Classical Nonequilibrium Molecular Dynamics Research Articles

Empirical interatomic potential development and classical molecular dynamics simulation of monolayer group-III monochalcogenides: insights into thermal transport properties

Abstract This research addresses the lack of comprehensive studies utilizing classical molecular dynamics simulations for monolayer group-III monochalcogenide materials. These materials, including GaS, GaSe, and InSe, have shown promise for diverse applications but lack well-defined empirical interatomic potentials in the literature. This study is concentrated on the development of empirical interatomic potential parameters for these materials using the particle swarm optimization method, filling a gap in the literature regarding classical molecular dynamics simulations. The parameters are optimized based on fundamental physical characteristics such as the lattice constants, bond lengths, phonon dispersions, and the equation of state, obtained from first-principles calculations. The developed potential parameters are then employed to predict lattice thermal conductivity through non-equilibrium classical molecular dynamics simulations, providing insights into the thermal transport properties of these materials.

Effect of the degree of polymerization and water content on the thermal transport phenomena in PEGDA hydrogel: a molecular-dynamics-based study.

A hydrogel is a 3D cross-linked polymer network that can absorb copious amounts of water or biological fluid. Due to their biocompatibility and non-toxicity, hydrogels have a wide range of applications in biomedical engineering. To develop hydrogels with superior thermal dissipation properties, atomistic-level studies are required to quantify the effect of the water content and the degree of polymerization. Classical mechanics-based non-equilibrium molecular dynamics (NEMD) simulations were performed in conjunction with a mathematical formulation developed by Müller-Plathe to explore the thermal conductivity of the poly(ethylene glycol)diacrylate (PEGDA) hydrogel. This work reveals that the thermal conductivity of the PEGDA hydrogel is enhanced with the increase in water content and approaches the value of the thermal conductivity of water at 85% water content in the hydrogel. The PEGDA-9 hydrogel, with a lower level of degree of polymerization, has a superior thermal conductivity than the PEGDA-13 and PEGDA-23 hydrogels. The lower level of degree of polymerization is associated with the higher mesh density of polymer chain network junctions that help to achieve the superior thermal conductivity at higher water contents. Increasing the water content improves the structural stability and compactness of the polymer chains, which can be further associated with the enhanced phonon transfer in PEGDA hydrogels. The work will help in the development of PEGDA-based hydrogels with superior thermal dissipation properties for tissue engineering.

Tracking structural solvent reorganization and recombination dynamics following e- photoabstraction from aqueous I- with femtosecond x-ray spectroscopy and scattering.

We present a sub-picosecond resolved investigation of the structural solvent reorganization and geminate recombination dynamics following 400nm two-photon excitation and photodetachment of a valence p electron from the aqueous atomic solute, I-(aq). The measurements utilized time-resolved X-ray Absorption Near Edge Structure (TR-XANES) spectroscopy and X-ray Solution Scattering (TR-XSS) at the Linac Coherent Light Source x-ray free electron laser in a laser pump/x-ray probe experiment. The XANES measurements around the L1-edge of the generated nascent iodine atoms (I0) yield an average electron ejection distance from the iodine parent of 7.4 ± 1.5 Å with an excitation yield of about 1/3 of the 0.1M NaI aqueous solution. The kinetic traces of the XANES measurement are in agreement with a purely diffusion-driven geminate iodine-electron recombination model without the need for a long-lived (I0:e-) contact pair. Nonequilibrium classical molecular dynamics simulations indicate a delayed response of the caging H2O solvent shell and this is supported by the structural analysis of the XSS data: We identify a two-step process exhibiting a 0.1ps delayed solvent shell reorganization time within the tight H-bond network and a 0.3ps time constant for the mean iodine-oxygen distance changes. The results indicate that most of the reorganization can be explained classically by a transition from a hydrophilic cavity with a well-ordered first solvation shell (hydrogens pointing toward I-) to an expanded cavity around I0 with a more random orientation of the H2O molecules in a broadened first solvation shell.

