Neurodevelopmental Disorder (NDD) Model

Neurodevelopmental disorders modeling using innovative isogeometric analysis, dynamic domain expansion and local refinement

Flow chart of the NDDs modeling pipeline

User Guide

This code is the implementation of the phase field model using isogeometric analysis to simulate neurodevelopmental disorders. Based on truncated T-spline with local refinements and dynamic domain expansion, the implementation uses PETSc library for MPI parallelization.

File structures

• 2D_solver_coarse: contains code for 2D Phase field model for NDDs using isogeometric method.
• 2D_solver_coarse_compCase: code modified for comparison cases in paper.
• 2D_solver_compareMatlab: code modified for comparison with previous Matlab code.
• 2D_solver_compareMatlab_AxonDiff: code modified for axon differentiation test.
• THS2D: truncated T-spline code by Xiaodong Wei.
• eigen-3.4.0: eigen-3.4.0 library for ease of use.
• genBatch: batch script generation for PSC HPC system
• nanoflann/1.5.5: nanoflann/1.5.5 library for ease of use.
• spline2D_src: 2D spline generation code for initialization by Angran Li

How to run (Assuming Linux environment)

1. Installation of PETSc (and its dependents), METIS, gcc, g++, gfortran, make.

2. Make and build THS2D, spline2D_src, and 2D_solver_XXXX that you want to run

   make clean

   make all

3. [petsc mpirun path] -n [number of threads] ./2DNG [number of neurons] [number of iterations] [input/output path] | tee -a [log file path]

   • example:

     /.../petsc/arch-linux-c-opt/bin/mpirun -n 32 ./2DNG 1 350000 ../io2D/ | tee -a ../io2D/log.txt

   • for comparison cases, replace number of neurons with case ID:

     /.../petsc/arch-linux-c-opt/bin/mpirun -n 32 ./2DNG K 350000 ../io2D/ | tee -a ../io2D/log.txt

Reference

1. K. Qian, G. O. Suarez, T. Nambara, T. Kanekiyo, A. S. Liao, V. A. Webster-Wood, Y. J. Zhang. Neurodevelopmental disorders modeling using innovative isogeometric analysis, dynamic domain expansion and local refinement. Computer Methods in Applied Mechanics and Engineering, 117534, 2025.
2. K. Qian, A. Liao, S. Gu, V. Webster-Wood, Y. J. Zhang. Biomimetic IGA Neuron Growth Modeling with Neurite Morphometric Features and CNN-Based Prediction, Computer Methods in Applied Mechanics and Engineering, 116213, 2023.
3. A. S. Liao, W. Cui, Y. J. Zhang, V. A. Webster-Wood, Semi-automated quantitative evaluation of neuron developmental morphology in vitro using the change-point test, Neuroinformatics 21:163–176, 2022.
4. K. Qian, A. Pawar, A. Liao, C. Anitescu, V. Webster-Wood, A. W. Feinberg, T. Rabczuk, Y. J. Zhang, Modeling neuron growth using isogeometric collocation based phase field method, Scientific Reports 12:8120, 2020.
5. X. Wei, Y. J. Zhang, T. J. R. Hughes. Truncated T-splines: Fundamentals and methods, Computer Methods in Applied Mechanics and Engineering, 316:349-372, 2017.