One-dimensional harmonic chain model of vibration-mode matching in solid-liquid interfacial thermal transport.

Understanding the atomistic mechanism of interfacial thermal transport at solid-liquid interfaces is a key challenge in thermal management at the nanoscale. A recent molecular-dynamics study demonstrated that interfacial thermal resistance (ITR) at the interface between a solid and a surfactant solution can be minimized by adjusting the molecular mass of the surfactant. In the present study, we explain the mechanism of this ITR minimization in view of vibration-mode matching using a one-dimensional (1D) harmonic chain model of a solid-liquid interface having an interfacial adsorption layer of surfactant molecules. The equation of motion for the 1D chain is described by a classical Langevin equation and is analytically solved by the nonequilibrium Green's function (NEGF) method. The resultant ITR is expressed in a form of vibrational matching, and its relationship to the overlap of the vibrational density of states is also discussed. The analysis leads to a conclusion that the damping coefficient η in the Langevin equation should be a finite and sufficiently large value to represent the rapid damping of vibration modes at solid-liquid interfaces. This conclusion provides a clue to seamlessly extend the conventional NEGF-phonon transmission picture of solid-solid interfacial thermal transport, which assumes η to be infinitesimal, to solid-liquid interfaces.

Computing the Work of Solid-Liquid Adhesion in Systems with Damped Coulomb Interactions via Molecular Dynamics: Approaches and Insights.

Recently, the dry-surface method [ Langmuir 2016, 31, 8335-8345] has been developed to compute the work of adhesion of solid-liquid and other interfaces using molecular dynamics via thermodynamic integration. Unfortunately, when long-range Coulombic interactions are present in the interface, a special treatment is required, such as solving additional Poisson equations, which is usually not implemented in generic molecular dynamics software, or as fixing some groups of atoms in place, which is undesirable most of the time. In this work, we replace the long-range Coulombic interactions with damped Coulomb interactions, and explore several thermal integration paths. We demonstrate that regardless of the integration path, the same work of adhesion values are obtained as long as the path is reversible, but the numerical efficiency differs vastly. Simple scaling of the interactions is most efficient, requiring as little as 8 sampling points, followed by changing the Coulomb damping parameter, while modifying the Coulomb interaction cutoff length performs worst. We also demonstrate that switching long-range Coulombic interactions to damped ones results in a higher work of adhesion by about 10 mJ/m2 because of slightly different liquid molecule orientation at the solid-liquid interface, and this value is mostly unchanged for surfaces with substantially different Coulombic interactions at the solid-liquid interface. Finally, even though it is possible to split the work of adhesion into van der Waals and Coulomb components, it is known that the specific per-component values are highly dependent on the integration path. We obtain an extreme case, which demonstrates that caution should be taken even when restricting to qualitative comparison.

Prediction of nanoscale thermal transport and adsorption of liquid containing surfactant at solid-liquid interface via deep learning.

HYPOTHESIS: Recent advances in deep learning (DL) have enabled high level of real-time prediction of thermophysical properties of materials. On the other hand, molecular dynamics (MD) have been long used as a numerical microscope to observe detailed interfacial conditions but require separate simulations that are computationally costly. Hence, it should be possible to combine MD and DL to obtain high resolution interfacial details at a low computational cost. EXPERIMENT: We proposed a novel DL encoding-decoding convolutional neural network (CNN) coupled with MD to realize the mapping from micro solid-liquid interface geometry to molecular temperature and density distribution of liquid containing surfactant. A multi-nanoscale optimization scheme was further proposed to reduce the uncertainty of DL prediction at the expense of local details to obtain more resilient predictors. FINDINGS: The statistical results showed that the proposed CNN had high prediction accuracy and could reproduce the heat transfer and adsorption phenomena under the influence of various factors including liquid composition, wettability, and solid surface roughness, while the computational efficiency was greatly improved. Our DL method with the support of multi-nanoscale learning strategies can achieve the fast and accurate visualization and prediction of various interfacial properties of liquid and assist for interfacial material design.

