Ultrafast molecular dynamics of biofuel extraction for microalgae and bacteria milking: Blocking membrane folding pathways to damaged lipid-bilayer conformations with nanomicelles,
Jean-Numa Gillet,
- DOI 10.1080/07391102.2014.907544
RG Source: Article Ultrafast molecular dynamics of biofuel extraction for micro...
Dear Mr. Gillet,
I recently became acquainted with your work through Research Gate. This paper was, to say the least, insightful for me. I am an early stage researcher and an even earlier stage user of MD techniques. This paper has a lot of biophysical analysis, so I kept my focus on the MD simulations. The system you have chosen is of particular interest to me. I have just started to see the effects of small fungal peptides that aggregate to form ion channels across membranes and cause leakage.
This might not work for you as the membrane damage is irreversible and is used by many fungal species to "takeover" rival species or even bacteria. However, the various quantities, like entropy or diffusion, that you have discussed in your paper with respect to simulation, provided a fresh outlook for me. Maybe after a lot of effort I can apply these to my calculations as well.
Another observation is the small simulation timescales in this study. I figured that large biosystems required larger times to at least attempt to traverse the conformational space. Your membrane system undergo big conformational changes in just 10-12 ns. Is it because NAMD provides some strategy for it?
As I am modeling my system, I can see almost no big movement even after 5-6 ns. I am sure I will have to extend it longer than 10 ns to actually observe something interesting. I use AmberTools16 for my studies. Your opinion would be valuable.
On the last note, it was a delight to read.
Congratulations!
Thank you for asking for my opinion. I like it. It is an excellent theoretical interpretation of the process. What do I miss is the experimental proof. I should read it once more to comment in a more professional mode. My basic question for the double check is to learn what happens with the cell after extraction, can it function further, can it use the residual solvent for energy reserve or should this (as being the raffinate of the extraction process) been processed for different purposes? This part of downstream operations make that hexane has been the preferred solvent. I recommend for reading.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biota
- Eukaryota
- Fungi