Dear LAMMPS developers and users:
I am glad to announce that my newest study using LAMMPS has been published on Journal of The Royal Society Interface: https://royalsocietypublishing.org/rsif/article/23/239/20251155/482038.
This work established an integrated mechano-physiological framework (CREST) for closed-loop control of the small intestinal transport. I used LAMMPS for the computational simulation of the mechanical part. Specifically, the RHEO package was used for fluid transport and the BPM package was used for simulating the viscoelasity of the intestinal wall. Thanks to LAMMPS’ convenient python module, I was able to couple LAMMPS with an external Python package (Brian2, for controller simulation) in parallel (How to use MPI in fix external - LAMMPS / LAMMPS General Discussion - Materials Science Community Discourse).
I also want to thank @akohlmey for his kind help. He replied to almost every question posted by me in time and always provided useful advice, saving me a lot of time.
LAMMPS is not only a powerful tool for molecular dynamics simulation, but also powerful for mesoscale/macroscale cases like this study. Moreover, it is easy to modify LAMMPS source code and add some user-defined functions. I referred to this book: Extending and Modifying LAMMPS Writing Your Own Source Code by Dr. Shafat Mubin and Jichen Li. Here you can get access to my source codes: Jasmine969/CREST_SUDA
Here is a video showing the coupled dynamics of the intestinal transport and neural control: Item - Intestinal transport under neural control from Closed-loop control of the small intestinal transport within an integrated mechano-physiological framework - The Royal Society - Figshare
Cheers,
Hong Zhu