Biomedical Modelling and Simulation

Owner	Master Physics and Astronomy (joint degree)
Coordinator	dr. I.H.M. van Stokkum
Part of	Master Physics and Astronomy, track Physics of Life and Health, year 1Master Computational Science (Joint Degree), year 1Master Physics and Astronomy (joint degree), track Biophysics and Biophotonics, year 1Master Computational Science (Joint Degree), year 2

Course manual 2018/2019

Course content

This course will start with a general overview the various types of models used to describe biomedical processes by parametric and non-parametric models using linear and non linear (differential) equations. Basic knowledge of vector and matrix calculations and differential equations is required but will be refreshed. During the course, attention will be paid to viscoelastic models, spectral analysis, compartment models, and models to describe molecular structures and their dynamic behaviour. Examples will concentrate on cardiovascular function: linear and nonlinear viscoelastic models of pressure volume relations, compartment models of the interaction between contractile proteins to simulate force and pressure development and a description of an ion pump for instance to import Ca-ions into the cell during an action potential. The introductory lectures will be combined and followed by practical courses in which, through exercises, experience will be gained of MatLab and Mathematica (4th generation computer languages). Finally students will be offered a choice of 1 out of 5 modelling problems to be solved in small groups, guided by a supervisor. At the end of the course each group will present and discuss their work with all participants and supervisors of the course.

Objectives

To gain knowledge of the most important theoretical and practical concepts in modelling and simulation of biomedical processes at different scales, ranging from macroscopic organ function, cellular function down to biochemical interactions and signaling pathways within cells. To gain experience with and to apply MatLab and Mathematica to acquire, analyse and evaluate biomedical signals and to model and simulate biomedical processes.

Teaching methods

• Lecture
• Computer lab session/practical training
• Presentation/symposium
• Self-study

Learning activities

Attendance

Requirements concerning attendance (OER-B).

In addition to, or instead of, classes in the form of lectures, the elements of the master’s examination programme often include a practical component as defined in article 1.2 of part A. The course catalogue contains information on the types of classes in each part of the programme. Attendance during practical components is mandatory.

Assessment

Item and weight	Details
Final grade
1 (100%) Tentamen

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Contact information

Coordinator

• dr. I.H.M. van Stokkum