A recently developed version of the Gibbs ensemble Monte Carlo
technique is used for the determination of
vapor−liquid equilibria of potential models for hydrogen sulfide.
By fitting to experimental saturation
properties of the substance, an optimized effective pair potential is
parametrized on the basis of an existing
four-site model of Lennard-Jones plus point charge type. The new
model reproduces well also the critical
properties and the structural characteristics of the
substance.
In a multiscale modeling approach, we present computer simulation results for a rectifying bipolar nanopore at two modeling levels. In an all-atom model, we use explicit water to simulate ion transport directly with the molecular dynamics technique. In a reduced model, we use implicit water and apply the Local Equilibrium Monte Carlo method together with the Nernst-Planck transport equation. This hybrid method makes the fast calculation of ion transport possible at the price of lost details. We show that the implicit-water model is an appropriate representation of the explicit-water model when we look at the system at the device (i.e., input vs. output) level. The two models produce qualitatively similar behavior of the electrical current for different voltages and model parameters. Looking at the details of concentration and potential profiles, we find profound differences between the two models. These differences, however, do not influence the basic behavior of the model as a device because they do not influence the z-dependence of the concentration profiles which are the main determinants of current. These results then address an old paradox: how do reduced models, whose assumptions should break down in a nanoscale device, predict experimental data? Our simulations show that reduced models can still capture the overall device physics correctly, even though they get some important aspects of the molecular-scale physics quite wrong; reduced models work because they include the physics that is necessary from the point of view of device function. Therefore, reduced models can suffice for general device understanding and device design, but more detailed models might be needed for molecular level understanding.
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 Ca2+ 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, Ca2+ exclusion, and Ca2+ 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.
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