Orientational Matching Diagram.

<p>A toy example illustrating the matching sphere orientational matching algorithm. A) Toy receptor with 4 matching spheres shown as circles and a toy ligand with 3 spheres shown as stars. B) The distance matrices constructed from these spheres are show in the upper right. C) The 2 possible orientational matches of the ligand spheres (as stars) onto the receptor spheres with a distance tolerance of 0.1 (assuming 3 matching nodes are used, in 3D this is usually 4). D) The additional two orientations produced when the distance tolerance is raised to 0.2.</p

Filtering efficiency model that includes the statistical randomness of non-woven fiber layers in facemasks

Facemasks have become important tools to fight virus spread during the recent COVID-19 pandemic, but their effectiveness is still under debate. We present a computational model to predict the filtering efficiency of an N95-facemask, consisting of three non-woven fiber layers with different particle capturing mechanisms. Parameters such as fiber layer thickness, diameter distribution, and packing density are used to construct two-dimensional cross-sectional geometries. An essential and novel element is that the polydisperse fibers are positioned randomly within a simulation domain, and that the simulation is repeated with different random configurations. This strategy is thought to give a more realistic view of practical facemasks compared to existing analytical models that mostly assume homogeneous fiber beds of monodisperse fibers. The incompressible Navier-Stokes and continuity equations are used to solve the velocity field for various droplet-laden air inflow velocities. Droplet diameters are ranging from 10 nm to 1.0 µm, which covers the size range from the SARS-CoV-2 virus to the large virus-laden airborne droplets. Air inflow velocities varying between 0.1 m·s−1 to 10 m·s−1 are considered, which are typically encountered during expiratory events like breathing, talking, and coughing. The presented model elucidates the different capturing efficiencies (i.e., mechanical and electrostatic filtering) of droplets as a function of their diameter and air inflow velocity. Simulation results are compared to analytical models and particularly compare well with experimental results from literature. Our numerical approach will be helpful in finding new directions for anti-viral facemask optimization

Compiler Optimizations.

<p>Compiler Optimizations.</p

DOCK score effects with varying degrees of orientational sampling.

<p>A) The crystal ligand from PDB Code 1VSO. The critical contacts are defined as 3 atoms from the ligand crystal structure making key polar contacts with the protein, highlighted with spheres. 4 poses of ZINC00013260 are shown in B through E, with increasing sampling going from left to right, better DOCK scores and lower critical contact RMSD (with the exception of the critical contact RMSD rising from Match Goal of 50 to 500). Protein is shown in gray, crystal ligand shown in purple and representative docked pose shown in green, with hydrogen bonds drawn according to UCSF Chimera defaults. An additional molecule, ZINC00374553, is similarly shown in subfigures F through I, with a similar trend of increasing DOCK energies and decreasing critical contact RMSD.</p

Ligand Building Explanations.

<p>At left, several conformations of a ligand built with electrostatics off. At right the same ligand built with electrostatics on. The MMFF94S energies from OMEGA are shown below each pose. The bottom conformation on either side is the lowest energy conformation according to either energy function. The scales at either side are the differences in energy score from the best conformation to the shown conformation, this is the energy window used in construction.</p

Common mental disorders in migrants in primary care services: an emerging issue for CLP

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Speed versus different measures for five levels of orientational sampling.

<p>Speed measured in mean time in hours across all 102 DUD-E Targets against three measures of docking performance: Adjusted logAUC, AUC and EF1. Data shown for the full MMFF94S energy function used in ligand bulding (Green Squares) as well as the energy function with electrostatics turned off (Orange Diamonds).</p