Modeling and Simulation in Systems Biology

The repository includes homework assignments (HW1-HW4) and a term project focused on environmental DNA modeling in the mesopelagic ocean.

Main Results

Homework 1: Numerical Methods

• Implementation of Euler method for solving ordinary differential equations

  

• Implementation of 4th order Runge-Kutta method showing improved accuracy

  

Homwwork 2-1: Michaelis-Menten Rate Law Derivation

• Check 3.7.3.pdf.

Homework 2-2: Enzyme Kinetics

• Michaelis-Menten kinetics model results

  

• Mass action kinetics model results

  

Homework 3: Flux Balance Analysis

• Flux variability analysis results (part 1)

  

• Flux variability analysis results (part 2)

  

• Flux distribution in metabolic network

  

Homework 4-1: Noisy Toggle Switch

• Bistability with varying alpha ($\alpha$) and initial values

  

  

  

Homework 4-2: Epidemiological Modeling

• Animated SIR model simulation for COVID-19

  

• Epidemic curve showing disease progression over time with varying infection probability and proportion of isolated individuals

  

Term Project: eDNA Modeling

• Parameter profiles for eDNA distribution

  

• Animated visualization of eDNA concentration changes over time

  

• Static snapshot of eDNA vertical distribution

  

• Effects of predator-prey interactions on eDNA transport

  

• Decomposition of mixed eDNA signals