Downslope migration of free-living corals (Scleractinia: Fungiidae) in typhoon-exposed reef habitats at Okinawa, Japan.

Offshore Onna Village, Okinawa Island, Japan, there is a large and densely covered coral assemblage of free-living mushroom corals (Scleractinia: Fungiidae) on a reef slope at depths from 20 m to 32 m, covering an area of approximately 350 × 40 m2. From previous research, it is known that migration distances of mushroom corals may depend on coral shapes, coral sizes, substrate, and bottom inclination. However, until now there have been no published examples of regular Fungiidae movement and behavior from typhoon-exposed coastlines, such as those in the western Pacific Ocean. Our surveys across three years offshore Onna Village show that mushroom corals always move in down-slope direction from shallow to deeper reef zones. The results indicated that mushroom corals migrated faster in autumn than in other seasons, and that oval-elongate fungiids, and particularly those with a smooth underside, migrated more quickly than species with other shapes. Surprisingly, we observed a negative relationship between the presence of typhoons and migration rates. We also observed active migration by fungiid individuals to escape situations in which they were threatened to become overgrown by Acropora corals, or when they needed to escape from burial underneath coral debris.

Effect of the in-plane aspect ratio of a graphene filler on anisotropic heat conduction in paraffin/graphene composites.

Enhancement of polymer thermal conductivity using nanographene fillers and clarification of its molecular-scale mechanisms are of great concern in the development of advanced thermal management materials. In the present study, molecular dynamics simulation was employed to theoretically show that the in-plane aspect ratio of a graphene filler can have a significant impact on the effective thermal conductivity of paraffin/graphene composites. Our simulation included multiple graphene fillers aggregated in a paraffin matrix. The effective thermal conductivity of a paraffin/graphene composite, described as a second-rank tensor in the framework of equilibrium molecular dynamics simulation, was calculated for two types of graphene fillers with the same surface area but in-plane aspect ratios of 1 and 10. The filler with the higher aspect ratio was found to exhibit a much higher thermal conductivity enhancement than the one with the lower aspect ratio. This is because a high in-plane aspect ratio strongly restricts the orientation of fillers when they aggregate and, consequently, highly ordered agglomerates are formed. On decomposing the effective thermal conductivity tensor into various molecular-scale contributions, it was identified that the thermal conductivity enhancement is due to the increased amount of heat transfer inside the graphene filler, particularly along the longer in-plane axis. The present result indicates a possibility of designing the heat conduction characteristics of a nanocomposite by customizing the filler shapes so as to control the aggregation structure of the fillers.

Cross-Plane and In-Plane Heat Conductions in Layer-by-Layer Membrane: Molecular Dynamics Study.

A material with anisotropic heat conduction characteristics, which is determined by molecular scale structure, provides a way of controlling heat flow in nanoscale spaces. As such, here, we consider layer-by-layer (LbL) membranes, which are an electrostatic assembly of polyelectrolyte multilayers and are expected to have different heat conduction characteristics between cross-plane and in-plane directions. We constructed models of a poly(acrylic acid)/polyethylenimine (PAA/PEI) LbL membrane sandwiched by charged solid walls and investigated their anisotropic heat conduction using molecular dynamics simulations. In the cross-plane direction, the thermal boundary resistance between the solid wall and the LbL membrane and that between the constituent PAA and PEI layers decrease with increasing degree of ionization (solid surface charge density and the number of electric charges per PAA/PEI molecule). When the degree of ionization is low, the cross-plane thermal conductivity of a constituent layer is higher than that of the bulk state. As the degree of ionization increases, however, the cross-plane thermal conductivity of PAA, a linear polymer, decreases because of the increase in the number of in-plane oriented polymer chains. In the in-plane direction, we investigated the heat conduction of each layer and found the enhancement of effective in-plane thermal conductivity again due to the in-plane oriented chain alignment. The heat conduction in the LbL membrane is three-dimensionally enhanced compared to those in the bulk states of the constituent polymers because of the electrostatic interactions in the cross-plane direction and the molecular alignment in the in-plane direction.

