Dynamic Monte Carlo simulation in mixtures

Application of Nano-SiO2 Reinforced Urea-Formaldehyde Resin and Molecular Dynamics Simulation Study

Nano-SiO₂ is a typical modifier used for urea-formaldehyde (UF) resins to balance the reduced formaldehyde content and maintain bond strength. However, the microstructure of UF resin and the interaction between UF resin and nano-SiO₂ are microscopic phenomena; it is difficult to observe and study its intrinsic mechanism in traditional experimental tests. In this work, the enhancement mechanism was explored by molecular dynamics simulations combined with an experiment of the effect of nano-SiO₂ additions on UF resin. The results showed that the best performance enhancement of UF resin was achieved when the addition of nano-SiO₂ was 3 wt%. The effects caused by different additions of nano-SiO₂ were compared and analyzed by molecular dynamics simulations in terms of free volume fraction, the radius of gyration, and mechanical properties, and the results were in agreement with the experimental values. Meanwhile, the changes in hydrogen bonding and radial distribution functions in these systems were counted to explore the interaction between nano-SiO₂ and UF resin. The properties of the UF resin were enhanced mainly through the large number of different forms of hydrogen bonds with nano-SiO₂, with the strongest hydrogen bond occurring between H_(SiO2)… O = _(PHMU).

Extraction of kinetics from equilibrium distributions of states using the Metropolis Monte Carlo method

The Metropolis Monte Carlo (MMC) method is used to extract reaction kinetics from a given equilibrium distribution of states of a complex system. The approach is illustrated by the folding/unfolding reaction for two proteins: a model β-hairpin and α-helical protein α_{3}D. For the β-hairpin, the free energy surfaces (FESs) and free energy profiles (FEPs) are employed as the equilibrium distributions of states, playing a role of the potentials of mean force to determine the acceptance probabilities of new states in the MMC simulations. Based on the FESs and PESs for a set of temperatures that were simulated with the molecular dynamics (MD) method, the MMC simulations are performed to extract folding/unfolding rates. It has been found that the rate constants and first-passage time (FPT) distributions obtained in the MMC simulations change with temperature in good agreement with those from the MD simulations. For α_{3}D protein, whose equilibrium folding/unfolding was studied with the single-molecule FRET method [Chung et al., J. Phys. Chem. A 115, 3642 (2011)1089-563910.1021/jp1009669], the FRET-efficiency histograms at different denaturant concentrations were used as the equilibrium distributions of protein states. It has been found that the rate constants for folding and unfolding obtained in the MMC simulations change with denaturant concentration in reasonable agreement with the constants that were extracted from the photon trajectories on the basis of theoretical models. The simulated FPT distributions are single-exponential, which is consistent with the assumption of two-state kinetics that was made in the theoretical models. The promising feature of the present approach is that it is based solely on the equilibrium distributions of states, without introducing any additional parameters to perform simulations, which suggests its applicability to other complex systems.

Separation Selectivity of CH4/CO2 Gas Mixtures in the ZIF-8 Membrane Explored by Dynamic Monte Carlo Simulations

Here we report a series of nonequilibrium dynamic Monte Carlo simulations combined with dual control volume (DCV-DMC) to explore the separation selectivity of CH₄/CO₂ gas mixtures in the ZIF-8 membrane with a thickness of up to about 20 nm. Meanwhile, an improved DCV-DMC approach coupled with the corresponding potential map (PM-DCV-DMC) is further developed to speed up the computational efficiency of conventional DCV-DMC simulations. Our simulation results provide the molecular-level density and selectivity profiles along the permeation direction of both CH₄ and CO₂ molecules in the ZIF-8 membrane, indicating that the parts near membrane surfaces at both ends play a key role in determining the separation selectivity. All densities initially show a sharp increase in the individual maximum within the first outermost unit cell at the feed side and follow a long fluctuating decrease process. Accordingly, the corresponding selectivity profiles initially display a long fluctuating increase in the individual maximum and follow a sharp decrease near the membrane surface at the permeation side. Furthermore, the effects of feed composition, temperature, and pressure on the relevant separation selectivity are also discussed in detail, where the temperature has a greater influence on the separation selectivity than the feed composition and pressure. More importantly, the predicted separation selectivities from our PM-DCV-DMC simulations are well consistent with previous experimental results.

Structural origin of enhanced translational diffusion in two-dimensional hard-ellipse fluids

The static correlations and diffusive dynamics of hard ellipses are investigated in the isotropic and nematic phases by Monte Carlo simulation. In particular, an enhancement of the translational diffusion with respect to the rotational diffusion is observed at an onset concentration φ_{on} within the isotropic phase, which is explained in terms of the formation of unstable nematic-like regions with a mean lifetime that exceeds the characteristic time of diffusion at φ_{on}. The relevance to the onset of spatially heterogeneous dynamics in supercooled glass-forming liquids is discussed.

Current and selectivity in a model sodium channel under physiological conditions: Dynamic Monte Carlo simulations

A reduced model of a sodium channel is analyzed using Dynamic Monte Carlo simulations. These include the first simulations of ionic current under approximately physiological ionic conditions through a model sodium channel and an analysis of how mutations of the sodium channel's DEKA selectivity filter motif transform the channel from being Na(+) selective to being Ca(2+) selective. Even though the model of the pore, amino acids, and permeant ions is simplified, the model reproduces the fundamental properties of a sodium channel (e.g., 10 to 1 Na(+) over K(+) selectivity, Ca(2+) exclusion, and Ca(2+) selectivity after several point mutations). In this model pore, ions move through the pore one at a time by simple diffusion and Na(+) versus K(+) selectivity is due to both the larger K(+) not fitting well into the selectivity filter that contains amino acid terminal groups and K(+) moving more slowly (compared to Na(+)) when it is in the selectivity filter.