also calculated and shows a minimum value in the same composition as the minimum value of the surface tension. [ABSTRACT FROM AUTHOR]

In this work, we have calculated self-diffusion and shear viscosity, two of the most important transport properties, of the spherical square-well (SW) fluid interacting with potential range $ \lambda = 1.5 \, \sigma $ λ = 1.5 σ. To this end, we have used a combination of molecular dynamics simulation and the continuous version of the square-well (CSW) intermolecular potential recently proposed by Zerón et al. [Mol. Phys. 116, 3355 (2018)]. In addition to that, we have also determined a number of equilibrium properties, including internal energy, compressibility factor, radial distribution function and coordination number. All properties are evaluated in a wide range of temperatures and densities, including subcritical and supercritical thermodynamic conditions. Results obtained in this work show an excellent agreement with available data reported in the literature and demonstrate that the CSW intermolecular potential can be used in molecular dynamics simulations to emulate SW transport properties with confidence. [ABSTRACT FROM AUTHOR]

For molecular dynamics simulations of hard particles, we define dynamic neighbours as the distinct particles that collide with a given reference one during a specific time interval. This definition allows us to determine the distribution of the number of dynamic neighbours, its average, and its standard deviation. We will show that regardless of the time window used to identify dynamic neighbours, their distribution is correlated with diffusion coefficients, structure, and configurational entropy. Thus, it is likely that the distribution of the number of dynamic neighbours may be employed as another tool to gain insights into the dynamic behaviour of hard-core systems. We tested this approach on 2D and 3D systems consisting of monodisperse and binary mixtures of hard disks and spheres. Results show that implementing dynamic neighbours to define order parameters can sharpen the signals where transitions take place. [ABSTRACT FROM AUTHOR]

Based on an equilibrium thermodynamic scheme, this work studies the separation of the Helmholtz free energy of a hard-disk system into its positional and orientational contributions. For the positional part, an accurate two dimensional version of the Carnahan-Starling equation of state is proposed, while a simple ansatz of the one particle partition function for the orientational part is proposed. The latter expression, which contains information about the probability of the norm of the six-fold orientational order parameter, is obtained through molecular dynamics simulations. Perhaps due to finite size effects, the ordering of the fluid is not a sudden phenomenon: the fluid-hexatic phase transition is preceded by a linear increase in the orientational contribution to the pressure of the fluid. A similar result is obtained for the hexatic-solid phase transition. Thus, the hexatic first-order phase transition is located between two linear ordering processes, consistent with the KTHNY theory. The proposed separation also predicts the existence of first order fluid-hexatic phase transition by using two procedures: the first, based on a purely bimodal probability density function, produces a pressure with a van del Waals-like first-order phase transition, while the second, considering density fluctuations, results in a flattened pressure phase transition. [ABSTRACT FROM AUTHOR]

In order to understand the enhancement mechanism of the interaction between functionalised carbon nanotubes and polymer matrix, and to investigate the effects of different functionalised carbon nanotubes on the properties of composites at the microscopic level, the models of pure polyurethane (PUR), carbon nanotubes/polyurethane (CNTs/PUR), hydroxyl-functionalised carbon nanotubes/polyurethane (CNTOH/PUR), and carboxyl-functionalised carbon nanotubes/polyurethane (CNTCOOH/PUR) systems were constructed, and molecular dynamics methods were used to simulate the effects of different functionalised carbon nanotubes on the mechanical properties of polyurethane composite systems. The effects of different functionalised carbon nanotubes on the properties of PUR composite systems were compared by analysing the properties of PUR and its composite systems in terms of free volume fraction (FFV), radial distribution function (RDF), binding energy, and density distribution of PUR around different functionalised carbon nanotubes. The effects of intermolecular interactions on the properties of the composite systems were elucidated at the microscopic level. The final simulation results show that the CNTCOOH/PUR composite system with added carboxylated CNTs has the highest tensile yield strength, compressive properties and modulus; the smallest free volume fraction; the strongest bonding energy between CNTCOOH and PUR matrix, the largest density distribution of PUR matrix around CNTCOOH, and the best interfacial interaction. [ABSTRACT FROM AUTHOR]

