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 other degree programs: via your respective study or examination office

For students of the IMPRS-CellDevoSys: via the PhD 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.

Grade scale:

All exams are graded in absolute terms w.r.t. the following pre-defined grade scale that remains constant over the years:

  • The top grade of 1.0 is reached with 80% of the maximum possible points
  • Half of that, i.e., 40% of the maximum possible points, are required to pass
  • Below 40%, or no-show, is a fail.
Between the top grade and the passing threshold, the grading scale is linear. In the end, grades are rounded to the nearest allowed grade according to the exam regulations: 1.0, 1.3, 1.7, 2.0, 2.3, 2.7, 3.0, 3.3, 3.7, 4.0, 5.0. The grades 0.7, 4.3, and 4.7 are not allowed. Any grade above 4.1 is a fail (see exam regulations). The maximum number of points that can be reached in the exam is given by the number of minutes the exam lasts (i.e., a 90 minute exam yields maximum 90 points). Points are distributed amongst the exam questions to reflect the number of minutes a good student would need to solve the problem. This provides some guidance for your time management in the exam. In order to reduce the risk of correction mistakes, all exams are checked by at least two independent, qualified assessors (typically professors or teaches with officially conferred examination rights). The exam review session (see below) is for you to come look at your exam paper and report correction mistakes you found.


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 other degree programs: via your respective examination office

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


Exam Review

You can come and look at your exam, and ask questions about its correction and the answers given during the exam review times. In order to accommodate for everyone's schedule, we offer three exam review dates at different times:

  • October 12, 2020, 2pm CANCELED DUE TO RAIN. NEW DATE: October 19, 2020, 10am
  • October 27, 10am
  • November 4, 4pm

Location for all exam reviews: Outdoors in the seating area in front of the Center for Systems Biology Dresden, Pfotenhauerstr. 108 (yellow building) (Maps Link). The review only takes place if there is no rain. In case of rain, a new date will be found. In order to participate, You MUST wear a face mask and you are only allowed to come forward one by one.

IMPORTANT: All students attending an exam review must fill in and sign the exam review form they are going to receive during the review. Undocumented exam reviews are not permitted.


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.