Biophysical Modeling with Matlab

1. Matlab Primer with Simple Statistical Analyses

• Coin Flip Experiment: Analyze the statistics of simultaneous coin flip experiments.
• Two-Dimensional Random Walk: Mean squared displacement and diffusion analysis.
• Matlab code.
• Detailed problem statement.

2. Repulsive Vicsek Simulation for EMT

• To capture cell migration physics in Epethelial-Mesenchymal Transitions (EMT).
• Matlab code (driver scripts: P1_Polarization.m, P2_MSD.m).
• Detailed problem statement.
• Plots and analysis.

3. Plant Tissue Structure Analysis

• Analyze the structure of plant tissues using voronoi diagrams.
• Matlab code.
• Detailed problem statement.
• Plots and analysis.

4. Machine Learning for Protein Decoy Detection

• Basic machine learning workflow in Matlab using the MNIST Handwritten Digits dataset.
• Regression using multi-layer perceptrons for protein decoy detection.
• Matlab code.
• Detailed problem statement.
• Plots and analysis.

5. Tumor Invasion Analysis

• Deformable particle model of tumor cell invasion into white adipose tissue (WAT).
• Thermalized soft-disk numerical model of tumor cell diffusion within WAT.
• Matlab code.
• Detailed problem statement.
• Plots and analysis.