Lithium-ion batteries are popular in the market due to their ability to charge and many applications in life. In these rechargeable batteries, Lithium ions move from the positive electrode to the negative electrode during charging and in the opposite direction during discharge. In the present research, the effect of external electric field amplitude (EEFA) with different ratios of 0.1, 0.2, 0.3, and 0.5 V/Å on the Li-ion-C-anode nanobattery was investigated by molecular dynamics (MD), and the effect of EEFA (0.1–0.5 V/Å) on the Mean squared displacement (MSD) was checked. It is concluded that for the Li-Li pair, the NN distance presents a slight tendency to decrease. Moreover, with the increase in the intensity of the EEFA, the number of mobile lithium ions increased from 60 to 183. Numerically, with increasing EEFA from 0.1–0.2, 0.3, and 0.5 V/Å, the MSD of lithium increased from 38.28–59.22, 89.91, and 113.04 nm2. This behaviour indicated that the lithiation of the carbon is occurring and that the lithium ions can diffuse through the carbon structure by breaking C–C bonds and forming a LiC alloy wall. [ABSTRACT FROM AUTHOR]

In this paper, the vacancy formation at the interface between different grains (Ag3Sn and βSn) induced by electromigration was investigated from the perspective of atom diffusion. To explain the micro-mechanism of void formation near the interface, the diffusion coefficient was specifically studied here via molecular dynamics (MD) simulation. By comparing the atom diffusion rates of atoms in βSn and Ag3Sn, a significant difference could be observed when the temperature is up to 400 K. The Sn atoms in βSn have a higher diffusion coefficient (8E − 9 cm2/s) than atoms in Ag3Sn (4E − 9 cm2/s), which indicated that the void would be prone to appear in βSn near the interface. Moreover, the effect of grain size and pressure on atom diffusivity was studied. Results show that the atom diffusivity depends heavily on the grain size of Ag3Sn. When the thickness of Ag3Sn is increased from 4 to 12 nm, this difference is significant when the temperature is only 375 K. On the other hand, the atom diffusion character of Ag3Sn and βSn changes substantially under constant pressure. The difference of the atom diffusion rate would be inhibited by pressure perpendicular to the interface, which indicated voids have less possibility to appear herein. [ABSTRACT FROM PUBLISHER]

Effective heat dissipation from nano-fluidic devices is sometimes necessary to ensure their performance and lifespan. In the molecular dynamics simulation of nanoscale convective heat transfer, thermostats cannot be directly applied to the fluid because of the non-uniform temperature distribution. Periodic boundary is typically utilised, but unrealistic axial heat conduction exists when there is a temperature difference between the outlet and images of inlet atoms. In this paper, the effect of axial conduction caused by periodic boundary is investigated through the Péclet number (Pe). Taking viscous dissipation into consideration, the magnitude of outlet thermal diffusion is observed to decrease with increasing Pe. The local average temperature of fluid changes in an exponential form except in the region close to the outlet. Results show that the contribution of outlet axial conduction to the local average temperature is less than 2.0% when Pe > 10. The main reason is that the magnitude of fluid velocity and viscous heat dissipation in nanochannels is much larger than that in macro-channels at the same Péclet number. [ABSTRACT FROM PUBLISHER]

Can a C60layer cover a surface of single-wall carbon nanotube (SWCNT) forming an exohedral pure-carbon hybrid with only van der Waals interactions? The aim of the present paper is to address this question and to demonstrate that the fullerene shell layer in such a bucky-corn structure can be stable. Theoretical study of the structure, stability and electronic properties of bucky-corn hybrids is reported for the shell of C60and C70molecules on an individual SWCNT, C60dimers on an individual SWCNT as well as C60molecules on SWNT bundles. The geometry and total energies of the bucky-corn hybrids were calculated by the molecular dynamics method, while the density functional theory method was used to simulate the electronic band structures. [ABSTRACT FROM AUTHOR]