Interfacial thermal transport between graphene and diamane

Similar to graphene, diamane is a single layer of diamond that has been investigated in recent years due to its peculiar mechanical, thermal, and electronic properties. Motivated by earlier work that showed an exceptionally high intra-plane thermal conductivity in diamane, in this work, we investigate the interfacial thermal resistance (R) between graphene and diamane using non-equilibrium classical molecular dynamics simulations. The calculated R for a pristine graphene and AB-stacked diamane at room temperature is 1.89 × 10-7Km2/W, which is comparable to other common graphene/semi-conductor bilayers. These results are understood in terms of the overlap of the phonon density of states between the graphene and diamane layers. We further explore the impact of stacking pattern, system temperature, coupling strength, in-plane tensile strain, and hydrogenation ratio on R. Intriguingly, we find that unlike single layer diamane, where the intra-plane thermal conductively is reduced by ∼50% under 5% strain, the inter-plane thermal conductance of the graphene-diamane bilayer is enhanced by ∼50% under 8% strain. The difference is caused by the opposite behavior between the inter- and intra-layer conductances as phonon relaxation time is decreased. The high intra-plane thermal conductivity and low inter-plane thermal resistance shows the high potential of using graphene-diamane heterostructures in electronic applications.

Chemisorbed vs physisorbed surface charge and its impact on electrokinetic transport: Carbon vs boron nitride surface.

The possibility of controlling electrokinetic transport through carbon and hexagonal boron nitride (hBN) nanotubes has recently opened new avenues for nanofluidic approaches to face outstanding challenges such as energy production and conversion or water desalination. The pH-dependence of experimental transport coefficients points to the sorption of hydroxide ions as the microscopic origin of the surface charge and recent ab initio calculations suggest that these ions behave differently on carbon and hBN, with only physisorption on the former and both physisorption and chemisorption on the latter. Using classical non-equilibrium molecular dynamics simulations of interfaces between an aqueous electrolyte and three models of hBN and graphite surfaces, we demonstrate the major influence of the sorption mode of hydroxide ions on the interfacial transport properties. Physisorbed surface charge leads to a considerable enhancement of the surface conductivity as compared to its chemisorbed counterpart, while values of the ζ-potential are less affected. The analysis of the MD results for the surface conductivity and ζ-potential in the framework of Poisson-Boltzmann-Stokes theory, as is usually done to analyze experimental data, further confirms the importance of taking into account both the mobility of surface hydroxide ions and the decrease in the slip length with increasing titratable surface charge density.

Interfacial thermal conductance between gold and SiO2: A molecular dynamics study

ABSTRACT Silica coating on a gold nanoparticle can improve its thermal application in cancer thermotherapy. In this paper, the interfacial thermal conductance between gold and silica is calculated utilizing classical non-equilibrium molecular dynamics. It is revealed that the results of molecular dynamics are different from what has been predicted by the conventional diffuse mismatch model. Furthermore, the interfacial thermal conductance between amorphous SiO2 and gold is approximately twice that of crystalline silica, which is explained by calculating the vibrational density of state mismatches. The interfacial thermal conductance variations in terms of van der Waals interaction strength between gold and silica are also investigated. It is revealed that the conductance increases by about 30% by increasing the simulation temperature from 300 to 700 K. The results of this paper can be useful in nanofluid systems, in addition to the application of silica-coated gold nanoparticles in cancer thermal therapy.

Quasi-Casimir coupling can induce thermal resonance of adsorbed liquid layers in a nanogap.

In a vacuum nanogap, phonon heat transfer can be induced by quasi-Casimir coupling in the absence of electromagnetic fields. However, it is unknown whether phonons can be transmitted across a nanogap via solid-like liquid layers adsorbed on solid surfaces. Here, we elucidate that phonon transmission across a nanogap can be induced by quasi-Casimir coupling via adsorbed liquid layers using classical nonequilibrium molecular dynamics simulation. We modulated the gap distance to verify the existence of quasi-Casimir coupling between interfacial solid-liquid or liquid-liquid layers. Thermal resonance can be induced between two liquid layers by quasi-Casimir coupling, agitating the co-occurrence of thermal resonance between interfacial solid layers, while a liquid monolayer disturbs the resonance. The thermal resonance between liquid layers results in a larger heat flux and thermal gap conductance compared with those in the vacuum gap case, while the liquid layer limits the acoustic phonon transmission in the interfacial solid layers. The fundamental understanding of quasi-Casimir heat transfer at the solid-liquid interface could pave the way for future nanoscale energy transport and thermal management.

