Molecular dynamics simulation of helium–argon gas mixture under various wall conditions

As computational capabilities increase, molecular dynamics (MD) simulations become important tools of simulating reality. These simulations are especially useful for compressible gas mixture problems. In this study, binary diffusion of helium and argon was examined using a hard-sphere MD simulation method. For the sake of computational speed, low spacing ratios were chosen. Binary mass diffusion of gases in two equally sized halves of a box was simulated for identical initial kinetic energies and number densities. It has been noted that a purely mass diffusion mechanism of different gases is not physically possible. The resultant gas mixtures of several diffusion simulations were used as initial conditions for combined heat transfer – Couette flow, and heating and cooling experiments. The results showed the interesting behaviour of the mixture, which was subjected to various wall conditions. Energy of heavier molecules is found to be more sensitive to the wall velocities and less sensitive to the wall temperatures than lighter molecules. Diffusion, heat transfer, viscosity and heat capacity coefficients are deduced as well.     

Computer Simulation Study of the Chemical Potential of Argon Adsorbed on Graphite

Abstract

A multilayer film of argon adsorbed on the basal plane of graphite at 103 K was simulated using isokinetic molecular dynamics. The local chemical potentials in the film were evaluated using three algorithms suggested in the literature: test particle insertion, real particle calculation and the ratio method, which relies on calculations of the local energy distribution functions for test and real particles. Although none of these was suitable for calculations involving the partially solidified first adsorbed layer, the test particle and the ratio method produced useful results for regions in the film corresponding to second and higher layers. The ratio method is shown to be the most realistic, giving constant local chemical potentials of reasonably high precision for all points other than in the first layer.     

Recommended gas transport properties of argon at low density using ab initio potential

The most important transport properties of argon have been calculated using classical kinetic theory expressions in conjunction with high-quality ab initio potential energy values computed by Patkowski and Szalewicz. Dilute gas transport properties have been calculated for the viscosity, thermal conductivity, self-diffusion coefficient and thermal diffusion factor from 83 to 10,000 K. Comparisons between experimental transport property data and values presently calculated indicate that the present theoretical predictions may be employed as recommended values for this set of transport properties over a wide temperature range.     

Methane bubbles in surface peat cores: in situ measurements

The quantification of greenhouse gas sources and sinks is important to understanding the impact of climate change. Methane (CH₄) is a potent greenhouse gas, which, on a global scale, is released largely as a product of anaerobic microbial decomposition and predominantly from wetlands. A zone of intense CH₄ production just below the water table is thought to contribute significantly to the overall flux from peat bogs. We describe the use of membrane inlet quadrupole mass spectrometry (QMS) to confirm the existence of bubbles, their gaseous concentrations and their localization at a fine spatial resolution within intact peat cores. We use the distribution of the noble gas argon (Ar) and the distinct QMS responses to dissolved and gaseous (bubble) phases to identify trapped bubbles with a resolution of 0.6 mm. Bubbles with CH₄ concentrations of up to 20 kPa were widely distributed in the upper 300 mm of the cores with ～11% of all profiles comprising bubbles. The dissolved concentrations responsible for the bubbles were on average 83±80 μm , indicating lower concentrations relative to other QMS studies. We suggest that if the distinction between dissolved and gaseous phases is not made in studies of CH₄ within peat profiles then the prominence of bubbles is likely to result in overestimates of dissolved CH₄ concentrations. Fluxes of CH₄ from peat as a result of drawdown or other perturbation are likely to be large, rapid and short lived because of bubble burst, and also larger than from peat without bubbles. We suggest that the dynamics of fluxes need to be modelled taking into account both gaseous and dissolved phases. Estimates of potential fluxes that assume CH₄ is dissolved are likely to overestimate fluxes if the gaseous phase has not been taken into account.     

Computation of elastic constants of solids using molecular simulation: comparison of constant volume and constant pressure ensemble methods

We compute the elastic stiffness tensor of fcc argon at 60 K and 1 bar using molecular simulation tools. Three different methods are investigated: explicit deformations of the simulation box, strain fluctuations at constant pressure and stress fluctuations at constant volume. Statistical ensemble sampling is done using molecular dynamics and Monte Carlo simulations. We observe a good agreement between the different methods and sampling algorithms excepted with molecular dynamics simulations in the (NpT) ensemble. There, we notice a strong dependence of the computed elastic constants with the barostat parameter, whereas molecular dynamics simulations in the (NVT) ensemble are not affected by the thermostat parameter.     

