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.


Contents

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.


Time/Place
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)
NO LECTURE / NO EXERCISE ON: MAY 21, 2019.


Format

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


Teachers

Lecture: Prof. Ivo F. Sbalzarini
Exercises: Aryaman Gupta


Exam

Date/Time: August 9, 2019 / 9am-11am

Place: APB/E005 and APB/E006

Format: written
Duration: 120 minutes


At the exam, the following may be used:
  • 4 A4 sheets (8 pages if you print duplex) of hand-written summary. We recommend writing the summary by hand, but it can also be machine-written. In the latter case, the font size must be 8 points or larger throughout.
  • A standard pocket calculator (devices with network or bluetooth access, as well as devices capable of storing and displaying documents are not allowed)
Items not adhering to these guidelines will be confiscated in their entirety at the beginning of the exam.


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: Script

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


Project

The student project will aim at implementing the Quorum Sensing model proposed by J. Müller et al. as described in this publicly available preprint. The final version of the paper is available from Springer Link with university access.