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 particlemesh methods for computer simulations, student project: simulation of a biological system.
Time/Place
Summer Term
Lecture: Mondays, 11:1012:40 (3. DS.), CSBD Seminar Room 1 (Pfotenhauerstr. 108) / FIRST LECTURE: APR 9, 2018
No lecture on May 7, May 21 (Pentecost), July 9 + 16
Exercises: Fridays, 1pm2:30pm, CSBD Room 121 (Pfotenhauerstr. 108), except:
 11th May: NO tutorial. There is no lecture on 7th of May either.
 18th May: Tutorial takes place at the Max Planck Institute of Molecular Cell Biology and Genetics in Seminar Room 2: enter the building, go up the spiral staircase to the second floor, the seminar room is directly opposite the stairs.
 29th May: Tutorial from 1st of June is shifted to Tuesday, 29th of May, 9:20  10:50 in APB2026 (AndreasPfitzmannBau, University main campus).
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
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 selfcheck questions, and the exercises:
 Lecture 1  Administration and Introduction (Admin Slides, Admin Handouts, Intro Slides, Intro Handouts, SelfTest Questions)
 Lecture 2  Dimensional Analysis (Slides, Handouts, SelfTest Questions, Exercise, Solution)
 Lecture 3  Modeling Dynamics: Reservoirs and Flows (Slides, Handouts, SelfTest Questions, Exercise, Solution)
 Lecture 4  Recap on Vector Calculus (Slides, Handouts, SelfTest Questions, Exercise, Solution)
 Lecture 5  Conservation Laws and Control Volume Methods (Slides, Handouts, SelfTest Questions, Exercise, Solution)
 Lecture 6  Particle Methods (Slides, Handouts, SelfTest Questions, Exercise, PositionsData File, Solution (ZIP))
 Lecture 7  Diffusion (Slides, Handouts, PSE/RW Slides, PSE/RW Handouts, SelfTest Questions, Exercise, Solution (ZIP))
 Lecture 8  ReactionDiffusion (Slides, Handouts, SelfTest Questions, Exercise, Solution (ZIP))
 Lecture 9  AdvectionDiffusion (Slides, Handouts, SelfTest Questions, Exercise, BacterialPos.dat, Solution (ZIP))
 Lecture 10  Flow (Slides, Handouts, SelfTest Questions, Exercise, Solution (ZIP))
 Lecture 11  PDEs (Slides, Handouts, SelfTest Questions, Exercise, Solution)
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.