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, APB-E007 (Computer Science Building)
Exercises: Tuesdays, 16:40-18:10h, APB-E006 (Computer Science Building) EXERCISES START APRIL 14, 2020
LECTURES AND EXERCISES WILL BE ONLINE FOR THE ENTIRE SEMESTER. They will be held as Zoom live screen-casts with the possibility to ask questions. Links will be announced here below (a separate link for every week) a day prior to the lecture. In order to keep this as close as possible to a real lecture experience, the webcasts are no recorded.


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: Justina Stark


Exam

Date/Time: 07. August 2020, 13:00h - 14:30h

Place: TRE/MATH/H, TRE Trefftz-Bau Haus A Hörsaalgeb., Zellescher Weg 16

Format: written
Duration: 90 minutes (reduced from 120 min due to Covid-19 room planning measures)

Persons who tested positive for Sars-Cov-2 or are experiencing Covid-19-like symptoms are not admitted to the exam. Distancing of 1,5m min is mandatory. All signs are must be strictly followed. The Covid-19 hygiene regulations for written exams at TU Dresden must be strictly followed.
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.


Registration to the exam

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

For students of the Computer Science programs: via lists circulated in the lecture, or via e-mail to Prof. Sbalzarini

For students of the IMPRS-CellDevoSys: via lists circulated in the lecture, or via e-mail to Prof. Sbalzarini


Exam Review
To be announced after 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.