Grand Canonical Molecular Dynamics Simulations Research Articles

Disentanglement of Surface and Confinement Effects for Diene Metathesis in Mesoporous Confinement.

We study the effects of a planar interface and confinement on a generic catalytically activated ring-closing polymerization reaction near an unstructured catalyst. For this, we employ a coarse-grained polymer model using grand-canonical molecular dynamics simulations with a Monte Carlo reaction scheme. Inspired by recent experiments in the group of M. Buchmeiser that demonstrated an increase in ring-closing selectivity under confinement, we show that both the interface effects, i.e., placing the catalyst near a planar wall, and the confinement effects, i.e., locating the catalyst within a pore, lead to an increase of selectivity. We furthermore demonstrate that curvature effects for cylindrical mesopores (2 nm < d < 12.3 nm) influence the distribution of the chain ends, leading to a further increase in selectivity. This leads us to speculate that specially corrugated surfaces might also help to enhance catalytically activated polymerization processes.

Grand-canonical molecular dynamics simulations powered by a hybrid 4D nonequilibrium MD/MC method: Implementation in LAMMPS and applications to electrolyte solutions.

Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed phases. A promising method [L. Belloni, J. Chem. Phys. 151, 021101 (2019)], one of the hybrid nonequilibrium molecular dynamics/Monte Carlo algorithms, was recently developed, which enables efficient computation of fluctuating number or charge density in dense fluids or ionic solutions. This method facilitates the exchange through an auxiliary dimension, orthogonal to all physical dimensions, by reducing initial steric and electrostatic clashes in three-dimensional systems. Here, we report the implementation of the method in LAMMPS with a Python interface, allowing facile access to grand-canonical molecular dynamics simulations with massively parallelized computation. We validate our implementation with two electrolytes, including a model Lennard-Jones electrolyte similar to a restricted primitive model and aqueous solutions. We find that electrostatic interactions play a crucial role in the overall efficiency due to their long-range nature, particularly for water or ion-pair exchange in aqueous solutions. With properly screened electrostatic interactions and bias-based methods, our approach enhances the efficiency of salt-pair exchange in Lennard-Jones electrolytes by approximately four orders of magnitude, compared to conventional grand-canonical Monte Carlo. Furthermore, the acceptance rate of NaCl-pair exchange in aqueous solutions at moderate concentrations reaches about 3% at the maximum efficiency.

Understanding Humidity-Enhanced Adhesion of Geckos: Deep Neural Network-Assisted Multi-Scale Molecular Modeling.

A higher relative humidity leads to an increased sticking power of gecko feet to surfaces. The molecular mechanism responsible for this increase, however, is not clear. Capillary forces, water mediating keratin-surface contacts and water-induced softening of the keratin are proposed as candidates. In previous work, strong evidence for water mediation is found but indirect effects via increased flexibility are not completely ruled out. This article studies the latter hypothesis by a bottom-up coarse-grained mesoscale model of an entire gecko spatula designed without explicit water particles, so that capillary action and water-mediation are excluded. The elasticity of this model is adjusted with a deep neural network to atomistic elastic constants, including water at different concentrations. Ourresults show clearly that on nanoscopic flat surfaces, the softening of keratin by water uptake cannot nearly account for the experimentally observed increase in gecko sticking power. Here, the dominant mechanism is the mediation of keratin-surface contacts by intervening water molecules. This mechanism remains important on nanostructured surfaces. Here, however, a water-induced increase of the keratin flexibility may enable the spatula to follow surface features smaller than itself and thereby increase the number of contacts with the surface. This leads to an appreciable but not dominant contribution to the humidity-increased adhesion. Recently, by atomistic grand-canonical molecular dynamics simulation, the room-temperature isotherm is obtained for the sorption of water into gecko keratin, to the authors' knowledge, the first such relation for any beta-keratin. In this work, it relates the equilibrium water content of the keratin to the ambient relativehumidity.

