CityUSimulation
Physical modeling for bacteria motions
Getting Started
Keywords:
- active matter, bacterial collective movement
Simulation softwares:
- gromacs
- lammps
- HOOMD-blue (http://glotzerlab.engin.umich.edu/hoomd-blue/)
HOOMD-blue:
- "you define particle initial conditions and interactions in a high-level python script"
- HOOMD-blue is a general-purpose particle simulation toolki. It scales from a single CPU core to thousands of GPUs
Hardware:
- Lenovo ThinkStation P920 Tower (80K HKD)
- Motherboard : P920 MB Intel Purley Dual CPU
- Processor : 2 x Intel Xeon GOLD 6136 Processor (24.75MB Cache, up to 3.70GHz)
- Memory Selection : 2 X 32GB DDR4 2666MHz ECC RDIMM
- 1st Graphic Card: P5000 16GB DVI+4DP HP L_EXT
Graphic Card:
- has 2560 CUDA parallel processing cores
Physical Observations:
- fast bacteria and slow bacteria together in a droplet, the fast bacteria gather at the boundary
- current simulation only observe this gathering effect of a few micro-meters, but the real-life observation is 2000 micro-meters
Literatures:
- 2014 EPL paper
- 2018 PRE paper
- experimental work by Chinese U collaborator - wu yilin's observation on bacteria
- and other more complicated and interesting collective motion of bateria
Theory:
- modeling bacteria = adding propulsion to common Brownian motion
HOOMD-blue:
- supports Brownian motion modeling out of the box, and can also add propulsion
- there is a simulation example in the package, and that is a sample simulation on bacteria motion
- github
- tutorials - from official website
- webinar1 - introduction to HOOMD-blue
- webinar2 - simulation of a polymer
Tasks
- (as of March 7th): cannot make gromacs use GPU
- install softwares on the Lenovo tower