Code about the microtubule comets project.
We are simulating the wetting of microtubules by proteins such as End-Binding (EB) proteins. We use a phase field approach. The phase separation is introduced via a double well potential (different potentials were tested, but we settled on a simple (phi-a)²(phi-b)² type of potential). The wetting is introduced via a surface energy h*phi. The microtubule is modeled as a solid cylinder.
We are simulating different situations considering cylindrical coordinates and assuming axisymmetry: -an infinite MT by using periodic boundary conditions along the x-axis. (Simulation_Static_...) -a growing MT with the simulation frame moving with the growing tip. (Simulation_Growing_...) -For both cases above, we are simulating the dynamics in the absence (noFlow) and presence (withFlows) of hydrodynamic flows. -We also introduce a chemical reaction term to induce droplet evaporation. (withEvaporation)
The dynamics of the phase field are governed by a Cahn-Hilliard equation while the dynamics of the hydrodynamic flows are governed by the Navier-Stokes equation.
We solve the Cahn-Hilliard equation with an upwind finite difference scheme and the Navier-Stokes equation with the Lattice Boltzmann Method.
The .csv files provide examples of parameter sets used in our simulations.
Software versions:
CUDA version:
CUDA runtime 12.3, artifact installation CUDA driver 12.8 NVIDIA driver 570.86.15
CUDA libraries:
- CUBLAS: 12.3.4
- CURAND: 10.3.4
- CUFFT: 11.0.12
- CUSOLVER: 11.5.4
- CUSPARSE: 12.2.0
- CUPTI: 21.0.0
- NVML: 12.0.0+570.86.15
Julia packages:
- CUDA.jl: 5.2.0
- CUDA_Driver_jll: 0.7.0+1
- CUDA_Runtime_jll: 0.11.1+0
- CUDA_Runtime_Discovery: 0.2.3
Toolchain:
- Julia: 1.8.5
- LLVM: 13.0.1
1 device: 0: Tesla P100-PCIE-12GB (sm_60, 11.899 GiB / 12.000 GiB available)
Package version:
Status ~/.julia/environments/v1.8/Project.toml
⌃ [336ed68f] CSV v0.10.12
⌃ [052768ef] CUDA v5.2.0
⌃ [a93c6f00] DataFrames v1.6.1
⌃ [31c24e10] Distributions v0.25.107
⌃ [7a1cc6ca] FFTW v1.8.0
⌃ [5789e2e9] FileIO v1.16.2
⌃ [4138dd39] JLD v0.13.4
[682c06a0] JSON v0.21.4
⌃ [ee78f7c6] Makie v0.20.7
[ade2ca70] Dates
[8bb1440f] DelimitedFiles
[37e2e46d] LinearAlgebra
[d6f4376e] Markdown
[de0858da] Printf
[9a3f8284] Random
[10745b16] Statistics
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