Connecting dynamic pore filling mechanisms with equilibrium and out of equilibrium configurations of fluids in nanopores.

In the present study, using dynamic mean field theory complemented by grand canonical molecular dynamics simulations, we investigate the extent to which the density distributions encountered during the dynamics of capillary condensation are related to those distributions at equilibrium or metastable equilibrium in a system at fixed average density (canonical ensemble). We find that the states encountered can be categorized as out of equilibrium or quasi-equilibrium based on the magnitude of the driving force for mass transfer. More specifically, in open-ended slit pores, pore filling via double bridging is an out of equilibrium process, induced by the dynamics of the system, while pore filling by single bridge formation is connected to a series of configurations that are equilibrium configurations in the canonical ensemble and that cannot be observed experimentally by a standard adsorption process, corresponding to the grand canonical ensemble. Likewise, in closed cap slits, the formation of a liquid bridge near the pore opening and its subsequent growth while the initially detached meniscus from the capped end remains immobilized are out of equilibrium processes that occur at large driving forces. On the other hand, at small driving forces, there is a continuous acceleration of the detached meniscus from the capped end, which is associated with complete reversibility in the limit of an infinitesimally small driving force.

High-Performance Carbon Molecular Sieves for the Separation of Propylene and Propane

High-performance carbon molecular sieves (CMSs) for the separation of propylene (C3H6) and propane (C3H8) were synthesized in this study by chemical vapor deposition (CVD) of benzene on the pore entrances of activated carbon. The C3H6 and C3H8 separation characteristics of the CMSs were controlled by altering the amount of carbon deposited during CVD, and the resulting characteristic curve featuring the kinetic selectivity of C3H6 over C3H8 as a function of the adsorption rate constant of C3H6 is considered to be the upper bound of the C3H6-C3H8 separation factor for current CMSs because of the presence of previously reported CMS data under this curve. Additionally, CMS models were constructed using grand canonical molecular dynamics (GCMD) simulations mimicking the process of CVD, which revealed that the kinetic selectivity of C3H6 over C3H8 strongly depended on the size of the pore entrances at the level of 0.01 nm, and that strict control of the pore-entrance size was crucial for obtaining high-performance CMSs for C3H6-C3H8 separation. This was essentially achieved by controlling the duration of CVD, which led to the experimental realization of CMSs with a C3H6 selectivity over C3H8 of >2000 and a high uptake rate of C3H6. A design guideline for the development of high-performance CMSs for C3H6-C3H8 separation was proposed based on theoretical calculations performed using idealized carbon structures, which extracted the characteristics of the CMS models obtained from the GCMD simulations.

Self-Assembly of Model Triblock Janus Colloidal Particles in Two Dimensions.

A simplified two-dimensional effective-solvent model of triblock Janus particles, consisting of three interaction sites in a linear configuration, a core particle, and two particles modeling the attractive patches at the poles, is developed to study the mechanism of nucleation and self-assembly in triblock Janus particles. The potential energy parameters are tuned against phase transition temperatures and free energy barriers to the nucleation of crystalline phases, calculated from our previous detailed model of Janus particles. Vapor-liquid equilibria and critical temperatures are calculated by grand-canonical molecular dynamics simulations for particles of different patch widths. With metadynamics, phase equilibria, mechanism of nucleation, and free energy barriers to nucleation are investigated. The minimum free energy path to nucleation indicates two steps. The first step, with a higher free energy increase, consists of the densification of the fluid into a disordered cluster. In the second step, of a lower free energy barrier, the inner particles of the disordered cluster reorient to form a crystalline nucleus. This two-step mechanism of nucleation of a kagome lattice is in complete agreement with the experiment and with our previous simulations using a detailed model of Janus particles. Large systems at a slight supersaturation generate multiple crystalline domains, which are misaligned at the grain boundaries. In complete agreement with the experiment and with previous simulation results, we observe a two-step mechanism for crystal growth: melting of the smaller (less stable) crystallites to a fluid followed by recrystallization at the surface of neighboring bigger (more stable) crystallites. A comparison of the present softer modeling of a Janus particle with harder models in the literature for self-assembly of Janus particles indicates that softer potentials stabilize open lattices (e.g., kagome) more than dense lattices (e.g., hexagonal). Also, experimental locations of phase transition points and barrier heights to nucleation are better reproduced by the present model than by the existing simple models.