Application of atomic stress to compute heat flux via molecular dynamics for systems with many-body interactions.

Although the computation of heat flux and thermal conductivity either via Fourier's law or the Green-Kubo relation has become a common task in molecular dynamics simulation, contributions of three-body and larger many-body interactions have always proved problematic to compute. In recent years, due to the success when applying to pressure tensor computation, atomic stress approximation has been widely used to calculate heat flux, where the lammps molecular dynamics package is the most prominent propagator. We demonstrated that the atomic stress approximation, while adequate for obtaining pressure, produces erroneous results in the case of heat flux when applied to systems with many-body interactions, such as angle, torsion, or improper potentials. This also produces incorrect thermal conductivity values. To remedy this deficiency, by starting from a strict formulation of heat flux with many-body interactions, we reworked the atomic stress definition which resulted in only a simple modification. We modified the lammps package accordingly to demonstrate that the new atomic stress approximation produces excellent results close to that of a rigid formulation.

All- and one-particle distribution functions at nonequilibrium steady state under thermal gradient.

We provide a concrete expression for the phase-space distribution function at nonequilibrium steady state under a constant thermal gradient, which is a typical system of the nonequilibrium molecular dynamics simulation of heat conduction. First, the phase-space distribution function of all particles in a local volume is formulated. Our formulation explicitly takes into account the entropy production due to the change in equilibrium thermodynamic variables in addition to the traditional entropy production described by the spatial gradients and fluxes of equilibrium thermodynamic variables. This treatment is necessary to explain the nonequilibrium response of a quantity that has no equilibrium correlation with mass and heat fluxes and is essential to correctly deduce one-particle distribution functions from the all-particle one. From the all-particle distribution function, we derive the Green-Kubo relations that express the one-particle distribution functions of density and velocity in terms of equilibrium correlation functions and verify these expressions using the molecular dynamics simulation of a Lennard-Jones liquid. These nonequilibrium one-particle distribution functions are sufficiently tractable for practical use, such as for the analytical evaluation of the nonequilibrium average of physical quantities.

Molecular dynamics investigation of surface roughness scale effect on interfacial thermal conductance at solid-liquid interfaces.

Non-equilibrium molecular dynamics simulations were conducted for solid-liquid-solid systems with nanometer scale grooved surfaces and an induced heat flux for a wide range of topology and solid-liquid interaction conditions to investigate the mechanism of solid-liquid heat transfer, which is the first work of such extensive detail done about the nanoscale roughness effect on heat transfer properties. Single-atom molecules were used for liquid, and the solid-liquid interaction was varied from superhydrophobic to superhydrophilic, while the groove scale was varied from single atom to several nanometers, while keeping the surface area twice that of a flat surface. Both Wenzel and Cassie wetting regimes with a clear transition point were observed due to the capillary effect inside larger grooves that were more than 5 liquid molecule diameters, while such transition was not observed at smaller scales. At the hydrophobic state, large scale grooves had lower interfacial thermal conductance (ITC) due to the Cassie regime, i.e., having unfilled grooves, while at the hydrophilic state, grooved surfaces had ITC about twice that of a flat surface, indicating an extended heat transfer surface effect regardless of the groove scale. At the superhydrophilic state, crystallization of liquid at the surface occurred, and the packing of liquid molecules had a substantial effect on ITC regardless of the groove scale. Finally, both potential energy of solid-liquid interaction and work of solid-liquid adhesion were calculated and were shown to be in similar relations to ITC for all groove scales, except for the smallest single-atom scale grooves, due to a different heat transfer mechanism.

Equivalence of the EMD- and NEMD-based decomposition of thermal conductivity into microscopic building blocks.