Molecular simulation of size-selective gas adsorption in idealised carbon nanotubes

Molecular simulations were used to examine the adsorption of diatomic molecules (nitrogen and oxygen) and similarly sized gases (argon and methane) in pores with van der Waals diameters similar in size to the gas diameters. Idealised carbon nanotubes were used to model generic pores, to better understand the effect of pore diameter on guest adsorption in the absence of defects, specific adsorption sites, or variations in pore diameter that often complicate studies of gas adsorption in other porous materials. Molecular dynamics simulations of open nanotubes show that argon and methane are able to enter tubes whose diameters are slightly smaller than the gas diameters. Diatomic gases are able to enter tubes that are significantly smaller than their kinetic diameters with the molecular axis aligned parallel to the nanotube. The results indicate that size-selective adsorption of these gases is theoretically possible, although differences in pore diameters of only a few tenths of an Angstrom are required. Grand canonical Monte Carlo simulations of a 3.38 Å nanotube indicate significant uptake by argon and oxygen, but not nitrogen or methane. The adsorption of nitrogen and methane gradually increases as the nanotube diameter approaches 4.07 Å, and all gases fully saturate a 4.54 Å nanotube. Of the nanotubes studied, the largest adsorption enthalpy for any gas corresponds to the 4.54 Å nanotube, with significantly lower enthalpies seen in the 5.07 Å nanotube. These results suggest an ideal pore diameter for each gas based on the gas–pore van der Waals interaction energies. Trends in the ideal diameter correlate with the minimum tube diameter accessible to each gas.     

Does Pattern Scan Laser (PASCAL) photocoagulation really induce less VEGF expression in murine retina than conventional laser treatment?

To investigate the differences in the mRNA and protein expression levels of vascular endothelial growth factor (VEGF) in murine retina between mice subjected to conventional laser (AG) and those subjected to Pattern Scan Laser (PASCAL) system. Male C57BL/6 mice were randomly assigned to one of three groups: Group 1 (G1) receiving retinal scatter laser photocoagulation using with AG photocoagulator (n = 16), Group 2 (G2) receiving retinal scatter laser photocoagulation using with PASCAL (n = 16) and Group 3 (G3) served as an untreated control group (n = 6). Molecular and morphological analyses of VEGF were performed on days 1, 2 and 5 by ELISA, real-time PCR and immuno-histochemical analysis. In samples which underwent AG (G1), when compared with the control group (G3), VEGF mRNA level increased 2.4 folds on day 2, whereas it decreased on day 5 (p □ 0.001). In samples which underwent PASCAL (G2), on the other hand, VEGF mRNA level increased 1.8 folds on day 1 and 2.2 folds on day 5 when compared with the control group (G3). In samples which underwent AG (G1), when compared with the control group (G3), VEGF protein level increased significantly on day 2, whereas it decreased on day 5 (p □ 0.001). In group G2, the VEGF levels in the sensory retina significantly increased as compared to control groups at both 2 and 5 days after laser photocoagulation using PASCAL laser (p = 0.012, both time points). The peak expressions of VEGF protein in samples which underwent PASCAL and conventional laser were found on day 5 and day 2 respectively. In retinas of PASCAL-treated mice, VEGF immunoreactivity gradually increased during the 5-day follow-up. However, in argon laser group, the strongest VEGF immunoreactivity was detected on day 2, then started to decrease on day 5. In summary, the expression of VEGF protein and mRNA gradually increase during a 5-day follow-up period in PASCAL-treated mouse eyes, whereas in AG group they reach their peak levels on the second day of follow-up and started decreasing after then. These results may also explain why the PASCAL system is less effective in regressing neovascularization in the clinic.     

Reconciliation of different simulation methods in the determination of the equilibrium branch for adsorption in pores

The recently proposed mid-density scheme [Liu Z, Herrera L, Nguyen VT, Do DD, Nicholson D. A Monte Carlo scheme based on mid-density in a hysteresis loop to determine equilibrium phase transition. Mol Simul. 2011; 37(11):932–939, Liu Z, Do DD, Nicholson D. A thermodynamic study of the mid-density scheme to determine the equilibrium phase transition in cylindrical pores. Mol Simul. 2012; 38(3):189–199] is tested against a method 2V-NVT (similar to the well-established gauge cell method) and the canonical ensemble (CE) method, using argon adsorption at 87 K in graphitic slit pores of infinite and finite length. In infinitely long pores, the equilibrium transition is vertical that is expected for an infinite system to have a first-order transition and this vertical transition was found to lie at the middle of the hysteresis loop and satisfies the well-known Maxwell rule of equal area. For pores of finite length, the equilibrium transitions are steep and are close to, but not exactly identical to, the desorption branch. This lends support to the conventional view that the desorption branch is nearest to equilibrium, although both adsorption and desorption branches are strictly speaking metastable; a view proposed originally by Everett [Everett DH. Capillary condensation and adsorption hysteresis. Berichte Der Bunsen-Gesellschaft [Phys Chem Chem Phys]. 1975; 79(9):732–734]. As a consequence, the Maxwell rule of equal area does not apply to finite systems. As the widely accepted CE and gauge cell methods do not falsify the mid-density scheme, this study lends strong support to the validity of this technique for the study of equilibria.