Overview


Modeling and Simulation of Biological Systems

Arne Nägel, G-CSC, Universität Frankfurt, Gillian Queisser, Temple University Philadelphia, and Gabriel Wittum, AMCS, CS KAUST together with Babett Lemke, G-CSC, Universität Frankfurt, and Dmitry Logashenko, AMCS, KAUST.

Biological systems are distinguished by their enormous complexity and variability. That is why mathematical modeling and computational simulation of those systems is very difficult, in particular thinking of detailed models which are based on first principles. The difficulties start with geometric modeling which needs to extract basic structures from highly complex and variable phenotypes, on the other hand also has to take the statistic variability into account. Moreover, the models of the processes running on these geometries are not yet well established, since these are equally complex and often couple many scales in space and time. Thus, simulating such systems always means to put the whole frame to test, from modeling to the numerical methods and software tools used for simulation. These need to be advanced in connection with validating simulation results by comparing them to experiments. 

To treat problems of this complexity, novel mathematical models, methods, and software tools are necessary. In recent years, such models, numerical methods, and tools have been developed, allowing to attack these problems. The School will introduce the models, the algorithms and demonstrate the effect of such advanced modeling and simulation approaches in practical problems from the life sciences. We will discuss problems like diffusion through human skin, reconstruction of geometry from microscopic data, signal processing in neurons, spreading of infectious diseases, and fermentation of biomass. 

The school will include theoretical and practical parts and will discuss the following topics:

  • Modeling with PDE
  • Discretization of PDE
  • Solvers for large sparse systems of algebraic equations
  • Modeling and Simulation of Diffusion through Human Skin
  • Modeling and Simulation of Signal Processing in Neurons
  • Modeling Biomass Fermentation

Agenda

October 11th - 20th, 2021

*The agenda is subject to change.

Monday, Oct 11th 

09:00  Introduction
10:30 Break
11:00 Modeling with PDE
12:30 Break
14:30 Practical
16:00 Break
16:30 Practical

 

Tuesday, Oct 12th 

09:00 Discretization of PDE 1
10:30 Break
11:00 Discretization of PDE 2
12:30 Break
14:30 Practical
16:00 Break
16:30 Practical

 

Wednesday, Oct 13th

09:00 Solvers for large sparse systems of algebraic equations
10:30 Break
11:00 Solvers for large sparse systems of algebraic equations
12:30 Break
14:30 Practical
16:00 Break
16:30 Practical

 

Thursday, Oct 14th

09:00 Modeling and Simulation of Diffusion through Human Skin 1
10:30 Break
11:00 Modeling and Simulation of Diffusion through Human Skin 2
12:30 Break
14:30 Practical
16:00 Break
16:30 Practical

 

Monday, Oct 17th

09:00 Modeling and Simulation of Signal Processing in Neurons 1
10:30 Break
11:00 Modeling and Simulation of Signal Processing in Neurons 2
12:30 Break
14:30 Practical
16:00 Break
16:30 Practical

 

Tuesday, Oct 18th

09:00 Modeling and Simulation of Signal Processing in Neurons 3
10:30 Break
11:00 Modeling and Simulation of Signal Processing in Neurons 4
12:30 Break
14:30 Practical
16:00 Break
16:30 Practical

 

Wednesday, Oct 19th

09:00 Modeling Biomass Fermentation 1
10:30 Break
11:00 Modeling Biomass Fermentation 2
12:30 Break
14:30 Practical
16:00 Break
16:30 Practical

 

Thursday, Oct 20th

09:00 Final Overview
10:30 Break
11:00 Final Overview