Nonequilibrium Molecular Simulations Research Articles

Molecular-level study of hydrophobic interactions during low-rank coal particle-bubble attachment

Particle-bubble attachment is a crucial part of coal and mineral flotation processes. The attachment of two different hydrophobic low-rank coal particles to bubble surface were simulated by a non-equilibrium molecular simulation method. Both particles were subjected to water film drainage resistance when approaching the bubble. Eventually, CPC (low-rank Coal Particle with mixed Collector adhered) jumped in and attached to bubble, but CP (low-rank Coal Particle) had only repulsive effect with bubble. The surface water film of CPC generated tiny hole under the entropy effect of water molecule rearrangement, and the presence of gas–water and oil–water interfacial tension promoted the rapid expansion of the hole until the water film rupture. The critical rupture thickness of the water film on CPC surface was about 1 nm and the rupture was completed in a very short time of 0.4 ns. The CPC jumped in and attached to the bubble surface under the action of oil–water interfacial tension. This suggests that the long-range hydrophobic force originates from the combined action of various interfacial tensions. Our results demonstrate the important role of interfacial tension in the attachment of hydrophobic particle to bubble, and contribute to the connection between microscopic and macroscopic mechanism of particle-bubble attachment.

Molecular mechanisms of thickness-dependent water desalination in polyamide reverse-osmosis membranes

Using non-equilibrium molecular simulations, we systematically elaborate the relationships among synthesis (membrane's thickness and morphology), atomic-scale transport mechanism, and separation performance (permeability and selectivity) for 3D-printed polyamide (PA) membranes. Results indicated that water diffusion, swelling ratio, water flux, and water permeance proportionally decrease with increasing membrane thickness (4.0–32.5 nm). PA membranes with different thicknesses can achieve almost 100% salt rejection over the simulation time. Importantly, water permeability exponentially decreases with increasing thickness, and 15 nm is identified as the critical membrane thickness for efficient water transport. The discontinuous water-available space spreads all over PA membranes with thicknesses greater than 5 nm, allowing water molecules to jump by way of the temporary open-and-close pores. However, the connected water-useable space exists in PA membranes with thicknesses below 5 nm, offering the continuous channels to dominate water transport. More significantly, pore distribution is more homogeneous as the thickness increases. The applied high pressures can lead to membrane compaction during reverse osmosis and the thicker membranes show a lower compression ratio. In short, these investigations provide molecular insights for effectively designing and manufacturing PA membranes for water desalination and treatment at the molecular level.

Bell-Evans model and steered molecular dynamics in uncovering the dissociation kinetics of ligands targeting G-protein-coupled receptors

Recently, academic and industrial scientific communities involved in kinetics-based drug development have become immensely interested in predicting the drug target residence time. Screening drug candidates in terms of their computationally predicted residence times, which is a measure of drug efficacy in vivo, and simultaneously assessing computational binding affinities are becoming inevitable. Non-equilibrium molecular simulation approaches are proven to be useful in this purpose. Here, we have implemented an optimized approach of combining the data derived from steered molecular dynamics simulations and the Bell-Evans model to predict the absolute residence times of the antagonist ZMA241385 and agonist NECA that target the A2A adenosine receptor of the G-protein-coupled receptor (GPCR) protein family. We have predicted the absolute ligand residence times on the timescale of seconds. However, our predictions were many folds shorter than those determined experimentally. Additionally, we calculated the thermodynamics of ligand binding in terms of ligand binding energies and the per-residue contribution of the receptor. Subsequently, binding pocket hotspot residues that would be important for further computational mutagenesis studies were identified. In the experiment, similar sets of residues were found to be in significant contact with both ligands under study. Our results build a strong foundation for further improvement of our approach by rationalizing the kinetics of ligand unbinding with the thermodynamics of ligand binding.