The main point of this paper concerns the theoretical characterisation of the effects induced by the intermolecular interaction on the electron density upon the formation of CH4-H2X (X=O,S) and CH4–Ng (Ng=Ar,Xe) complexes. The work has been stimulated by recent molecular scattering beams experiments, which point out differences in both strength and anisotropy of the intermolecular potential between CH4–H2X respect to reference CH4–Ng systems. Herein, attention is focused on the electronic charge polarisation and particularly charge transfer (CT) effects between involved partners, directly related to the topology of the full potential energy surface. The modification of electron density and the occurrence of CT have been evaluated via the charge displacement function worked out by high levelab initiocalculations. Moreover, in the case of a specific configuration of CH4–H2O system, we define the leading interaction components, including their relative stabilising role and test our intermolecular potential model with reference toab initiocalculations. The results obtained indicate that CT clearly affects the strength and the anisotropy of CH4–H2O complex, and covers a minor and negligible role for CH4–H2S and the noble gas complexes, respectively. [ABSTRACT FROM AUTHOR]

Solid–fluid boundary conditions are strongly influenced by a number of factors, including the intrinsic properties of the solid/fluid materials, surface roughness, wettability, and the presence of interfacial nanobubbles (INBs). The interconnected nature of these factors means that they should be considered jointly. This paper employs molecular dynamics (MD) simulation in a series of studies aimed at elucidating the influence of wettability in boundary behaviour and the accumulation of interfacial gas. Specifically, we examined the relationship between effective slip length, the morphology of nanobubbles, and wettability. Two methods were employed for the promotion of hydrophobicity between two structured substrates with similar intrinsic contact angles. We also compared anisotropic and isotropic atomic arrangements in the form of graphite and Si(100), respectively. A physical method was employed to deal with variations in surface roughness, whereas a chemical method was used to adjust the wall–fluid interaction energy (ϵwf). We first compared the characteristic properties of wettability, including contact angle and fluid density within the cavity. We then investigated the means by which variations in solid–fluid interfacial wettability affect interfacial gas molecules. Our results reveal that the morphology of INB on a patterned substrate is determined by wettability as well as the methods employed for the promotion of hydrophobicity. The present study also illustrates the means by which the multiple effects of the atomic arrangement of solids, surface roughness, wettability and INB influence effective slip length. [ABSTRACT FROM PUBLISHER]

Vibronic coupling in the energetically lowest first four electronic states of CH2F+2is studied in this paper. A model 4×4 Hamiltonian is constructed in a diabatic electronic representation employing normal coordinates of vibrational modes and standard vibronic coupling theory. Extensiveab initioquantum chemistry calculations are carried out to determine the parameters of the Hamiltonian and energetic ordering of the electronic states. The topographical features of the latter are examined at length and several conical intersections are established. Nuclear dynamics calculations on coupled electronic states are carried out from first principles by propagating wave packet. Theoretically calculated broad band vibronic structure of the four states are found to be in good accord with the experimental results. [ABSTRACT FROM AUTHOR]

In this paper, we present molecular dynamics calculations of the Frank elastic constants, and associated time correlation functions, in nematic liquid crystals. We study two variants of the Gay–Berne potential, and use system sizes of half a million molecules, significantly larger than in previous studies of elastic behaviour. Equilibrium orientational fluctuations in reciprocal (k-) space were calculated, to determine the elastic constants by fitting at low |k|; our results indicate that small system size may be a source of inaccuracy in previous work. Furthermore, the dynamics of the Gay–Berne nematic were studied by calculating time correlation functions of components of the order tensor, together with associated components of the velocity field, for a set of wave vectorsk. Confirming our earlier work, we found exponential decay for splay and twist correlations, and oscillatory exponential decay for the bend correlation. In this work, we confirm similar behaviour for the corresponding velocity components. In all cases, the decay rates, and oscillation frequencies, were found to be accurately proportional tok2for smallk, as predicted by the equations of nematodynamics. However, the observation of oscillatory bend fluctuations, and corresponding oscillatory shear flow decay, is in contradiction to the usual assumptions appearing in the literature, and in standard texts. We discuss the advantages and drawbacks of using large systems in these calculations. [ABSTRACT FROM PUBLISHER]

