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).
2 SWS lecture, 2 SWS exercise, selfstudy
Programs / Modules
M.Sc. Computational Modeling and Simulation, Modules: CMSCLSMOS
B.Sc. Computer Science, Module: INFB510
Diplom Computer Science, Module: INFD510
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 IMPRSCellDevoSys: via the program office
Teachers
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
 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  ReactionDiffusion
 Lecture 9  AdvectionDiffusion
 Lecture 10  Flow
 Lecture 11  PDEs
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.