Shock resistance capability of multi-principal elemental alloys as a function of lattice distortion and grain size

This article aims to study the shock resistance capability of multi-element alloys. In this study, we utilized nonequilibrium molecular dynamics-based simulations with an embedded atom method potential to predict the deformation governing mechanism in a multi-elemental alloy system subjected to shock loading. The evolution of shock front width, longitudinal stress, shear stress, and dislocation density were investigated for different polycrystalline multi-element systems containing different mean grain sizes of 5, 10, and 18 nm, respectively. In order to quantify the effect of lattice distortion, average atom (A-atom) potential for quinary (high entropy) and ternary (medium entropy) configurations was also developed in this work. The random composition of multi-element alloys was replaced with single atom-based A-atom arrangements to study the effect of lattice distortion on shock resistance capabilities of high entropy alloy and medium entropy alloy. It was predicted from simulations that a higher value of lattice distortion component in the CoCrCuFeNi alloy leads to provide superior resistance against shock wave propagation as compared to the ternary alloy CrFeNi. In nanocrystalline configurations, dislocations, and stacking faults, only dislocations governed the deformation mechanics in monocrystalline configurations. The simulations indicate that grain size significantly affects the rates of generation of secondary/partial dislocations, hence affecting the stresses and the deformation mechanism of the structures.

Thermal conductance of the water-gold interface: The impact of the treatment of surface polarization in non-equilibrium molecular simulations.

Interfacial thermal conductance (ITC) quantifies heat transport across material-fluid interfaces. It is a property of crucial importance to study heat transfer processes at both macro- and nanoscales. Therefore, it is essential to accurately model the specific interactions between solids and liquids. Here, we investigate the thermal conductance of gold-water interfaces using polarizable and non-polarizable models. Both models have been fitted to reproduce the interfacial tension of the gold-water interface, but they predict significantly different ITCs. We demonstrate that the treatment of polarization using Drude-like models, widely employed in molecular simulations, leads to a coupling of the solid and liquid vibrational modes that give rise to a significant overestimation of the ITCs. We analyze the dependence of the vibrational coupling with the mass of the Drude particle and propose a solution to the artificial enhancement of the ITC, preserving at the same time the polarization response of the solid. Based on our calculations, we estimate ITCs of 200 MW/(m2 K) for the water-gold interface. This magnitude is comparable to that reported recently for gold-water interfaces [279 ± 16 MW/(m2 K)] using atomic fluctuating charges to account for the polarization contribution.

Effect of lattice distortion and nanovoids on the shock compression behavior of (Co-Cr-Cu-Fe-Ni) high entropy alloy

In this article, non-equilibrium molecular dynamics-based simulations were performed to study the effect of shock compression on the deformation governing mechanism of high entropy alloys (HEA). Quinary configuration of the alloy containing (Co-Cr-Cu-Fe-Ni) as primary elements were considered, and interaction between them was simulated with the help of embedded atom method potential. Hugoniot curves between P-Up and Us-Up were captured for HEA that agrees qualitatively and quantitatively with results reported using higher fidelity simulations and experimental techniques. Single-crystal HEA was subjected to shock compression and ultra-short pulse at piston velocities above and below the Hugoniot elastic limit. To capture the dynamics of the shock wave propagation in single-crystal HEA, spectra-temporal distribution of pressure and velocities were captured as a function of time from the onset of the shock wave. It was predicted from atomistic simulations that the insertion of voids in the path of shock front helps in dispersing the energy, as well as reducing the speed of shock propagation. Voids significantly affect the shock deformation governing mechanism in the crystal of HEA, and onset plastic deformation, even at piston velocities below the Hugoniot elastic limit. To capture the effect of lattice distortion in HEA, average atom configuration was also developed. It was predicted from the simulations that the effect of lattice distortion helps in blunting the shock front and diluting its speed of propagation. The lattice distortion effect is more dominant at lower simulation temperatures and lower piston impact velocities.

