A molecular dynamics study on heat conduction characteristics in DPPC lipid bilayer

In this paper, nonequilibrium molecular dynamics simulations were performed on a single component 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine lipid bilayer in order to investigate the thermal conductivity and its anisotropy. To evaluate the thermal conductivity, we applied a constant heat flux to the lipid bilayer along and across the membrane with ambient water. The contribution of molecular interaction to the heat conduction was also evaluated. Along the bilayer plane, there is little transfer of thermal energy by the interaction between lipid molecules as compared with the interaction between water molecules. Across the bilayer plane, the local thermal conductivity depends on the constituents (i.e., water, head group, and tail group of lipid molecule) that occupy the domain. Although the intramolecular transfer of thermal energy in the tail groups of lipid molecules works efficiently to promote high local thermal conductivity in this region, the highest thermal resistance appears at the center of lipid bilayer where acyl chains of lipid molecules face each other due to a loss of covalent-bond and low number density. The overall thermal conductivities of the lipid bilayer in the directions parallel and perpendicular to the lipid membrane have been compared, and it was found that the thermal conductivity normal to the membrane is higher than that along the membrane, but it is still smaller than that of bulk water.     

Modifying thermal transport in electrically conducting polymers: effects of stretching and combining polymer chains

If their thermal conductivity can be lowered, polyacetylene (PA) and polyaniline (PANI) offer examples of electrically conducting polymers that can have potential use as thermoelectrics. Thermal transport in such polymers is primarily influenced by bonded interactions and chain orientations relative to the direction of heat transfer. We employ molecular dynamics simulations to investigate two mechanisms to control the phonon thermal transport in PANI and PA, namely, (1) mechanical strain and (2) polymer combinations. The molecular configurations of PA and PANI have a significant influence on their thermal transport characteristics. The axial thermal conductivity increases when a polymer is axially stretched but decreases under transverse tension. Since the strain dependence of the thermal conductivity is related to the phonon scattering among neighboring polymer chains, this behavior is examined through Herman's orientation factor that quantifies the degree of chain alignment in a given direction. The conductivity is enhanced as adjacent chains become more aligned along the direction of heat conduction but diminishes when they are orthogonally oriented to it. Physically combining these polymers reduces the thermal conductivity, which reaches a minimum value for a 2:3 PANI/PA chain ratio.     

The phase change property of lauric acid confined in carbon nanotubes as nano-encapsulated phase change materials

Lauric acid (LA) impregnates in carbon nanotubes (CNTs), resulting in nano-encapsulated phase change materials (PCMs). TEM and DSC results both indicate that the filling of LA into CNTs is realized by the vacuum infiltration method. A further study of nano-encapsulated PCMs at the molecular level is investigated by molecular dynamics simulations. From the axial view of CNTs, LA molecules always keep a circular distribution inside CNTs with a radius of about 4.8 Å. The analysis on radial distribution function, the end-to-end distance and the torsion angle simultaneously verifies that the order degree of LA molecules is improved due to the nano-confined effect of CNTs. The diffusion coefficient of LA is enhanced in CNTs. The energy flux and thermal conductivity of LA molecules in CNTs are higher than those of pure LA at the same temperature. These results fully indicate the heat and mass transfer of LA in CNTs could be enhanced. The current research could contribute to a deep understanding nanoscale thermal science and to potential application in heat dissipation of nanodevices.

     

Effect of chain length of self-assembled monolayers in dip-pen nanolithography using molecular dynamics simulations

The pattern transfer mechanism of an alkanethiol self-assembled monolayer (SAM) with different chain lengths during the dip-pen nanolithography (DPN) process and pattern characterizations are studied using molecular dynamics (MD) simulations. The mechanisms of molecular transference, alkanethiol meniscus characteristics, surface adsorbed energy, transfer number, and pattern formation are evaluated during the DPN process at room temperature. The simulation results clearly show that the molecular transfer ability in DPN is strongly dependent on the chain length. Shorter molecules have significantly better transport and diffusion abilities between the meniscus and substrate surface, and the transport period can be maintained longer. The magnitude of adsorbed energy increases with chain length, so many more molecules can be transferred to the surface when shorter molecules are used. After deposition, the magnitude of the adsorbed area and pattern height decrease with increasing chain length.     

