Nonequilibrium versus equilibrium molecular dynamics for calculating the thermal conductivity of nanofluids

Journal of Thermal Analysis and Calorimetry - Both equilibrium and nonequilibrium molecular dynamics (EMD and NEMD, respectively) methods have been used to predict the thermal conductivity of...     

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%.     

Phonon thermal conductivity in nanolaminated composite metals via molecular dynamics

We use nonequilibrium molecular dynamics to characterize the phonon contribution to thermal conduction of Al nanostructures and the role of interfaces in metallic nanocomposites. We characterize the lattice thermal conductivity of pure Al samples as a function of size and temperature from which we obtain, using kinetic theory, the temperature dependence of the phonon mean free path. We also calculated the thermal conductivity of AlAl* and AlNi nanolaminate composites (where Al* differs from Al only in its mass) for various periodic sizes and compositions as well as the associated interfacial thermal resistivities (ITRs). We find that simple, additive models provide good estimates of the thermal conductivities of the nanocomposites in terms of those of the individual components and interfaces if size effects on the behavior of the individual components are considered. The additive models provide important insight to the decrease in thermal conductivity of the nanolaminates as their periodicity (thickness of a bilayer) is reduced to a size comparable with the phonon mean free path and break down when this characteristic size is reduced further. At this point the system can be regarded as homogeneous and the conductivity increases with decreasing periodicity of the laminates. We also observe that the ITR depends on the direction of the heat flux; this is the first molecular level characterization of such thermal diode behavior in a realistic three dimensional material.     

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.     

Thermal conductivity of solid argon from molecular dynamics simulations

The thermal conductivity of solid argon in the classical limit has been calculated by equilibrium molecular dynamic simulations using the Green-Kubo formalism and a Lennard-Jones interatomic potential. Contrary to previous theoretical reports, we find that the computed thermal conductivities are in good agreement with experimental data. The computed values are also in agreement with the high-temperature limit of the three-phonon scattering contribution to the thermal conductivity. We find that finite-size effects are negligible and that phonon lifetimes have two characteristic time scales, so that agreement with kinetic theory is obtained only after appropriate averaging of the calculated phonon lifetimes.     

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.     

Determining equilibrium constants for dimerization reactions from molecular dynamics simulations

With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.     

On the mechanisms of ionic conductivity in BaLiF3: a molecular dynamics study

The mechanisms of ionic conductivity in BaLiF(3) are investigated using molecular simulations. Direct molecular dynamics simulations of (quasi) single crystalline super cell models hint at the preferred mobility mechanism which is based on fluoride interstitial (and to a smaller extent F(-) vacancy) migration. Analogous to previous modeling studies, the energy related to Frenkel defect formation in the ideal BaLiF(3) crystal was found as 4-5 eV which is in serious controversy to the experimentally observed activation barrier to ionic conductivity of only 1 eV. However, this controversy could be resolved by incorporating Ba(2+)? Li(+) exchange defects into the elsewise single crystalline model systems. Indeed, in the neighborhood of such cation exchange defects the F(-) Frenkel defect formation energy was identified to reduce to 1.3 eV whilst the cation exchange defect itself is related to a formation energy of 1.0 eV. Thus, our simulations hint at the importance of multiple defect scenarios for the ionic conductivity in BaLiF(3).     

First-principle molecular dynamics calculation of selenium clusters

The equiliblium structures of small selenium clusters are obtained via first-principle molecular dynamics calculations based on the linearized-augmented-plane-wave (LAPW) method. Resulting equiliblium structures show a good agreement with experimental data and other firstprinciple calculations.     

A cage effect in collision-induced light absorption from a molecular dynamics calculation

A computer experiment on a two-dimensional Lorentz gas is described for which the autocorrelation function of the induced dipole moment exhibits an extremely long positive tail. It is argued that this tail can be ascribed to the trapping of particles in irregular cages.     

The approximate calculation of the process of equilibrium dynamics of desorption

Conclusions The relationship between processes of equilibrium dynamics and kinetics of desorption and adsorption was discussed.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 9, pp. 1882–1886, September, 1971.     

On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm

Widely used programs for molecular dynamics simulation of (bio)molecular systems are the Verlet and leapfrog algorithms. In these algorithms, the particle velocities are less accurately propagated than the positions. Important quantities for the simulation such as the temperature and the pressure involve the squared velocities at full time steps. Here, we derive an expression for the squared particle velocity at full time step in the leapfrog scheme, which is more accurate than the standardly used one. In particular, this allows us to show that the full time step kinetic energy of a particle is more accurately computed as the average of the kinetic energies at previous and following half steps than as the square of the average velocity as implemented in various molecular dynamics codes. Use of the square of the average velocity introduces a systematic bias in the calculation of the instantaneous temperature and pressure of a molecular dynamics system. We show the consequences when the system is coupled to a thermostat and a barostat.     