Electric Field Effects on Photoelectrochemical Water Splitting: Perspectives and Outlook

The grand challenges in renewable energy lie in our ability to comprehend efficient energy conversion systems, together with dealing with the problem of intermittency via scalable energy storage systems. Relatively little progress has been made on this at grid scale and two overriding challenges still need to be addressed: (i) limiting damage to the environment and (ii) the question of environmentally friendly energy conversion. The present review focuses on a novel route for producing hydrogen, the ultimate clean fuel, from the Sun, and renewable energy source. Hydrogen can be produced by light-driven photoelectrochemical (PEC) water splitting, but it is very inefficient; rather, we focus here on how electric fields can be applied to metal oxide/water systems in tailoring the interplay with their intrinsic electric fields, and in how this can alter and boost PEC activity, drawing both on experiment and non-equilibrium molecular simulation.

Beyond Bell's law: model free transition rate estimation from nonequilibrium trajectories

Biological machines at the nanoscale regulate the rate at which they transition from one long-lived functional state to another by channeling chemical and mechanical energy from external forces and noisy environments. Here we discuss a concrete tradeoff, imposed by statistical physics, between the extent to which such transitions can be sped-up and the work required to do so. We use a model cooperatively (un)folding protein to illustrate how such a guiding principle can be put to use inferring transition rates from nonequilibrium force spectroscopy experiments and molecular simulation.

Molecular Simulation of External Electric Fields on the Crystal State: A Perspective

Unpacking the mechanistic insights into how externally applied electric fields affect the physicochemical properties of crystals represents a challenge of great importance for a plethora of natural phenomena, in addition to a broad array of industrial operations and technologies. As such, the key goals in such field effect studies centre around how thermodynamic and kinetic relaxation processes in crystals are affected, including charge carrier conduction and energy transfer processes, and this is a very recent area of fundamental scrutiny. Indeed, in recent years, there has been a steadily mounting number of reports of field-manipulated crystal-state phenomena. Taking as the background a range of natural phenomena, phenomenological theory, state-of-the-art experiments and technological observations, the present review examines the role of nonequilibrium molecular simulation in its scrutiny of intra-crystal phenomena from an atomistic viewpoint, in addition to providing a framework for a predictive molecular design philosophy by which to refine field crystal understanding.

Dynamical Water Ingress and Dissolution at the Amorphous-Crystalline Cellulose Interface.

The use of cellulose has considerable promise in a wide range of industrial applications but is hampered by degradation in mechanical properties due to ambient moisture uptake. Existing models of equilibrium moisture content can predict the impact of these effects, but at present, the dynamical, atomic-scale picture of water ingress into cellulose is lacking. The present work reports nonequilibrium molecular simulations of the interface between cellulose and water aimed at capturing the initial stages of two simultaneous dynamical processes, water ingress into cellulose and cellulose dissolution into water. These simulations demonstrate that the process depends on the temperature and chain length in the amorphous region, where high temperatures can induce more mass exchange and short chains can easily detach from amorphous cellulose. A cooperative mechanism that involves both chemical and physical aspects, namely, hydrogen bonding and chain intertwining, respectively, is proposed to interpret the incipient dual ingress/dissolution process. Outcomes of this work will provide a foundation for cellulose functionalization strategies to impede moisture uptake and preserve the mechanical properties of nanocellulose in applications.

Molecular Simulation of Crystallisation in External Electric Fields: A Review

Elucidating the underlying mechanisms of molecular solidification in both homo- and hetero-geneous systems is of paramount importance for a large swathe of natural phenomena (whether on Earth or throughout the Universe), as well as a whole litany of industrial processes. One lesser-studied aspect of these disorder-order transitions is the effect of external applied fields, shifting both thermodynamic driving forces and underlying kinetics, and, indeed, fundamental mechanisms themselves. Perhaps this is nowhere more apparent than in the case of externally-applied electric fields, where there has been a gradually increasing number of reports in recent years of electro-manipulated crystallisation imparted by such electric fields. Drawing motivations from both natural phenomena, state-of-the-art experiments and, indeed, industrial applications, this review focusses on how non-equilibrium molecular simulation has helped to elucidate crystallisation phenomena from a microscopic perspective, as well as offering an important, predictive molecular-design approach with which to further refine in-field-crystallisation operations.