Exploration of the Adsorption Kinetics of Surfactants at the Water-Oil Interface via Grand-Canonical Molecular Dynamics Simulations.

It is well-known that surfactants tend to aggregate into clusters or micelles in aqueous solutions due to their special structures, and it is difficult for the surfactant molecules involved in the aggregation to move spontaneously to the oil-water interface. In this article, we developed a new grand-canonical molecular dynamics (GCMD) model to predict the saturated adsorption amount of surfactant with constant concentration of surfactant molecules in the bulk phase, which can prevent surfactants aggregating in the bulk phase and get the atomic details of the interfacial structural change with increase of the adsorption amount through a single GCMD run. The adsorption of anionic surfactant sodium dodecyl sulfate (SDS) at the heptane-water interface was studied to validate the model. The saturated adsorption amount obtained from the GCMD simulation is consistent with the experimental results. The adsorption kinetics of SDS molecules during the simulation can be divided into three stages: linear adsorption stage, transition adsorption stage, and dynamic equilibrium stage. We also carried out equilibrium molecular dynamics (EMD) simulations to compare with GCMD simulation. This GCMD model can effectively reduce the simulation time with correct prediction of the interfacial saturation adsorption. We believe the GCMD method could be especially helpful for the computational study of surfactant adsorption under complex environments or emulsion systems with the adsorption of multiple types of surfactants.

Friends, Foes, and Favorites: Relative Interactions Determine How Polymer Brushes Absorb Vapors of Binary Solvents.

Polymer brushes can absorb vapors from the surrounding atmosphere, which is relevant for many applications such as in sensing and separation technologies. In this article, we report on the absorption of binary mixtures of solvent vapors (A and B) with a thermodynamic mean-field model and with grand-canonical molecular dynamics simulations. Both methods show that the vapor with the strongest vapor–polymer interaction is favored and absorbs preferentially. In addition, the absorption of one vapor (A) influences the absorption of another (B). If the A–B interaction is stronger than the interaction between vapor B and the polymers, the presence of vapor A in the brush can aid the absorption of B: the vapors absorb collaboratively as friends. In contrast, if the A–polymer interaction is stronger than the B–polymer interaction and the brush has reached its maximum sorption capacity, the presence of A can reduce the absorption of B: the vapors absorb competitively as foes.

Grand Canonical Investigation of the Quasi Liquid Layer of Ice: Is It Liquid?

In this study, the solid-vapor equilibrium and the quasi liquid layer (QLL) of ice Ih exposing the basal and primary prismatic faces were explored by means of grand canonical molecular dynamics simulations with the monatomic mW potential. For this model, the solid-vapor equilibrium was found to follow the Clausius-Clapeyron relation in the range examined, from 250 to 270 K, with a Δ Hsub of 50 kJ/mol in excellent agreement with the experimental value. The phase diagram of the mW model was constructed for the low pressure region around the triple point. The analysis of the crystallization dynamics during condensation and evaporation revealed that, for the basal face, both processes are highly activated, and in particular cubic ice is formed during condensation, producing stacking-disordered ice. The basal and primary prismatic surfaces of ice Ih were investigated at different temperatures and at their corresponding equilibrium vapor pressures. Our results show that the region known as QLL can be interpreted as the outermost layers of the solid where a partial melting takes place. Solid islands in the nanometer length scale are surrounded by interconnected liquid areas, generating a bidimensional nanophase segregation that spans throughout the entire width of the outermost layer even at 250 K. Two approaches were adopted to quantify the QLL and discussed in light of their ability to reflect this nanophase segregation phenomena. Our results in the μVT ensemble were compared with NPT and NVT simulations for two system sizes. No significant differences were found between the results as a consequence of model system size or of the working ensemble. Nevertheless, certain advantages of performing μVT simulations in order to reproduce the experimental situation are highlighted. On the one hand, the QLL thickness measured out of equilibrium might be affected because of crystallization being slower than condensation. On the other, preliminary simulations of AFM indentation experiments show that the tip can induce capillary condensation over the ice surface, enlarging the apparent QLL.