A gentler approach to RNEMD: nonisotropic velocity scaling for computing thermal conductivity and shear viscosity

We present a new method for introducing stable nonequilibrium velocity and temperature gradients in molecular dynamics simulations of heterogeneous systems. This method extends earlier reverse nonequilibrium molecular dynamics (RNEMD) methods which use momentum exchange swapping moves. The standard swapping moves can create nonthermal velocity distributions and are difficult to use for interfacial calculations. By using nonisotropic velocity scaling (NIVS) on the molecules in specific regions of a system, it is possible to impose momentum or thermal flux between regions of a simulation while conserving the linear momentum and total energy of the system. To test the method, we have computed the thermal conductivity of model liquid and solid systems as well as the interfacial thermal conductivity of a metal-water interface. We find that the NIVS-RNEMD improves the problematic velocity distributions that develop in other RNEMD methods.     

Reverse nonequilibrium molecular dynamics simulation of thermal conductivity in nanoconfined polyamide-6,6

A new molecular dynamics simulation method, with coupling to external baths, is used to perform equilibrium simulations on polyamide-6,6 trimers nanoconfined between graphene surfaces, in equilibrium with the bulk polymer. The method is coupled with the reverse nonequilibrium molecular dynamics simulation technique to exchange heat in the direction normal to the surfaces. To be able to study the effect of confinement on the heat conductance in nanoconfined pores, in this work a number of simulations on systems with different pore sizes are done. It is concluded that the coefficient of heat conductivity depends on the degree of polymer layering between the surfaces and on the pore width. Our results further indicate a considerable temperature drop at the interface between the surfaces and polymer. The calculated Kapitza lengths depend on the intersurface distance and on the layering of the polymer nanoconfined between the surfaces.     

Spectra analysis for macromolecular systems: Chain‐length effects in polymer particles

A complete set of frequencies for the density of states spectrum g(ω) is obtained for 6000‐atom polymer particles involving all 18,000 degrees of freedom. We efficiently generate the particle using molecular dynamics and molecular mechanics, and systematically analyze the spectra and thermal properties as a function of chain lengths: from one to 100 monomers. The density of states spectrum g(ω) shows a higher number of low‐frequency modes for the polymer particle with a smaller chain length, which results in a higher heat capacity at low temperature. Gibbs free energy was also calculated for the formation of a particle from a crystal as a function of temperature to evaluate thermal stability of those systems. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 1812–1823, 2000     

Equilibrium and nonequilibrium molecular dynamics simulations of the thermal conductivity of molten alkali halides

The thermal conductivity of molten NaCl and KCl was calculated through the Evans-Gillan nonequilibrium molecular dynamics (NEMD) algorithm and Green-Kubo equilibrium molecular dynamics (EMD) simulations. The EMD simulations were performed for a "binary" ionic mixture and the NEMD simulations assumed a pure system for reasons discussed in this work. The cross thermoelectric coefficient obtained from Green-Kubo EMD simulations is discussed in terms of the homogeneous thermoelectric power or Seebeck coefficient of these materials. The thermal conductivity obtained from NEMD simulations is found to be in very good agreement with that obtained through Green-Kubo EMD simulations for a binary ionic mixture. This result points to a possible cancellation between the neglected "partial enthalpy" contribution to the heat flux associated with the interdiffusion of one species through the other and that part of the thermal conductivity related to the coupled fluxes of charge and heat in "binary" ionic mixtures.     

Thermal conductivity of molten alkali halides from equilibrium molecular dynamics simulations

The thermal conductivity of molten sodium chloride and potassium chloride has been computed through equilibrium molecular dynamics Green-Kubo simulations in the microcanonical ensemble (N,V,E). In order to access the temperature dependence of the thermal conductivity coefficient of these materials, the simulations were performed at five different state points. The form of the microscopic energy flux for ionic systems whose Coulombic interactions are calculated through the Ewald method is discussed in detail and an efficient formula is used by analogy with the methods used to evaluate the stress tensor in Coulombic systems. The results show that the Born-Mayer-Huggins-Tosi-Fumi potential predicts a weak negative temperature dependence for the thermal conductivity of NaCl and KCl. The simulation results are in agreement with part of the experimental data available in the literature with simulation values generally overpredicting the thermal conductivity by 10%-20%.     