Thermal rectification in asymmetric two-phase nanowires

Thermal rectification based on a new strategy of nanostructuration has been assessed with nonequilibrium molecular dynamics and wave-packet propagation simulations. The use of asymmetric crystalline-core/amorphous-conical-shell nanowires creates a direction-dependent thermal conductivity due to variable axial and radial phonon propagation/confinement. The origin of this effect is related to the combination of a crystalline/amorphous interface parallel to the heat flux, together with the variable amount of amorphous coating due to the conical shell of the nanowire. Physical insights of the rectification are given by the mean free path of phonons, the axial and radial energy transfer, the energy diffusivity, and the vibrational density of states restricted to different constitutive elements of the nanowire.

Stability of force-driven shear flows in nonequilibrium molecular simulations with periodic boundaries.

We analyze the hydrodynamic stability of force-driven parallel shear flows in nonequilibrium molecular simulations with three-dimensional periodic boundary conditions. We show that flows simulated in this way can be linearly unstable, and we derive an expression for the critical Reynolds number as a function of the geometric aspect ratio of the simulation domain. Approximate periodic extensions of Couette and Poiseuille flows are unstable at Reynolds numbers two orders of magnitude smaller than their aperiodic equivalents because the periodic boundaries impose fundamentally different constraints on the flow. This instability has important implications for simulating shear rheology and for designing nonequilibrium simulation methods that are compatible with periodic boundary conditions.

Hydrodynamic slip can align thin nanoplatelets in shear flow

The large-scale processing of nanomaterials such as graphene and MoS2 relies on understanding the flow behaviour of nanometrically-thin platelets suspended in liquids. Here we show, by combining non-equilibrium molecular dynamics and continuum simulations, that rigid nanoplatelets can attain a stable orientation for sufficiently strong flows. Such a stable orientation is in contradiction with the rotational motion predicted by classical colloidal hydrodynamics. This surprising effect is due to hydrodynamic slip at the liquid-solid interface and occurs when the slip length is larger than the platelet thickness; a slip length of a few nanometers may be sufficient to observe alignment. The predictions we developed by examining pure and surface-modified graphene is applicable to different solvent/2D material combinations. The emergence of a fixed orientation in a direction nearly parallel to the flow implies a slip-dependent change in several macroscopic transport properties, with potential impact on applications ranging from functional inks to nanocomposites.

Taming the thermodiffusion of alkali halide solutions in silica nanopores.

Thermal fields give rise to thermal coupling phenomena, such as mass and charge fluxes, which are useful in energy recovery applications and nanofluidic devices for pumping, mixing or desalination. Here we use state of the art non-equilibrium molecular simulations to quantify the thermodiffusion of alkali halide solutions, LiCl and NaCl, confined in silica nanopores, targeting diameters of the order of those found in mesoporous silica nanostructures. We show that nanoconfinement modifies the thermodiffusion behaviour of the solution. Under confinement conditions, the solutions become more thermophilic, with a preference to accumulate at hot sources, or thermoneutral, with the thermodiffusion being inhibited. Our work highlights the importance of nanoconfinement in thermodiffusion and outlines strategies to tune mass transport at the nanoscale, using thermal fields.

Topological Methods for Polymeric Materials: Characterizing the Relationship Between Polymer Entanglement and Viscoelasticity.