Thermal conductivity of a material can be comprehended as being composed of microscopic building blocks relevant to the energy transfer due to a specific microscopic process or structure. The building block is called the partial thermal conductivity (PTC). The concept of PTC is essential to evaluate the contributions of various molecular mechanisms to heat conduction and has been providing detailed knowledge of the contribution. The PTC can be evaluated by equilibrium molecular dynamics (EMD) and non-equilibrium molecular dynamics (NEMD) in different manners: the EMD evaluation utilizes the autocorrelation of spontaneous heat fluxes in an equilibrium state whereas the NEMD one is based on stationary heat fluxes in a non-equilibrium state. However, it has not been fully discussed whether the two methods give the same PTC or not. In the present study, we formulate a Green-Kubo relation, which is necessary for EMD to calculate the PTCs equivalent to those by NEMD. Unlike the existing theories, our formulation is based on the local equilibrium hypothesis to describe a clear connection between EMD and NEMD simulations. The equivalence of the two derivations of PTCs is confirmed by the numerical results for liquid methane and butane. The present establishment of the EMD-NEMD correspondence makes the MD analysis of PTCs a robust way to clarify the microscopic origins of thermal conductivity.

Shifting communities after-- typhoon damage on an upper mesophotic reef in Okinawa, Japan.

Very few studies have been conducted on the long-term effects of typhoon damage on mesophotic coral reefs. This study investigates the long-term community dynamics of damage from Typhoon 17 (Jelawat) in 2012 on the coral community of the upper mesophotic Ryugu Reef in Okinawa, Japan. A shift from foliose to bushy coral morphologies between December 2012 and August 2015 was documented, especially on the area of the reef that was previously recorded to be poor in scleractinian genera diversity and dominated by foliose corals. Comparatively, an area with higher diversity of scleractinian coral genera was observed to be less affected by typhoon damage with more stable community structure due to less change in dominant coral morphologies. Despite some changes in the composition of dominant genera, the generally high coverage of the mesophotic coral community is facilitating the recovery of Ryugu Reef after typhoon damage.

Structure and Mass Transport Characteristics at the Intrinsic Liquid-Vapor Interfaces of Alkanes.

In this paper, an instantaneous interface definition has been used to study the intrinsic structure and self-diffusion coefficient in the vicinity of the liquid-vapor interfaces of decane and tetracosane at three different temperatures using molecular dynamics simulations, and the results have been compared with those obtained on the basis of the conventional Gibbs dividing surface (time- and space-averaged interface). The alkane molecules were modeled using the united atom NERD force field. Partial layered structures of alkane molecules at the liquid-vapor interface are observed as a pinned structure of alkane liquids based on the intrinsic interface. This kind of characteristic has not been observed in the density profiles obtained based on the Gibbs dividing surface. By examining the orientation order parameter and radius of gyration of the alkane molecules, it was observed that the alkane molecules were preferentially oriented to be more parallel to the intrinsic interface than to the Gibbs dividing surface, and the shape of the alkane molecules is slightly changed in the vicinity of the liquid-vapor interfaces. The self-diffusion coefficient parallel to the intrinsic interface was examined using the Green-Kubo relation, where the projection of the velocity in the parallel direction to the local intrinsic interface is used in the velocity correlation function. It was found that the self-diffusion coefficient in the direction parallel to the intrinsic interface changes as the position approaches the interface in a more obvious manner as compared with the self-diffusion coefficient obtained with respect to the Gibbs dividing surface. These results suggest that the use of an instantaneous interface definition allowed us to capture sharp variations in transport properties which are originating due to steeper structure at the liquid-vapor interfaces.

Self-diffusion Coefficient and Structure of Binary n-Alkane Mixtures at the Liquid-Vapor Interfaces.