Thermal relaxation mechanism and role of chemical functionalization in fullerene solutions

Using molecular-dynamics simulations we investigate thermal relaxation of C60 and C84 molecules suspended in octane liquid. Pristine fullerenes exhibit relatively slow relaxation due to weak thermal coupling with the liquid. A comparison of the interfacial transport characteristics obtained from relaxation simulations with those obtained from equilibrium simulations and fluctuation-dissipation theorem analysis demonstrates that the relaxation process involves two main steps: (i) energy flow from high- to low-frequency modes within the fullerene, and (ii) energy flow from low-frequency fullerene modes to the liquid. Functionalization of fullerenes with alkene chains leads to significant reduction of the thermal relaxation time. The relaxation time of functionalized fullerenes becomes independent from the functionalizing chain length beyond approximately 10 carbon segments; this can be understood in terms of thermal conductivity along the chain and heat transfer between the chain and the solvent.     

Concentration dependences of heat conductivity coefficients of inert gases in narrow pores

Calculation of the transfer of molecules in porous systems requires self-consistent expressions describing the kinetic transfer coefficients for various concentrations and temperatures. The concentration dependences of heat conductivity and self-diffusion coefficients for fluids with different densities, ranging from rarefied gases to liquids, were considered in terms of a unified model. For monoatomic gases (argon), the model takes into account two energy transfer channels, namely, the vacancy mechanism and energy transfer through collisions of molecules. The former channel is characteristic of rarefied gases, while the latter is noted for condensed phases. The energy parameters of the model were determined on the basis of data on the heat conductivity coefficient in the bulk phase. The heat conductivity coefficient follows a linear temperature dependence for low density; in the medium and large density regions, these dependences follow a more complex pattern that changes depending on temperature. The influence of the interaction of atoms with the pore walls on the concentration dependences of the heat conductivity coefficients was investigated for different total amounts of the adsorbate. These coefficients depend appreciably on the distance to the pore wall and on the direction of heat transfer.     

Transport Coefficients Of Ar—Kr Mixtures by Molecular Dynamics Computer Simulation

Abstract

Equilibrium molecular dynamics computer simulations have been used to determine the transport coefficients of model Ar—Kr mixtures, which are represented by Lennard-Jones pair potentials with Lorentz—Berthelot rules for the cross-species interactions. The component self-diffusion and mutual-diffusion coefficients are calculated from time correlation functions and mean square displacements. Time correlation functions are used to evaluate the shear and bulk viscosity, thermal conductivity and the thermal diffusion coefficient (Soret/Dufour coefficient). In the case of the thermal transport coefficients, the partial enthalpy of the two species is required at each state point to define the heat flux rigorously. We obtain this and the partial volume (and species resolved chemical potential) using particle-exchange (and particle insertion) techniques implemented in separate [NPT] simulations at the same state point.

The viscoelasticity of the fluids is characterised by the relaxation times for bulk and shear stress relaxation. The results are for dense liquids close to the triple point temperature and density. Agreement with experiment and previous simulation is particularly good for the density of the mixtures, the shear modulus, shear viscosity, shear stress relaxation time and thermal conductivity. As for the single component noble gas fluids (simulated and experiment) there is a significant qualitative difference in the temperature and, for mixtures, composition dependence of the bulk viscosity.     

Investigation of nanocomposite PNIPAm-g-graphene with pre-lower critical solution temperature rapid thermal response function for chip adaptive cooling: A molecular dynamics and computational fluid dynamics simulations