Clay Swelling in Dry Supercritical Carbon Dioxide: Effects of Interlayer Cations on the Structure, Dynamics, and Energetics of CO2 Intercalation Probed by XRD, NMR, and GCMD Simulations

In situ X-ray diffraction (XRD) and nuclear magnetic resonance (NMR) experiments combined with molecular dynamics simulations using the grand canonical ensemble [grand canonical molecular dynamics (GCMD)] show that the cation size, charge, and solvation energy play critical roles in determining the interlayer expansion of smectite clay minerals when exposed to dry supercritical scCO2 (scCO2) under conditions relevant to petroleum reservoirs and geological CO2 sequestration conditions. The GCMD results show that the smectite mineral, hectorite, containing interlayer alkali and alkaline earth cations with small ionic radii and high solvation energies (e.g., Na+ and Ca2+) does not intercalate CO2 and that the fully collapsed interlayer structure is the most energetically stable configuration. With Cs+ and Ba2+, the monolayer structure is the stable configuration, and CO2 should spontaneously enter the interlayer. With Cs+, there is not even an energy barrier for CO2 intercalation, in agreement with the XRD a...

Molecular simulations of water adsorption and transport in mesopores with varying hydrophilicity arrangements.

The adsorption and transport of water in an open cylindrical mesopore with two different inner surface arrangements of hydrophilicities were examined by molecular simulations. The first model has a weak hydrophilic surface at both entrances of the pore and a stronger hydrophilic surface in the mid-section. The second pore has stronger hydrophilic surfaces at the entrances and weaker in the middle region. The simulation results show that the water adsorption isotherms obtained from Grand Canonical Monte Carlo simulations and pore filling curves acquired from Grand Canonical Molecular Dynamics simulations change depending on the arrangement of the strong and weak hydrophilic surfaces. In the first model, water condensation focuses on the mid-section forming a liquid bridge or a film, which creates a concave meniscus accelerating subsequent adsorption within the pore. Two bridges form in the entrance regions, where a cavity naturally occurs in between the films, in the second model. The different filling and emptying mechanisms clearly change the adsorption-desorption characteristics for the two pore types, but the second type generally showed faster transitions overall. Flux and meniscus analysis also reveals a circulating flow at the menisci of the interfaces within the pore. The results are expected to be valuable in understanding the effects of interior surface modification of nanopores in future applications.

Confined fluid and the fluid-solid transition: Evidence from absolute free energy calculations

The debate on whether an organic fluid nanoconfined by mica sheets will undergo a fluid-to-solid transition as the fluid film thickness is reduced below a critical value has lasted over two decades. Extensive experimental and simulation investigations have thus far left this question only partially addressed. In this work, we adapt and apply absolute free energy calculations to analyze the phase behavior of a simple model for nanoconfined fluids, consisting of spherical Lennard-Jones (LJ) molecules confined between LJ solid walls, which we use in combination with grand-canonical molecular dynamics simulations. Absolute Helmholtz free energy calculations of the simulated nanoconfined systems directly support the existence of order-disorder phase transition as a function of decreasing wall separation, providing results in close agreement with previous experiments and detailed atomistic simulations.