In this paper, Monte Carlo (MC) simulation has been used to study the swelling pattern of Na-montmorillonite (Na-Mnt), Mg-montmorillonite (Mg-Mnt), and Na/Mg-mixture montmorillonite (4NaMg-Mnt; 2Na2Mg-Mnt). The molecular simulation was performed in the NVT (number of molecules, volume and temperature are constant) ensemble at normal temperature (300 K) and 225, 300, and 340 bar over an H2O content 147, 196, and 294 mg g−1of clay. The simulations reproduce the swelling pattern of Na-Mnt and Mg-Mnt. The predicted spacing of the Na/Mg-Mnt mixtures is closely related to that of Mg-Mnt and confirms the results reported in the literature for Na-rich/Mg-poor Mnt. The results of the water adsorption and the swelling properties on the system Na-Mnt, Mg-Mnt, and the Na/Mg-Mnt mixtures are reflected with a transformation to two-hydrate stages. The probability of the coordination number of Na+, Mg2+, and mixtures tends to increase with an increasing amount of H2O molecules, but decreases with increasing pressure. The cation–oxygen distances (Na–O or Mg–O) show two signals, corresponding to the first and second coordination shells, which indicates that the ions behave as in bulk water. [ABSTRACT FROM PUBLISHER]

The understanding of the flow and heat transfer processes for fluid through micro- and nanochannels becomes imperative due to its wide application in micro- and nano-fluidic devices. In this paper, the method to simulate the convective heat transfer process in molecular dynamics is improved based on a previous study. With this method, we simulate a warm dense fluid flowing through a cold parallel-plate nanochannel with constant wall temperature. The characteristics of the velocity and temperature fields are analysed. The temperature difference between the bulk average temperature of fluid and the wall temperature decreases in an exponential form along the flow direction. The Nusselt number for the laminar flow in parallel-plate nanochannel is smaller than its corresponding value at macroscale. It could be attributed to the temperature jump at the fluid–wall interface, which decreases the temperature gradient near the wall. The results also reveal that the heat transfer coefficient is related to the surface wettabilities, which differs from that in the macroscopic condition. [ABSTRACT FROM PUBLISHER]

We report a new permutationally invariant polynomial (PIP) fit to CCSD(T)/aug-cc-pVTZ energies for $ \hbox {CH}_5^{+} $ CH 5 + that provides fast analytical forces, unlike the original PIP fit of 2006. The new fit, which is slightly more precise than the previous one, is used in classical molecular dynamics, diffusion Monte Carlo and path integral molecular dynamics calculations of CH and HH radial distribution functions (RDFs) at temperatures of 10 and $ 50\,\hbox {K} $ 50 K . Corresponding RDFs are also reported for $ \hbox {CD}_{3}\hbox {H}_{2}^{+} $ CD 3 H 2 + . The well-known quantum localisation of the H atoms to the diatomic site from previous and present DMC calculations is maintained at $ 10\,\hbox {K} $ 10 K but shows additional delocalisation to the ' $ \hbox {CH}_{3}^{+} $ CH 3 + ' site at $ 50\,\hbox {K} $ 50 K . [ABSTRACT FROM AUTHOR]