Temperature-sensitive hydrogels have been widely used for rapid adaptive cooling in electronic device thermal management with promising applications. However, existing temperature-sensitive hydrogels can only regulate the flow in the chip cooling system after the ambient temperature reaches their lower critical solution temperature (LCST). Before reaching LCST, effective rapid heat dissipation for electronic chips is not achievable. This study aims to develop a temperature-sensitive hydrogel that can provide assisted adaptive cooling for electronic chips before reaching its LCST. This requires the hydrogel to have a thermal conductivity far surpassing existing hydrogel materials. Using the temperature-sensitive hydrogel PNIPAm and graphene molecules as base materials, this research utilized molecular dynamics simulations to graft graphene molecules onto PNIPAm molecules in different ways, resulting in the temperature-sensitive hydrogel material PNIPAm-g-graphene. Non-equilibrium molecular dynamics (NEMD) was employed to calculate the thermal conductivity of this material under different temperature conditions. The results indicate that the thermal conductivity of PNIPAm-g-graphene can reach up to 1.95474 W/m K (graphene grafted at  CH₃ functional group, temperature at 280 K). Compared to the thermal conductivity of PNIPAm under the same conditions (0.45 W/m K), the increase in thermal conductivity is significant, demonstrating excellent thermal conductivity compared to PNIPAm. Subsequently, this study analyzed the underlying mechanisms of different thermal conductivities in materials obtained by grafting graphene molecules at different points using the method of overlap in Phonon Density of States Curves (PDOS) from the perspective of interfacial thermal conduction. Finally, through computational fluid dynamics (CFD) simulations, this study investigates the chip's adaptive cooling performance with PNIPAm-g-graphene material. The results show that, compared to traditional temperature-sensitive hydrogels, PNIPAm-g-graphene can achieve efficient adaptive cooling of chip hotspots before the cooling fluid temperature reaches its LCST value. This finding is significant for the field of chip cooling. The study proposes a new method for rapid, adaptive cooling of chip hotspots and explores its feasibility from the perspectives of molecular dynamics and CFD simulation. It holds importance in the thermal management of electronic devices and the rapid adaptive cooling of electronic chips.     

Efficient light harvesting in dye-endcapped conjugated polymers probed by single molecule spectroscopy

The development of sophisticated microscopic models of energy transfer in linear multichromophoric systems such as conjugated polymers is rarely matched by suitable experimental studies on the microscopic level. To assess the roles of structural, temporal, and energetic disorder in energy transfer, single molecule spectroscopic investigations of the elementary processes leading to energetic relaxation in conjugated polymers are desirable. We present a detailed study of energy transfer processes occurring in dye-endcapped conjugated polymer molecules on the single molecule level. These processes are mostly masked in ensemble investigations. Highly efficient intramolecular energy transfer along a single polyindenofluorene chain to a perylene endcap occurs in many instances and is resolved in real time. We further consider the spectral emission characteristics of the single molecule, the polarization anisotropy which reveals the chain conformation, the fluorescence intermittency, and the temperature dependence and conclude that the efficiency of energy transfer in the ensemble is controlled by the statistics of the individual molecules. The weak thermal activation of energy transfer indicates the involvement of vibrational modes in interchromophoric coupling. Whereas backbone-endcap coupling is strong, the rate-limiting step for intramolecular energy transfer is the migration along the backbone. The results are particularly relevant to understanding undesired exciton trapping on fluorenone defects in polyfluorenes.     

Transport properties of 2F <==> F2 in a temperature gradient as studied by molecular dynamics simulations

We calculate transport properties of a reacting mixture of F and F(2) from results of non-equilibrium molecular dynamics simulations. The reaction investigated is controlled by thermal diffusion and is close to local chemical equilibrium. The simulations show that a formulation of the transport problem in terms of classical non-equilibrium thermodynamics theory is sound. The chemical reaction has a large effect on the magnitude and temperature dependence of the thermal conductivity and the interdiffusion coefficient. The increase in the thermal conductivity in the presence of the chemical reaction, can be understood as a response to an imposed temperature gradient, which reduces the entropy production. The heat of transfer for the Soret stationary state was more than 100 kJ mol(-1), meaning that the Dufour and Soret effects are non-negligible in reacting mixtures. This sheds new light on the transport properties of reacting mixtures.     

A comparison of Coulombic interaction methods in non-equilibrium studies of heat transfer in water

We investigate the impact of the treatment of electrostatic interactions on the heat conduction of liquid water. With this purpose, we report a series of non-equilibrium molecular dynamics computer simulations of the Modified Central Force Model of water. We consider both the Ewald summation approach, which includes the full range of the electrostatic interactions, and the Wolf method, which uses a cutoff to truncate the long range contributions. It is shown that the relaxation of the temperature profiles towards the stationary state solution and the equation of state of the liquid are not affected by the treatment of the electrostatic interactions. However, the truncation of the interactions results in lower internal energy fluxes as well as lower thermal conductivities. We also find that the anomalous increase of the thermal conductivity of water with temperature is reproduced by the different methods considered in this work, showing that this physical behavior is independent of the treatment of the long range electrostatic interactions.     