Grand canonical steady-state simulation of nucleation

Grand canonical molecular dynamics (GCMD) is applied to the nucleation process in a metastable phase near the spinodal, where nucleation occurs almost instantaneously and is limited to a very short time interval. With a variant of Maxwell's demon, proposed by McDonald [Am. J. Phys. 31, 31 (1963)], all nuclei exceeding a specified size are removed. In such a steady-state simulation, the nucleation process is sampled over an arbitrary time span and all properties of the metastable state, including the nucleation rate, can be obtained with an increased precision. As an example, a series of GCMD simulations with McDonald's demon is carried out for homogeneous vapor to liquid nucleation of the truncated-shifted Lennard-Jones (tsLJ) fluid, covering the entire relevant temperature range. The results are in agreement with direct nonequilibrium MD simulation in the canonical ensemble. It is confirmed for supersaturated vapors of the tsLJ fluid that the classical nucleation theory underpredicts the nucleation rate by two orders of magnitude.

Concurrent triple-scale simulation of molecular liquids

We present a triple-scale simulation of a molecular liquid, in which the atomistic, coarse-grained, and continuum descriptions of the liquid are concurrently coupled. The presented multiscale approach, which covers the length scales ranging from the micro- to macroscale, is a combination of two dual-scale models: a particle-based adaptive resolution scheme (AdResS), which couples the atomic and mesoscopic scales, and a hybrid continuum-molecular dynamics scheme (HybridMD). The combined AdResS-HybridMD scheme successfully sorts out the problem of large molecule insertion in the hybrid particle-continuum simulations of molecular liquids. The combined model is shown to correctly describe the hydrodynamics within a hybrid particle-continuum framework. The presented approach opens up the possibility to perform efficient grand-canonical molecular dynamics simulations of truly open molecular liquid systems.

Temperature control algorithms in dual control volume grand canonical molecular dynamics simulations of hydrogen diffusion in palladium

The effectiveness of five temperature control algorithms for dual control volume grand canonical molecular dynamics is investigated in the study of hydrogen atom diffusion in a palladium bulk. The five algorithms, namely, Gaussian, generalized Gaussian moment thermostat (GGMT), velocity scaling, Nosé-Hoover (NH), and its enhanced version Nosé-Hoover chain (NHC) are examined in both equilibrium and nonequilibrium simulation studies. Our numerical results show that Gaussian yields the most inaccurate solutions for the hydrogen-palladium system due to the high friction coefficient generated from the large velocity fluctuation of hydrogen, while NHC, NH, and GGMT produce the most accurate temperature and density profiles in both equilibrium and nonequilibrium cases with their feedback control mechanisms. However, this feedback control also overestimates the self-diffusion coefficients in equilibrium systems and the diffusion coefficient in nonequilibrium systems. Velocity scaling thermostat produces slight inhomogeneities in the temperature and density profiles, but due to the dissipated heat accumulated in the control volumes it still yields accurate self-diffusion coefficients that are in good agreement with the experimental data at a wide range of temperatures while others tend to deviate.

Modeling fluid diffusion using the lattice density functional theory approach: counterdiffusion in an external field

The dependence of the diffusivity on temperature, pressure, and composition is not understood well; consequently, data is preferred significantly over correlations in most practical situations. Even in dilute gases, the contributions of attractions and repulsions to the diffusivity are difficult to understand on a molecular level without performing simulations. We have developed a Lattice Density Functional Theory (LDFT) approach for modeling diffusion to supplement existing methods that are very rigorous but computationally demanding. The LDFT approach is analogous to the van der Waals equation in how it accounts for molecular interactions in that it has first-order corrections to ideal behavior; it is an extension of the Equilibrium LDFT for adsorption and phase behavior. In this work, the LDFT approach is presented and demonstrated by modeling the problem of color counterdiffusion in an externally-applied potential field. This potential field, in combination with the intermolecular potential function, creates a diffusion regime in which repulsions cause oscillations in the density profile. Using the LDFT approach, the oscillations were described and attributed to nearest-neighbor and next nearest-neighbor interactions. The LDFT approach gives qualitative and quantitative agreement with dual control-volume Grand Canonical Molecular Dynamics simulations.