We develop topological methods for characterizing the relationship between polymer chain entanglement and bulk viscoelastic responses. We introduce generalized Linking Number and Writhe characteristics that are applicable to open linear chains. We investigate the rheology of polymeric chains entangled into weaves with varying topologies and levels of chain density. To investigate viscoelastic responses, we perform non-equilibrium molecular simulations over a range of frequencies using sheared Lees–Edwards boundary conditions. We show how our topological characteristics can be used to capture key features of the polymer entanglements related to the viscoelastic responses. We find there is a linear relation over a significant range of frequencies between the mean absolute Writhe and the Loss Tangent . We also find an approximate inverse linear relationship between the mean absolute Periodic Linking Number and the Loss Tangent . Our results show some of the ways topological methods can be used to characterize chain entanglements to better understand the origins of mechanical responses in polymeric materials.

Viscosity of a highly compressed methylated alkane via equilibrium and nonequilibrium molecular dynamics simulations

Recent experiments have established the glass-forming ability of methylated alkanes. While temperature effects on the glass transition have been extensively studied under ambient pressure, the impact of pressure on molecular mobility at ambient temperature has received less attention. In this work, we use a combination of equilibrium and nonequilibrium molecular simulation methods to determine the viscosity of 2,2,4-trimethylhexane at 293 K and for pressures ranging from 0.1 MPa to 1 GPa, shedding light on the interplay between structural, thermodynamic and transport properties, leading to the increase in viscosity by several orders of magnitude at high pressure.

Unexpected thermal conductivity enhancement in pillared graphene nanoribbon with isotopic resonance

Thermal transport in nanoribbon based nanostructures is critical to advancing its applications. Wave effects of phonons can give rise to controllability of heat conduction in nanostructures beyond that by particle scattering. In this paper, by introducing pillars to form structural resonance, we systematically studied the thermal conductivity of graphene nanoribbon based phononic metamaterials (GNPM) through non-equilibrium molecular dynamical simulation. Interestingly, it is found that the thermal conductivity of GNPM is counter intuitively enhanced by isotope engineering, which is strong contrast to the common notion that isotope engineering reduces thermal conductivity.Further mode analysis and atomic Green function calculation reveal that the unexpected increasing in thermal conductivity originates from the breaking of the resonant hybridization wave effect between the resonant modes and the propagating modes induced by isotope engineering. Besides, factors including the system width and pillar height can also efficiently tune the thermal conductivity of GNPM. This abnormal mechanism provides a new dimension to manipulate phonon transport in nanoribbon based nanostructures through wave effect.

Acoustothermal Atomization of Water Nanofilms.

We report nonequilibrium molecular simulations of the vibration-induced heating of nanoscale-thick water layers on a metal substrate. In addition to experimentally confirmed acoustothermal evaporation, we observe hitherto unmapped nucleate and film boiling regimes, accompanied by the generation of unprecedented heat fluxes [∼O(10^{9}) W/m^{2}]. We develop a universal scaling parameter to classify the heat-transfer regimes and to predict the thickness of the residual nonevaporating liquid layer. The results find broad application to systems involving drying, coatings, and sprays.

Thermostat effect on water transport dynamics across CNT membranes

Whereas numerous experimental and simulation studies have been contributed to the investigation of fluid transport across membranes in the past decades, there is a significant discrepancy between experiments and simulations in the magnitude of fluid permeability and the degree of flow rate enhancement. Here, we show that one of the causes of the discrepancy is the variety of thermostating object, via which the temperature of fluid flow in non-equilibrium molecular simulations is controlled. By thermostating either the water system or the membrane material with Langevin method, we examine the temperatures of water flows in two types of membranes, the amounts of absorbed water molecules, fluid velocities, slip lengths and water fluxes. We show that thermostating the CNT membrane brings overall enhanced water flow than directly thermostating the water system. Moreover, increasing the temperature coupling time in the thermostat gives rise to an enhancement of water flux, while weakens the stability of system temperature. In addition to explaining the disparate simulation results on fluid transport in nanopores, this work provides guidelines for diagnosing the setting of NEMD simulations.