Numerical investigation of molecular nano-array in potential-energy profile for a single dsDNA

Parallel computing for mobilities in periodic geometries

We examine methods for calculating the effective mobilities of molecules driven through periodic geometries in the context of particle-based simulation. The standard formulation of the mobility, based on the long-time limit of the mean drift velocity, is compared to a formulation based on the mean first-passage time of molecules crossing a single period of the system geometry. The equivalence of the two definitions is derived under weaker assumptions than similar conclusions obtained previously, requiring only that the state of the system at subsequent period crossings satisfy the Markov property. Approximate theoretical analyses of the computational costs of estimating these two mobility formulations via particle simulations suggest that the definition based on first-passage times may be substantially better suited to exploiting parallel computation hardware. This claim is investigated numerically on an example system modeling the passage of nanoparticles through the slit-well device. In this case, the traditional mobility formulation is found to perform best when the Péclet number is small, whereas the mean first-passage time formulation is found to converge much more quickly when the Péclet number is moderate or large. The results suggest that, given relatively modest access to modern GPU hardware, this alternative mobility formulation may be an order of magnitude faster than the standard technique for computing effective mobilities of biomolecules through periodic geometries.

Forced diffusion of water molecules through aquaporin-5 biomembrane; a molecular dynamics study

Aquaporins (AQPs) are protein channels located across the cell membrane which conduct the water permeation through the cell membrane. Different types of AQPs exist in human organs and play vital roles, as the malfunction of such protein membranes can lead to life-threatening conditions. A specific type of AQP, identified as AQP5, is particularly essential to the generation of saliva, tears and pulmonary secretions. We have adopted Molecular Dynamics (MD) simulation to analyze the water permeation and diffusion in AQP5 structure in a 0.5 microsecond simulation time window. The MD numerical simulation shows the water permeability of the human AQP5 is in the nominal range for other members of human aquaporins family. In addition, we have considered the effect of the osmotic water diffusion and the diffusion occurred by pressure gradient on the protein membrane. The water permeability grows monotonically as the applied pressure on the solvent increases. Furthermore, the forced diffusion increases the minimum radius of Selectivity Filter (SF) region of region AQP5 up to 20% and consequently the permeability coefficients enhance enormously compared to osmotic self-diffusion in AQP5 tetramer. Finally, it is revealed that the MD simulation of human AQP5 provides useful insights into the mechanisms of water regulation through alveolar cells under the different physical conditions; osmotic self-diffusion and forced diffusion condition.