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Ion channels are proteins that play a significant role in physiological processes, including neuronal excitability and signal transduction. However, the precise mechanisms by which these proteins facilitate ion diffusion through cell membranes are not well understood. This is because experimental techniques to characterize ion channel activity operate on a time scale too large to understand the role of the various protein conformations on diffusion. Meanwhile, computational approaches operate on a time scale too short to rationalize the observed behavior at the microscopic scale. In this paper, we present a continuous-time random walk model that aims to bridge the scales between the atomistic models of ion channels and the experimental measurement of their conductance. We show how diffusion slows down in complex systems by using 3D lattices that map out the pore geometry of two channels: Nav1.7 and gramicidin. We also introduce spatial and dynamic site disorder to account for system heterogeneity beyond the mean field approximation. Computed diffusion coefficients show that an increase in spatial disorder slows down diffusion kinetics, while dynamic disorder has the opposite effect. Our results imply that microscopic or phenomenological models based on the potential of mean force data overlook the functional importance of protein dynamics on ion diffusion through channels. [ABSTRACT FROM AUTHOR]

Polarizable force fields crucially enhance the modeling of macromolecules in polar media. Here, we present new parameters to model six common monosaccharides with the polarizable AMOEBA force field. These parameters yield a thinner, but denser, hydration layer than that previously reported. This denser hydration layer results in eliminating non-physical aggregation of glucose in water—an issue that has plagued molecular dynamics simulations of carbohydrates for decades. [ABSTRACT FROM AUTHOR]

Water contributes to the structure of bone by coupling hydroxyapatite to collagen over the hierarchical levels of tissue organization. Bone water exists in two states, bound or mobile, each accomplishing different roles. Although many experimental studies show that the amount of bound water correlates with bone strength, a molecular understanding of the interactions between hydroxyapatite, collagen and water is missing. In this work, we unveil the water adsorption properties of bone tissues at the nanoscale using advanced density functional theory methods. We demonstrate that environmental factors such as collagen conformation or degree of confinement, rather than the surface itself, dictate the adsorption mode, strength and density of water on hydroxyapatite. While the results derived in this paper come from a simplified model of bone tissues, they are consistent with experimental observations and constitute a reasonable starting point for more realistic models of bone tissues. For example, we show that environmental changes expected in aging bone lead to reduced water adsorption capabilities, which is consistent with weaker bones at the macroscale. Our findings provide a new interpretation of molecular interactions in bone tissues with the potential to impact bone repair strategies. [ABSTRACT FROM AUTHOR]