The self-diffusion coefficient and molecular-scale structure of several binary n-alkane liquid mixtures in the liquid-vapor interface regions have been examined using molecular dynamics simulations. It was observed that in hexane-tetracosane mixture hexane molecules are accumulated in the liquid-vapor interface region and the accumulation intensity decreases with increase in a molar fraction of hexane in the examined range. Molecular alignment and configuration in the interface region of the liquid mixture change with a molar fraction of hexane. The self-diffusion coefficient in the direction parallel to the interface of both tetracosane and hexane in their binary mixture increases in the interface region. It was found that the self-diffusion coefficient of both tetracosane and hexane in their binary mixture is considerably higher in the vapor side of the interface region as the molar fraction of hexane goes lower, which is mostly due to the increase in local free volume caused by the local structure of the liquid in the interface region.

Hydrodynamic consideration of the finite size effect on the self-diffusion coefficient in a periodic rectangular parallelepiped system.

In the present study, we use molecular dynamics (MD) simulations to provide an insight into the system size effect on the self-diffusion coefficient of liquids in the periodic rectangular parallelepiped system, from the hydrodynamic perspective. We have previously shown that in the rectangular box system, the diffusivity exhibits anomalous behaviors, i.e., the diffusion tensor appears to be anisotropic despite the bulk liquid simulation and the diffusion component in the direction along the short side of rectangular box with a high aspect ratio exceeding the diffusivity in the infinite system [Kikugawa et al., J.Chem. Phys. 142, 024503 (2015)]. So far, the size effect on the diffusivity has been intensively studied in the cubic system and has been interpreted quite well by the theoretical considerations employing the hydrodynamic interaction. Here, we have extended the hydrodynamic theory to be applied to periodic rectangular box systems and compared the theoretical predictions with MD simulation results. As a result, the diffusivity predicted by the hydrodynamic theory shows good agreement with the MD results. In addition, the system size effect was examined in a rod-shaped rectangular box in which the two shorter side lengths were equivalent and a film-type rectangular box in which the two longer side lengths were equivalent. It is of interest that we found that the aspect ratio, at which the diffusivity coincides with that in the infinite system, is a universal constant independent of the cross-sectional area for the rod system or the thickness for the film system. By extracting the universal structure in the hydrodynamic description, we also suggested a simplified approximate model to accurately predict the size effect on the diffusivity over a practical range of aspect ratios.

Local thermal transport of liquid alkanes in the vicinity of α-quartz solid surfaces and thermal resistance over the interfaces: A molecular dynamics study.

Thermal transport in liquid n-alkanes in the vicinity of α-quartz substrates and thermal boundary resistance between the liquid n-alkanes and the α-quartz substrates have been investigated using nonequilibrium molecular dynamics simulations. The study considers two liquid alkanes, methane and decane, and three crystal orientations of α-quartz substrate terminated with -H or -OH groups. The local thermal conductivity (LTC), defined in the same manner as with macroscopic thermal conductivity, is used to measure the efficiency of thermal energy transport of the liquids in the vicinity of the solid surface. The variations in the LTC of the liquid alkanes in the layered region next to the surface of the substrate were examined. The modeled LTC values of the alkanes were found to oscillate in the solid-liquid interface region. These fluctuations were typically proportional to the oscillations in the local density profile. The correlation between the thermal conductivity and density was linear in the bulk liquid region. The correlation between LTC and local density in the first adsorption layer is not a straightforward extension of that of the bulk liquid, which is mostly due to the specific molecular-scale ordering structure that occurs in the liquids formed by the proximity of the solid substrate. Thermal boundary resistance between the liquid alkanes and the quartz substrate was also evaluated. It was observed that thermal boundary resistance is relatively large when the in-plane molecular-scale structure in the first adsorption layer is sparse, and is lower when the liquid structure is dense in the adsorption layer.

Effects of molecular structure on microscopic heat transport in chain polymer liquids.

In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7Tc) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs.

Effect of the computational domain size and shape on the self-diffusion coefficient in a Lennard-Jones liquid.

