Spatiotemporal Modeling and Simulation

Introduction to spatiotemporal modeling and simulation

This course teaches modeling techniques for spatially resolved systems. You will learn to account for the geometry of a system and for transport in space. After repetition of the basics from mathematics and physics, you will model processes such as diffusion and flow, and simulate them in the computer.


dimensionality analysis, causality diagrams, vector fields, particle methods, governing equations for diffusion and flow, hybrid particle-mesh methods for computer simulations, student project: simulation of a biological system.

Summer Term

Lecture: Tuesdays, 14:50-16:20h, CSBD Seminar Room Ground Floor (Pfotenhauerstr. 108)
Exercises: Tuesdays, 16:40-18:10h, CSBD Seminar Room Ground Floor (Pfotenhauerstr. 108)


2 SWS lecture, 2 SWS exercise, self-study

Programs / Modules

M.Sc. Computational Modeling and Simulation, Modules: CMS-CLS-MOS

B.Sc. Computer Science, Module: INF-B-510

Diplom Computer Science, Module: INF-D-510

Registration to the course

For students of the Master program "Computational Modeling and Simulation: via CampusNet SELMA

For students of the Computer Science programs: via jExam

For students of the IMPRS-CellDevoSys: via the program office


Lecture: Prof. Ivo F. Sbalzarini
Exercises: Karl Hoffmann

Learning goals
  • Analysis of the dynamic behavior of biological or physical systems with spatial structure

  • Formulation of a model of the system behavior

  • Computer simulation of the model using numerical methods

Special remarks

We focus on biological systems. The taught methods and concepts are, however, applicable in a much broader sense.

Lecture language: ENGLISH

Please find below the lecture syllabus, the slides, the self-check questions, and the exercises:
  • Lecture 1 - Administration and Introduction
  • Lecture 2 - Dimensional Analysis
  • Lecture 3 - Modeling Dynamics: Reservoirs and Flows
  • Lecture 4 - Recap on Vector Calculus
  • Lecture 5 - Conservation Laws and Control Volume Methods
  • Lecture 6 - Particle Methods
  • Lecture 7 - Diffusion
  • Lecture 8 - Reaction-Diffusion
  • Lecture 9 - Advection-Diffusion
  • Lecture 10 - Flow
  • Lecture 11 - PDEs

Full lecture notes can be found here: Script (PDF).


The student project will aim at implementing the Quorum Sensing model proposed by J. Müller et al. as described in this publicly available preprint.