Transport of a liquid water and methanol mixture through carbon nanotubes under a chemical potential gradient

In this work, we report a dual-control-volume grand canonical molecular dynamics simulation study of the transport of a water and methanol mixture under a fixed concentration gradient through nanotubes of various diameters and surface chemistries. Methanol and water are selected as fluid molecules since water represents a strongly polar molecule while methanol is intermediate between nonpolar and strongly polar molecules. Carboxyl acid (-COOH) groups are anchored onto the inner wall of a carbon nanotube to alter the hydrophobic surface into a hydrophilic one. Results show that the transport of the mixture through hydrophilic tubes is faster than through hydrophobic nanotubes although the diffusion of the mixture is slower inside hydrophilic than hydrophobic pores due to a hydrogen network. Thus, the transport of the liquid mixture through the nanotubes is controlled by the pore entrance effect for which hydrogen bonding plays an important role.

Molecular dynamics simulations of transport and separation of carbon dioxide-alkane mixtures in carbon nanopores.

The configurational-bias Monte Carlo method, which is used for efficient generation of molecular models of n-alkane chains, is combined for the first time with the dual control-volume grand-canonical molecular-dynamics simulation, which has been developed for studying transport of molecules in pores under an external potential gradient, to investigate transport and separation of binary mixtures of n-alkanes, as well as mixtures of CO2 and n-alkanes, in carbon nanopores. The effect of various factors, such as the temperature of the system, the composition of the mixture, and the pore size, on the separation of the mixtures is investigated. We also report the preliminary results of an experimental study of transport and separation of some of the same mixtures in a carbon molecular-sieve membrane with comparable pore sizes. The results indicate that, for the mixtures considered in this paper, even in very small carbon nanopores the energetic effects still play a dominant role in the transport and separation properties of the mixtures, whereas in a real membrane they are dominated by the membrane's morphological characteristics. As a result, for the mixtures considered, a single pore may be a grossly inadequate model of a real membrane, and hence one must resort to three-dimensional molecular pore network models of the membrane.

Grand canonical molecular dynamics simulations of transport diffusion in geometrically heterogeneous pores

Most transport diffusion simulation studies are carried out in single pores with simple geometries such as slit-like pores or straight cylindrical pores. Such models are gross simplifications of the structure of real, geometrically heterogeneous adsorbents. We carried out grand canonical molecular dynamics simulations of binary, counter diffusing CH4/CF4 mixtures in different cylindrical model pores with pore radii ranging from 11 to 23 A. Each of these pore models represents a feature that can be found in real adsorbents such as pores with amorphous surfaces, pores with a change in the cross-sectional area, pores with kinks and simple pore networks. The results were compared to simulation results in straight pores with homogeneous surfaces to investigate the extent to which transport diffusion can be represented by these simplified model pores. Our results show that transport diffusion is hardly influenced by the different pore structures studied in this work. The simulation results can be reproduced by straight pores if the correct average radius, flow length and enclosing gradient are chosen.

Transport diffusion of liquid water and methanol through membranes

In this work, we carried out dual-control-volume grand canonical molecular dynamics simulations of the transport diffusion of liquid water and methanol to vacuum under a fixed chemical potential gradient through a slit pore consisting of Au(111) surfaces covered by −CH3 or −OH terminated self-assembled monolayers (SAMs). Methanol and water are selected as model fluid molecules because water represents a strongly polar molecule while methanol is intermediate between nonpolar and strongly polar molecules. Surface hydrophobicity is adjusted by varying the terminal group of −CH3 (hydrophobic) or −OH (hydrophilic) of SAMs. We observed for the first time from simulations the convex and concave interfaces of fluids transporting across the slit pores. Results show that the characteristics of the interfaces are determined by the interactions between fluid molecules and surfaces. The objective of this work is to provide a fundamental understanding of how these interactions affect transport diffusion.