Implications of the Interface Modeling Approach on the Heat Transfer across Graphite–Water Interfaces

In this investigation, the thermal transport across graphite–water interfaces was studied by means of nonequilibrium classical molecular dynamics (NEMD) simulations. The main focus of this work was...

Simulating Surfactant–Iron Oxide Interfaces: From Density Functional Theory to Molecular Dynamics

Understanding the behavior of surfactant molecules on iron oxide surfaces is important for many industrial applications. Molecular dynamics (MD) simulations of such systems have been limited by the absence of a force field (FF), which accurately describes the molecule-surface interactions. In this study, interaction energies from density functional theory (DFT) + U calculations with a van der Waals functional are used to parameterize a classical FF for MD simulations of amide surfactants on iron oxide surfaces. The original FF, which was derived using mixing rules and surface Lennard-Jones (LJ) parameters developed for nonpolar molecules, was shown to significantly underestimate the adsorption energy and overestimate the equilibrium adsorption distance compared to DFT. Conversely, the optimized FF showed excellent agreement with the interaction energies obtained from DFT calculations for a wide range of surface coverages and molecular conformations near to and adsorbed on α-Fe2O3(0001). This was facilitated through the use of a Morse potential for strong chemisorption interactions, modified LJ parameters for weaker physisorption interactions, and adjusted partial charges for the electrostatic interactions. The original FF and optimized FF were compared in classical nonequilibrium molecular dynamics simulations of amide molecules confined between iron oxide surfaces. When the optimized FF was employed, the amide molecules were pulled closer to the surface and the orientation of the headgroups was more similar to that observed in the DFT calculations. The optimized FF proposed here facilitates classical MD simulations of anhydrous amide-iron oxide interfaces in which the interactions are representative of accurate DFT calculations.

Thermal Transport across SiC-Water Interfaces.

Thermal transport across interfaces made of 3C-type silicon carbide (SiC) and water was investigated by means of nonequilibrium classical molecular dynamics. The effects of different crystallographic planes and atomic surface terminations were studied, as it pertains to interfacial heat transfer. Hydrophilic and hydrophobic conditions were analyzed by modifying the interfacial bonding strength between the solid and liquid phases. The formation of structures in the liquid molecules close to the solid substrate was observed and found that such structures are sensitive to the uppermost atomic layer termination, the wettability condition, and the temperature of the system. It was found that the interfacial heat transfer and the wetting properties are not universally related and to obtain a more comprehensive description, it is required to include the structuring observed in the liquid phase at the interface. A reconciliation of the thermal boundary conductance calculations was found after the density depletion length was utilized as the descripting parameter.

Computational investigation of non-covalent interactions in 1-butyl 3-methylimidazolium/bis(trifluoromethylsulfonyl)imide [bmim][Tf2N] in EMD and NEMD.

Non-covalent interactions (NCIs) play a crucial role in the behavior and properties of ionic liquids (ILs). These interactions are particularly important for non-equilibrium properties such as the change in viscosity due to shearing forces (shear viscosity). Therefore, a detailed understanding of these interactions can improve our understanding of these important classes of liquids. Here, we have employed quantum mechanical energy decomposition analysis (EDA) and NCI analysis to investigate a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. EDA based on symmetry-adapted perturbation theory (SAPT) for the complete monomers, as well as fragment SAPT (FSAPT), for the functional fragments has been carried out. In general, the electrostatic component comprises ≈80% of the intermolecular interaction, and significant contributions from other components (induction and dispersion) are also observed, especially for interactions involving bifurcated hydrogen bonds. The FSAPT analysis suggests that caution is warranted when employing simplified assumptions for non-bonded interactions, e.g., focusing only on hydrogen bonds between functional fragments, since this view may not provide a complete picture of the complicated interactions between the ions. In non-equilibrium molecular dynamics, the total interaction energies of some fragments have a significant qualitative change as the shear rate increases. Our results indicate that the inter-fragment interactions play a fundamental role in the viscous behavior of ILs, suggesting that the exclusive use of geometric criteria to analyze inter-molecular interactions in these systems is not sufficient to investigate shear-thinning effects.