Molecular dynamics simulations of the thermal conductivity of methane hydrate

Nonequilibrium molecular dynamics simulations with the nonpolarizable SPC/E (Berendsen et al., J. Phys. Chem. 1987, 91, 6269) and the polarizable COS/G2 (Yu and van Gunsteren, J. Chem. Phys. 2004, 121, 9549) force fields have been employed to calculate the thermal conductivity and other associated properties of methane hydrate over a temperature range from 30 to 260 K. The calculated results are compared to experimental data over this same range. The values of the thermal conductivity calculated with the COS/G2 model are closer to the experimental values than are those calculated with the nonpolarizable SPC/E model. The calculations match the temperature trend in the experimental data at temperatures below 50 K; however, they exhibit a slight decrease in thermal conductivity at higher temperatures in comparison to an opposite trend in the experimental data. The calculated thermal conductivity values are found to be relatively insensitive to the occupancy of the cages except at low (T相似文献   

Nonequilibrium versus equilibrium molecular dynamics studies of solvation dynamics after photoexcitation of OCIO

The results of our earlier work [C. Brooksby, O. V. Prezhdo, and P. J. Reid, J. Chem. Phys. 119, 9111 (2003)] rationalizing the surprisingly weak solvent dependence of the dynamics following photoexcitation of chlorine dioxide in water, chloroform, and cyclohexane are thoroughly tested. Comparisons are made between equilibrium and nonequilibrium solvent response, equilibrium response in the ground and excited electronic states, as well as the cumulant and direct evaluation of the optical response function. In general, the linear response and cumulant approximations are found to hold, although minor deviations are found with all solvents. The ground state, linear response, and cumulant data show best agreement with experiment, most likely due to the better tested ground-state force field and the robust behavior of the linear response and cumulant approximations. The main conclusion of our earlier work explaining the weak solvent dependence by the domination of the van der Waals interaction component remains intact within the more advanced treatments. However, the molecular origin of this surprising experimental observation is different in water and chloroform compared to cyclohexane.     

Direct effect of nanoparticles on the thermal conductivity of CuO-water nanofluid in a phase transition phenomenon using molecular dynamics simulation

Journal of Thermal Analysis and Calorimetry - The thermal behavior of CuO-water nanofluid is examined on an aluminum surface. The dimensions of simulation boxes are...     

Solvation dynamics of Hoechst 33258 in water: an equilibrium and nonequilibrium molecular dynamics study

Integrated within an appropriate theoretical framework, molecular dynamics (MD) simulations are a powerful tool to complement experimental studies of solvation dynamics. Together, experiment, theory, and simulation have provided substantial insight into the dynamic behavior of polar solvents. MD investigations of solvation dynamics are especially valuable when applied to the heterogeneous environments found in biological systems, where the calculated response of the environment to the electrostatic perturbation of the probe molecule can easily be decomposed by component (e.g., aqueous solvent, biomolecule, ions), greatly aiding the molecular-level interpretation of experiments. A comprehensive equilibrium and nonequilibrium MD study of the solvation dynamics of the fluorescent dye Hoechst 33258 (H33258) in aqueous solution is presented. Many fluorescent probes employed in experimental studies of solvation dynamics in biological systems, such as the DNA minor groove binder H33258, have inherently more conformational flexibility than prototypical fused-ring chromophores. The role of solute flexibility was investigated by developing a fully flexible force-field for the H33258 molecule and by simulating its solvation response. While the timescales for the total solvation response calculated using both rigid (0.16 and 1.3 ps) and flexible (0.17 and 1.4 ps) models of the probe closely matched the experimentally measured solvation response (0.2 and 1.2 ps), there were subtle differences in the response profiles, including the presence of significant oscillations for the flexible probe. A decomposition of the total response of the flexible probe revealed that the aqueous solvent was responsible for the overall decay, while the oscillations result from fluctuations in the electrostatic terms in the solute intramolecular potential energy. A comparison of equilibrium and nonequilibrium approaches for the calculation of the solvation response confirmed that the solvation dynamics of H33258 in water is well-described by linear response theory for both rigid and flexible models of the probe.