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The following movies highlight the visual output of calculations, simulations, and modeling by Computational Sciences staff in various research areas: the gas diffusion pathways in [Fe-Fe] hydrogenase, the electronic structure of a CdSe tetrapod, and the visualization of room air flow.
Gas Diffusion Pathways in [Fe-Fe] Hydrogenase
The following two movies demonstrate the separate trajectories, as calculated by molecular dynamics simulations, of hydrogen and oxygen gas diffusion outwards from the catalytic site (the site of Hydrogen production) of Clostridium Pasteurianum hydrogenase I (CpI).
[Fe-Fe]-hydrogenases are enzymes that catalyze the production of molecular hydrogen and as such offer a promise of a means for affordable large-scale production of hydrogen as a source of renewable energy. However, hydrogen production is deactivated if oxygen molecules enter the catalytic site.
For this reason, the objective of the molecular dynamics research was to investigate the possible pathways taken by hydrogen and oxygen across the Cpl Hydrogenase. If the pathways by which oxygen enters the enzyme can be identified it could open the possibility of creating an engineered version of hydrogenase in which these pathways are closed thereby decreasing the hydrogenases's sensitivity towards oxygen. However, it is also imperative that the exit of hydrogen is not limited to the same pathways as the oxygen which would the hydrogen exit from the catalytic site being blocked in engineered versions of the protein.
The results of these simulations are displayed in the following movies.
In both movies the blue ribbons show the backbone of overall protein structure of Clostridium Pasteurianum hydrogenase I (CpI). Highlighted atoms are the inorganic metal clusters, Fe-S clusters in yellow (S) and green (Fe) spheres. In the center is the catalytic center called H-cluster where the hydrogen production reaction occurs. The green sticks are the residues lining up the major pathways identified by the simulations of both gases.
However as demonstrated by the oxygen simulation movie it can be seen that the pathways of oxygen diffusion from the catalytic site are limited to the major pathways highlighted by the green stick representation whereas in the hydrogen simulation movie it can be seen that there exists alternative pathways of hydrogen diffusion.
CdSe Tetrapod Electronic Structure
The movie shows the electronic structure calculations of branched CdSe nanocrystals. This is made by spherical joints in cubic zincblende structure and the rods (arms) in hexagonal wurtzite structure. The electronic structure was calculated by an empirical pseudopotential method. The calculated charge density is shown by volume visualization. The lowest conduction band state is localized in four outer joints highlighted in orange.
- Electronic structure calculations of branched CdSe nanocrystals (MPG 2.4 MB)
Room Air Flow Visualizations
The following two movies compare and contrast conditions required for optimal room ventilation.
The objective in providing adequate room ventilation is to obtain fresh air circulation throughout the room and maintain an even temperature throughout.
The first movie demonstrates the results obtained using an input air speed of 2mps and temperature of 130F. Using these parameters the air circulation is stratified i.e. there is limited air flow in the lower regions of the room and the temperature variation throughout the room is significant (10K).
The second movie demonstrates the results obtained using a higher input air speed of 4mps and a lower temperature of 90F. In contrast to the first model, air circulates throughout the room, and there exists no great temperature variation (a variation of 0.5K is shown).
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