We investigated the proportional relationship between the diffusion coefficient and the viscosity coefficient and excess entropy in Lennard-Jones fluids. Based on the theoretical basis of Dzugutov and Bell et al., we came up with a new expression. Using molecular dynamics simulation to calculate the radial distribution function (RDF), the reduced diffusion coefficient D* and the reduced shear viscosity coefficient η* in the state of reduced density ρ* = 0.5 and the reduced temperature range of 1 ≤ T* ≤ 2.8. The two body excess entropy S2 was calculated from RDF. The results showed that the reduced diffusion coefficient and the reduced viscosity coefficient and the excess entropy present the exponential scaling behaviour. Our results supported the notion put forth by Dzugutov and Bell et al. but had different adjust parameters. The dependence of the reduced diffusion coefficient on the reduced temperature are also explored, they qualitatively exhibited a 2/3 power function relationship. In addition, we have quantitatively calculated the relation schema of ln(η*)-ln(D*/T*) in Lennard-Jones fluids that with LJ potential (n = 12) without considering the influence of the packing fraction and found that the reduced diffusion coefficient and reduced viscosity satisfy the new Stokes–Einstein relationship proposed by Ohtori et al. [ABSTRACT FROM AUTHOR]

We have first investigated a feasibility of a malt-particle collision dynamics (MPCD) method by addressing whether or not the translational and rotational Brownian motion is activated at a physically reasonable level. From the results with respect to the root mean square velocities, we conclude that the MPCD method is a quite feasible simulation technique for a suspension composed of magnetic cubic particles. Then we have applied the MPCD simulation method to a quasi-2D system of magnetic cubic particles in order to control a regime change in the internal structure of particle aggregates by means of the strength and direction of a uniform applied magnetic field. In the case of a magnetic field applied in a certain direction from the 2D plane, a regime change in the internal structure of large densely-packed clusters into a regular configuration is more effectively attained than a magnetic field applied along the 2D plane. [ABSTRACT FROM AUTHOR]

The 3D reference interaction site model (3DRISM) is a powerful tool to study the thermodynamic and structural properties of liquids. However, for hydrophobic solutes, the inhomogeneity of the solvent density around them poses a great challenge to the 3DRISM theory. To address this issue, we have previously introduced the hydrophobic-induced density inhomogeneity theory (HI) for purely hydrophobic solutes. To further consider the complex hydrophobic solutes containing partial charges, here we propose the D2MSA closure to incorporate the short-range and long-range interactions with the D2 closure and the mean spherical approximation, respectively. We demonstrate that our new theory can compute the solvent distributions around real hydrophobic solutes in water and complex organic solvents that agree well with the explicit solvent molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

In this work, we evaluate the liquid-vapour coexistence diagram and the critical point for two different ranges, λ = 1.5 and 2.0 σ of the square-well dimer fluid, using two different simulation methods: (1) In the critical point vicinity, we use a new algorithm, based on transition rates, that can obtain the chemical potential as a function of the density at a given temperature and (2) Molecular Dynamics simulations using the direct coexistence technique for temperatures far below the critical region. The transition rate method has been proposed by Sastre and was used for the evaluation of the critical temperature of square-well monomers with high accuracy. The simulations in the low-temperature region were carried out using molecular dynamics simulations with the direct coexistence method and a continuous version of the square-well potential proposed recently by Zerón et al. [ABSTRACT FROM AUTHOR]

Square-well (SW) potential is likely the simplest potential describing attractive and repulsive interactions. However, its discontinuous functional form makes it difficult to be used in Molecular Dynamics (MD) simulation, particularly with commercial MD packages. Recently, Zerón and collaborators [Mol. Phys.116, 3355 (2018)] have presented a parameterisation of the SW potential that allows its use for simulation packages since the intermolecular potential and force are described by continuous mathematical functions. It was validated for SW spheres. In this work, we use this reported continuous SW potential to describe for the first time the equilibrium and interfacial properties of SW chains, with potential ranges of λ = 1.5 and 1.75. Simulations for tetramers interacting with λ = 1.5 are compared with available computational data in the literature, which has allowed to validate the method for molecular chain systems. Besides, a systematic study for the potential range of λ = 1.75 has not been addressed so far, which represents valuable information for instance to discern whether different microscopic theories are capable of describing this type of system. In particular, we assess the effect of temperature, chain length, and potential range on the calculated properties, namely density profiles, coexistence densities, vapour pressures, surface tensions and critical points. Overall, with increasing the chain length, the width of the envelope of the coexistence phase increases, which results in an increase of the surface tension as well as the critical temperature at the same time that the vapour pressure and the interfacial width decrease. [ABSTRACT FROM AUTHOR]