Thermal conductivity of carbon nanotube-polyamide-6,6 nanocomposites: reverse non-equilibrium molecular dynamics simulations

The thermal conductivity of composites of carbon nanotubes and polyamide-6,6 has been investigated using reverse non-equilibrium molecular dynamics simulations in a full atomistic resolution. It is found, in line with experiments, that the composites have thermal conductivities, which are only moderately larger than that of pure polyamide. The composite conductivities are orders of magnitude less than what would be expected from nai?ve additivity arguments. This means that the intrinsic thermal conductivities of isolated nanotubes, which exceed the best-conducting metals, cannot be harnessed for heat transport, when the nanotubes are embedded in a polymer matrix. The main reason is the high interfacial thermal resistance between the nanotubes and the polymer, which was calculated in addition to the total composite thermal conductivity as well as that of the subsystem. It hinders heat to be transferred from the slow-conducting polymer into the fast-conducting nanotubes and back into the polymer. This interpretation is in line with the majority of recent simulation works. An alternative explanation, namely, the damping of the long-wavelength phonons in nanotubes by the polymer matrix is not supported by the present calculations. These modes provide most of the polymers heat conduction. An additional minor effect is caused by the anisotropic structure of the polymer phase induced by the nearby nanotube surfaces. The thermal conductivity of the polymer matrix increases slightly in the direction parallel to the nanotubes, whereas it decreases perpendicular to it.     

Exploration on regulating factors for proton transfer along hydrogen-bonded water chains.

Proton transfer along a single-file hydrogen-bonded water chain is elucidated with a special emphasis on the investigation of chain length, side water, and solvent effects, as well as the temperature and pressure dependences. The number of water molecules in the chain varies from one to nine. The proton can be transported to the acceptor fragment through the single-file hydrogen-bonded water wire which contains at most five water molecules. If the number of water molecule is more than five, the proton is trapped by the chain in the hydroxyl-centered H(7)O(3) (+) state. The farthest water molecule involved in the formation of H(7)O(3) (+) is the fifth one away from the donor fragment. These phenomena reappear in the molecular dynamics simulations. The energy of the system is reduced along with the proton conduction. The proton transfer mechanism can be altered by excess proton. The augmentation of the solvent dielectric constant weakens the stability of the system, but favors the proton transfer. NMR spin-spin coupling constants can be used as a criterion in judging whether the proton is transferred or not. The enhancement of temperature increases the thermal motion of the molecule, augments the internal energy of the system, and favors the proton transfer. The lengthening of the water wire increases the entropy of the system, concomitantly, the temperature dependence of the Gibbs free energy increases. The most favorable condition for the proton transfer along the H-bonded water wire is the four-water contained chain with side water attached near to the acceptor fragment in polar solvent under higher temperature.     

Thermal physics in carbon nanotube growth kinetics

The growth of single wall carbon nanotubes (SWNTs) mediated by metal nanoparticles is considered within (i) the surface diffusion growth kinetics model coupled with (ii) a thermal model taking into account heat release of carbon adsorption-desorption on nanotube surface and carbon incorporation into the nanotube wall and (iii) carbon nanotube-inert gas collisional heat exchange. Numerical simulations performed together with analytical estimates reveal various temperature regimes occurring during SWNT growth. During the initial stage, which is characterized by SWNT lengths that are shorter than the surface diffusion length of carbon atoms adsorbed on the SWNT wall, the SWNT temperature remains constant and is significantly higher than that of the ambient gas. After this stage the SWNT temperature decreases towards that of gas and becomes nonuniformly distributed over the length of the SWNT. The rate of SWNT cooling depends on the SWNT-gas collisional energy transfer that, from molecular dynamics simulations, is seen to be efficient only in the SWNT radial direction. The decreasing SWNT temperature may lead to solidification of the catalytic metal nanoparticle terminating SWNT growth or triggering nucleation of a new carbon layer and growth of multiwall carbon nanotubes.     

二酰胺吡啶修饰杯[4]芳烃与脂肪二羧酸主客体相互作用的理论研究

本文用分子力学和分子动力学方法对二酰胺吡啶修饰杯[4]芳烃与脂肪二羧酸的主客体相互作用进行了研究.