Molecular dynamics study of thermal resistance of solid-liquid interface in contact with single layer of nanoparticles

In a nanoscale system, thermal resistance at a solid-liquid interface can be considerable. Nanoparticle deposition on the solid-liquid interface is able to influence the solid-liquid interfacial thermal resistance (ITR). The influence of the nanoparticle layer on the thermal resistance can be critical, for an example, in a heat transfer of nanoparticle suspension fluids. In the present study, by means of non-equilibrium classical molecular dynamics (MD) method, we numerically investigated changes in the solid-liquid ITR, liquid density near the interface, heat flux components through single layer of carbon nanoparticles. Under the present conditions, the carbon nanoparticle layers on the solid-liquid interface influenced the liquid density and the heat transport near the solid-liquid interface, and the ITR. The ITR decreased, as the liquid density in the nanoparticle layer increased. The change in the liquid density near the solid-liquid interface was one of significant factors that affected the ITR. When the nanoparticle layer significantly decreased the ITR, the energy transport from the wall to the nanoparticles was enhanced, and the energy transfer inside the nanoparticles increased. Therefore, the nanoparticles were able to extract and store the thermal energy from the solid wall, which decreased the ITR.

Spectral Analysis of the Heat Flow Across Crystalline and Amorphous Si–Water Interfaces

Nonequilibrium classical molecular dynamics simulations were employed to investigate thermal transport across crystalline and amorphous silicon (a-Si) surfaces in contact with water for different interfacial bonding strengths. A spectral analysis of heat transfer across the different interfaces revealed the characteristics of the phonon modes contributing to thermal transport. Low-frequency modes contributed the most in hydrophobic interfaces, while a shift toward contribution from higher frequency modes was found for hydrophilic surfaces. The shift to higher frequency modes was not significant for a-Si and crystalline Si(111) interfaces. In-plane phonon modes significantly contributed to heat transfer in Si(100), less significantly in a-Si, and had a minimum contribution in Si(111) hydrophilic interfaces. While the wettability and solid–liquid bonding strength failed in explaining these observations, the interfacial liquid density depletion helped to understand the differences between Si(100) and a-Si in...

Lattice Thermal Conductivity of Pristine Si Nanowires: Classical Nonequilibrium Molecular Dynamics Study

ABSTRACTWe investigate lattice thermal conductivities of Si nanowires (SiNWs) based on classical nonequilibrium molecular dynamics (NEMD) simulations. The SiNWs are supposed to have a crystalline diamond structure and extend along the [001] axial direction with the {100} sidewall facets on which the surface Si atoms are all dimerized and fully passivated by hydrogen. Various sizes in the square cross section are considered, and the lengths are varied to find the diffusive limits of the lattice thermal conductivities. The upper limits of the diffusive lattice thermal conductivities of SiNWs are 11.2, 16.0, 22.8, and 28.0 W/mK for SiNWs with widths of 2.7, 4.9, 8.1, and 11.3 nm, respectively. The mode-averaged mean free paths of phonons are 50, 52, 63, and 80 nm for the SiNWs, respectively, which are 7–19 times longer than the SiNW widths.

Thermal Conductivity of Monolayer MoSe2 and MoS2

Two-dimensional (2D) MoSe2 and MoS2 monolayers, two prototype transition metal dichalcogenides (TMDCs) materials, have attracted growing interest as promising 2D semiconductors. In this work, thermal conductivity (κ) of the monolayer MoSe2 is computed using large-scale classical nonequilibrium molecular dynamics (NEMD) simulations for the first time. The predicted κ of monolayer MoSe2 with infinite length (or MoSe2 2D sheets) are 43.88 ± 1.33 and 41.63 ± 0.66 W/(m·K) in armchair and zigzag directions, respectively. These simulation results are further confirmed by independent simulations using the Green–Kubo method (GKM), which yield computed κ of 44.38 ± 2.08 and 44.63 ± 2.50 W/(m·K), respectively. For 2D MoS2 sheet, the computed κ based on the NEMD method are 101.43 ± 1.13 and 110.30 ± 2.07 W/(m·K), respectively, in armchair and zigzag directions, whereas those based on the GKM are 102.32 ± 6.05 and 108.74 ± 6.68 W/(m·K), respectively. The predicted κ values of MoS2 monolayer are 2 times larger than those of MoSe2 monolayer. Both types of 2D monolayers exhibit isotropic properties in thermal conduction. Effects of system dimensions, heat flux, and temperature on κ are investigated comprehensively. The predicted κ value increases monotonically with the system length but decreases with temperature.