In the present study, molecular dynamics (MD) simulations on the monatomic Lennard-Jones liquid in a periodic boundary system were performed in order to elucidate the effect of the computational domain size and shape on the self-diffusion coefficient measured by the system. So far, the system size dependence in cubic computational domains has been intensively investigated and these studies showed that the diffusion coefficient depends linearly on the inverse of the system size, which is theoretically predicted based on the hydrodynamic interaction. We examined the system size effect not only in the cubic cell systems but also in rectangular cell systems which were created by changing one side length of the cubic cell with the system density kept constant. As a result, the diffusion coefficient in the direction perpendicular to the long side of the rectangular cell significantly increases more or less linearly with the side length. On the other hand, the diffusion coefficient in the direction along the long side is almost constant or slightly decreases. Consequently, anisotropy of the diffusion coefficient emerges in a rectangular cell with periodic boundary conditions even in a bulk liquid simulation. This unexpected result is of critical importance because rectangular fluid systems confined in nanospace, which are present in realistic nanoscale technologies, have been widely studied in recent MD simulations. In order to elucidate the underlying mechanism for this serious system shape effect on the diffusion property, the correlation structures of particle velocities were examined.

Typhoon damage on a shallow mesophotic reef in Okinawa, Japan.

Little is known about effects of large storm systems on mesophotic reefs. This study reports on how Typhoon 17 (Jelawat) affected Ryugu Reef on Okinawa-jima, Japan in September 2012. Benthic communities were surveyed before and after the typhoon using line intercept transect method. Comparison of the benthic assemblages showed highly significant differences in coral coverage at depths of 25-32 m before and after Typhoon 17. A large deep stand of Pachyseris foliosa was apparently less resistant to the storm than the shallower high diversity area of this reef. Contradictory to common perception, this research shows that large foliose corals at deeper depths are just as susceptible to typhoon damage as shallower branching corals. However, descriptive functional group analyses resulted in only minor changes after the disturbance, suggesting the high likelihood of recovery and the high resilience capacity of this mesophotic reef.

Energy dissipation in non-isothermal molecular dynamics simulations of confined liquids under shear.

Energy is commonly dissipated in molecular dynamics simulations by using a thermostat. In non-isothermal shear simulations of confined liquids, the choice of the thermostat is very delicate. We show in this paper that under certain conditions, the use of classical thermostats can lead to an erroneous description of the dynamics in the confined system. This occurs when a critical shear rate is surpassed as the thermo-viscous effects become prominent. In this high-shear-high-dissipation regime, advanced dissipation methods including a novel one are introduced and compared. The MD results show that the physical modeling of both the accommodation of the surface temperature to liquid heating and the heat conduction through the confining solids is essential. The novel method offers several advantages on existing ones including computational efficiency and easiness of application for complex systems.

Heat conduction in chain polymer liquids: molecular dynamics study on the contributions of inter- and intramolecular energy transfer.

In this paper, the molecular mechanisms which determine the thermal conductivity of long chain polymer liquids are discussed, based on the results observed in molecular dynamics simulations. Linear n-alkanes, which are typical polymer molecules, were chosen as the target of our studies. Non-equilibrium molecular dynamics simulations of bulk liquid n-alkanes under a constant temperature gradient were performed. Saturated liquids of n-alkanes with six different chain lengths were examined at the same reduced temperature (0.7T(c)), and the contributions of inter- and intramolecular energy transfer to heat conduction flux, which were identified as components of heat flux by the authors' previous study [J. Chem. Phys. 128, 044504 (2008)], were observed. The present study compared n-alkane liquids with various molecular lengths at the same reduced temperature and corresponding saturated densities, and found that the contribution of intramolecular energy transfer to the total heat flux, relative to that of intermolecular energy transfer, increased with the molecular length. The study revealed that in long chain polymer liquids, thermal energy is mainly transferred in the space along the stiff intramolecular bonds. This finding implies a connection between anisotropic thermal conductivity and the orientation of molecules in various organized structures with long polymer molecules aligned in a certain direction, which includes confined polymer liquids and self-organized structures such as membranes of amphiphilic molecules in water.