This computational study characterises charge-transfer-to-solvent (CTTS) states of aqueous thiocyanate anion using equation-of-motion coupled-cluster methods combined with electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) scheme. Equilibrium sampling was carried out using classical molecular dynamics (MD) with standard force-fields and QM/MM ab initio molecular dynamics (AIMD) using density functional theory. The two calculations yield significantly different local structure around solvated SCN − . Because of the diffuse character of CTTS states, they are very sensitive to the local structure of solvent around the solute and its dynamic fluctuations. Owing to this sensitivity, the spectra computed using MD and AIMD based snapshots differ considerably. This sensitivity suggests that the spectroscopy exploiting CTTS transitions can provide an experimental handle for assessing the quality of force-fields and density functionals. By combining CTTS-based spectroscopies with reliable theoretical modeling, detailed microscopic information of the solvent structure can be obtained. We present a robust computational protocol for modeling spectra of solvated anions and emphasise the use of an ab initio characterization of individual electronic transitions as CTTS or local excitations. [ABSTRACT FROM AUTHOR]

The mechanical qualities of single – and multi-layer CH3NH3XI3 (X = Pb, Sn, Mn) perovskite structures have been computed using the LAMMPS programme via the molecular dynamics' method. The LAMMPS analysis code is the keystone for computing mechanical characteristics in simulations. The stress–strain curves of the simulated atomic structures are offered for tests in the X and Y directions. The stress–strain curves were significantly computed by employing the loading technique and the deform command during the computational tests. Mechanical data was retrieved by inducing deformation in the simulated structures. The stress–strain curves for the single – (SL) and the multi-layer (ML) CH3NH3XI3 at various temperature and pressure values in the X and Y directions were also produced and compared, after applying a maximum stress (ultimate strength) using a load. Molecular dynamics (MD) simulations using LAMMPS software showed that layered perovskite materials possess high flexibility compared to the non-layered perovskite materials, which is essential in perovskite solar cells. The studied atomic structures thus provided the significant mechanical properties for designing proficient perovskite solar cells via the MD simulation. [ABSTRACT FROM AUTHOR]

The receptor-interacting serine/threonine protein kinase 1 (RIPK1) is tightly related to Digestive System Neoplasms genesis. Therefore, inhibitors that target RIPK1 have gained popularity in today's anti-cancer therapy. Molecular docking, molecular dynamics simulations, and molecular mechanics/Poisson-Boltzmann surface area calculations were used to investigate the binding mode and inhibition mechanism of five 4,5-dihydropyrazole derivatives with RIPK1 in the present work. The results showed that the five inhibitors mainly interacted with RIPK1 through van der Waals interaction and were stably present in the hydrophobic pocket next to the ATP-binding pocket. During the simulation, the inhibitor 2R with opposite chirality displayed a significant flip-flop in the binding pose, causing the key residue Asp156 to not easily maintain the inactive conformation, affecting its inhibitory ability. Inhibitors with identical chirality but different 1-substituents could exert noncompetitive inhibition via three pathways. First of all, the inhibitor interacted directly with ATP, influencing its γ -phosphate position. Second, it altered the conformation of Lys45, which was crucial for both ATP binding and γ -phosphate transfer. And then it affected the conformation of the P-loop and ß1 sheet, resulting in differences in substrate peptide recognition. The results can provide a theoretical basis for the design of such inhibitors in the future. [ABSTRACT FROM AUTHOR]