Coarse-grained lipid membranes: A teaser of upcoming MD simulation stuff!

in #steemstem3 years ago (edited)

Hi friends... To be honest I am overwhelmed with many things recently. And few days back my tinkering became official work(Well... Kinda). Few of you might have seen my previous post. So I will elaborate a little bit more about how I started these projects, what am I intending to post, etc.

How I started this work?

I was applying for postdoctoral positions when I was about to wrap up my Ph.D. I was always fascinated by lipid membrane simulations. And, then I got selected as a postdoctoral researcher to a group that does coarse-grained lipid simulations, etc. So I was supposed to learn a new tool called LAMMPS software. Out of pure curiosity and free time I got during these COVID19 days I started working on replicating my postdoc supervisor's model in LAMMPS[1]. I extended it to vesicles too. You can see the details in the paper. Also, I am planning to write about these adventures in an upcoming series.

My upcoming plan for articles

  • Description of the lipid model
  • How to set up a coarse-grained vesicle using moltemplate/LAMMPS/topotools/VMD
  • How to generate customized forcefield files for the simulations
  • How to set up the simulations
  • More details like analysis/interpretation of results and things according to how project evolves.

Screen Capture of simulations

Here is a screen capture video from my work. The coarse-grained lipid vesicle was simulated in LAMMPS under NVE ensemble and visualized in VMD software. I will explain the technical details in the upcoming articles.

Can you see the spherical vesicle getting a lot of sharp edges in the video? Physicists call them DEFECTS. These defects are assumed to form due to the rigidity in the lipid trimer. I will talk about them in the coming articles. @scienceangel : I don't know if you are seeing this. Do you remember our discussion about lipid flipflops? These simulations capture that phenomenon. I will show those too. Wait for it. :)

Till then bye bye!



This post was shared in the Curation Collective Discord community for curators, and upvoted and reblogged by the @c-squared community account after manual review.
@c-squared runs a community witness. Please consider using one of your witness votes on us here
This post has been voted on by the HiveSTEM curation team and voting trail. It is elligible for support from @curie and @minnowbooster.

If you appreciate the work we are doing, then consider supporting our witness @stem.witness. Additional witness support to the curie witness would be appreciated as well.

For additional information please join us on the SteemSTEM discord and to get to know the rest of the community!

Thanks for having used the app. This granted you a stronger support from SteemSTEM. Note that including @steemstem in the list of beneficiaries of this post could have yielded an even more important support.