Influence of interfacial interactions on deformation mechanism and interface viscosity in α-chitin–calcite interfaces

The interfaces between organic and inorganic phases in natural materials have a significant effect on their mechanical properties. This work presents a quantification of the interface stress as a function of interface chemical changes (water, organic molecules) in chitin–calcite (CHI–CAL) interfaces using classical non-equilibrium molecular dynamics (NEMD) simulations and steered molecular dynamics (SMD) simulations. NEMD is used to investigate interface stress as a function of applied strain based on the virial stress formulation. SMD is used to understand interface separation mechanism and to calculate interfacial shear stress based on a viscoplastic interfacial sliding model. Analyses indicate that interfacial shear stress combined with shear viscosity can result in variations to the mechanical properties of the examined interfacial material systems. It is further verified with Kelvin–Voigt and Maxwell viscoelastic analytical models representing viscous interfaces and outer matrix. Further analyses show that overall mechanical deformation depends on maximization of interface shear strength in such materials. This work establishes lower and upper bounds of interface strength in the interfaces examined.

Heat Transport in Double-Bond Linear Chains of Fullerenes**Supported by the National Natural Science Foundation of China under Grant Nos 11004082 and 11005048, and the Natural Science Foundation of Guangdong Province under Grant No 2014A030313367.

Heat transport in one kind of double-bond linear chains of fullerenes (C60's) is investigated by the classical nonequilibrium molecular dynamics method. It is found that the negative differential thermal resistance (NDTR) is more likely to occur at larger temperature difference and shorter length. In addition, with the increase of the length, the thermal conductivity of the chains increases, and NDTR region shrinks and vanishes in the end. The temperature profiles reveal that a large temperature jump exists at a high-temperature boundary of the chains when NDTR occurs. These results may be helpful for designing thermal devices where low-dimensional C60 polymers can be used.

Interfacial Thermal Resistance and Thermal Rectification in Graphene with Geometric Variations of Doped Nitrogen: A Molecular Dynamics Study

Using classical non-equilibrium molecular dynamics simulations (NEMD), the interfacial thermal resistance and thermal rectification of nitrogen-doped zigzag graphene (NDZG) are investigated. Two different structural models about nitrogen-doped graphene are constructed. It is found that the interfacial thermal resistance at the location of nitrogen-doping causes severe reduction in thermal conductivity of the NDZG. Thermal rectification of the triangular single-nitrogen-doped graphene (SNDG) decreases with increasing temperature. However, thermal rectification is not detected in the parallel various–nitrogen-doped graphene (VNDG). These results suggest that SNDG might be a promising structure for thermal device.

A boron nitride nanotube peapod thermal rectifier

The precise guidance of heat from one specific location to another is paramount in many industrial and commercial applications, including thermal management and thermoelectric generation. One of the cardinal requirements is a preferential conduction of thermal energy, also known as thermal rectification, in the materials. This study introduces a novel nanomaterial for rectifying heat—the boron nitride nanotube peapod thermal rectifier. Classical non-equilibrium molecular dynamics simulations are performed on this nanomaterial, and interestingly, the strength of the rectification phenomenon is dissimilar at different operating temperatures. This is due to the contingence of the thermal flux on the conductance at the localized region around the scatterer, which varies with temperature. The rectification performance of the peapod rectifier is inherently dependent on its asymmetry. Last but not least, the favourable rectifying direction in the nanomaterial is established.

First principles nonequilibrium plasma mixing

We have performed nonequilibrium classical and quantum-mechanical molecular dynamics simulations that follow the interpenetration of deuterium-tritium (DT) and carbon (C) components through an interface initially in hydrostatic and thermal equilibrium. We concentrate on the warm, dense matter regime with initial densities of 2.5-5.5 g/cm3 and temperatures from 10 to 100 eV. The classical treatment employs a Yukawa pair-potential with the parameters adjusted to the plasma conditions, and the quantum treatment rests on an orbital-free density functional theory at the Thomas-Fermi-Dirac level. For times greater than about a picosecond, the component concentrations evolve in accordance with Fick's law for a classically diffusing fluid with the motion, though, described by the mutual diffusion coefficient of the mixed system rather than the self-diffusion of the individual components. For shorter times, microscopic processes control the clearly non-Fickian dynamics and require a detailed representation of the electron probability density in space and time.