SMTK20001U Advanced Physiological Modelling

Volume 2021/2022

MSc Programme of Biomedical Engineering - Restricted elective in the Technological Specialization

MSc Quantitative Biology and Disease Modelling - Restricted elective in the Technological Specialization


The course aims to provide overview of current research topics in mathematical physiology by synthesizing a coherent description of the physiological background with realistic mathematical models and their analysis. The program will give students the opportunity to develop mathematical and computer modeling skills, whilst at the same time will introduce students to cutting-edge experimental techniques and computational algorithms. A wide variety of topics are touched upon: from cellular signaling and biological rhythms to neuronal and vascular networks.

Learning Outcome

After participating in the course, the student must demonstrate the following abilities at a sufficient level:


  • Understand mathematical/physics concepts (dynamical systems, oscillation theory, network theory, synchronization theory, statistics, survival analysis)

  • Understand computational algorithms behind Matlab/Python/R scripts related to biosimulations

  • Explain topology and dynamics of biological networks and their relevance to normal and pathological conditions

  • Understand what assumptions and simplifications are needed to build a model

  • Understand underlying signaling mechanisms and corresponding control parameters in a model related to a certain disease


  • Review scientific literature on physiological modeling and related data analysis, critically assess the use of methods and obtained results

  • Assess complex networks of the human body by treating a sequence problems at the intracellular, intercellular, whole organ and systemic levels

  • Perform theoretical and computational analysis of dynamical patterns of physiological models and reveal parameters responsible for pathological conditions

  • Optimize/develop computation algorithms to perform biosimulations

  • Convey a physiological problem solving into a report and a Power Point presentation


  • To formulate mechanism-based and data-driven models and choose appropriate computational methods to investigate them

  • To interpret dynamical features of the biomedical systems in term of biology and mathematics

  • To integrate fundamental knowledge from physics, mathematics and biology to provide better understanding of regulatory mechanisms at different levels of organization

Lecture notes and scientific papers

Lectures, class/home assignments
  • Category
  • Hours
  • Lectures
  • 24
  • Preparation
  • 226
  • Project work
  • 24
  • Total
  • 274
2,5 ECTS
Type of assessment
Course participation
Participation in all written and oral assignments through the course and approval of the final written report
All aids allowed
Marking scale
passed/not passed
Censorship form
No external censorship
Criteria for exam assesment

To obtain the course certificate the student must be able to


  • Understand underlying mathematical/physics concepts 
  • Understand advanced computational algorithms used for modeling
  • Explain biological background of the model
  • Understand regulatory mechanisms of biological rhythms/networks and their mathematical models



  • Discuss modeling approaches depending on the purpose of study
  • Reproduce, modify and simulate models from scientific literature
  • Discuss reproducibility and comparability of relevant computational models
  • Apply mathematical/physical concept to particular biomedical problem
  • Formulate a model and discuss its possible simplifications/​extension and dynamics
  • Develop algorithms to perform simulations
  • Improve scientific writings in English language