Molecular Modeling of Surfactant Molecules Along an Organic/Water Interface

in chemistry •  7 years ago  (edited)

Here are some images generated from simulation files using the Visual Molecular Dynamics program (VMD). The surfactant molecules in the image are sodium dodecanoate, the organic layer is carbon tetrachloride, the aqueous layer is water, and the divalent cations in the aqueous layer are calcium (yellow) with chloride counterions (blue). Screen Shot 2017-07-14 at 2.07.13 PM.png

Let me know in the comments if this type of molecular modeling research interests you. I have tons of more theoretical data to share on this specific chemical system. OpenMM was used to perform the simulations in python. The simulations were ran using Nvidia CUDA architecture GPUs. Each simulation of 25ns takes about 5 days with every step in the simulation at 0.5 femtoseconds (10^-15 seconds). This system was studied in order to look at how the presence of divalent cations along the interface can change the interfacial width of the system.

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Do you have a video of simulations?

Yes I do have a couple videos. I'm working on uploading them soon!

@sunshine11 : Do you work in molecular dynamics? I never found any active users who do MD here. In case you know other steemit users who do MD, please let me know. I work in computational biophysics. Uses NAMD and VMD. Good article btw. Please have a look at my articles too. I am going to start writing on MD. Good luck.

Yes I am currently doing research for Pacific University, Oregon in the computational chemistry department using molecular dynamics! A couple of my fellow student lab-mates or going to be a part of the STEEM community soon. Good to here some other MD enthusiasts on here!

Cool. Great to know that. In case you are creating some MD related group, inform me too.🙂 I am following you.