Subject description - A6M33MOS

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A6M33MOS Modeling and Simulation
Roles:P Extent of teaching:2P+2C
Department:13133 Language of teaching:CS
Guarantors:  Completion:Z,ZK
Lecturers:  Credits:5
Tutors:  Semester:Z


The modelling techniques being frequently used in biomedical engineering and corresponding software tools: Matlab-Simulink, Modelica. Techniques of modelling and processes associated with them. Types of models, continuous and discrete time models, linear and nonlinear models with lumped parameters, models and their implementation in program environment. Formalization and model creation for a selected system, its identification, verification and interpretation. Equilibrium states (homeostasis) and their inquiry by simulation. Models of open and feedback systems. Use of fuzzy-neuronal models in biomedicine. Models of separate systems and whole constellations being defined in biomedical engineering. Models of cellular and physiological control, population models. Application of models for artificial organs production.

Study targets:

The goul of the course is to teach studentes modelling techniques being frequently used in biomedical engineering.

Course outlines:

1. Mathematical modelling in BMI - examples of composition of physiological systems models.
2. Static analysis of physiological systems and processes. Examples: cardiac output control, glycemy control, acidobasic equilibrium control, chemical control of ventilation.
3. Time-domain analysis of linear regulation processes in physiological systems. Linearized model of breathing mechanics, dynamics of the neuromuscular reflex arc.
4. Frequency-domain analysis of linear regulation processes in physiological systems. Frequency response of circulation control and glycemy control models.
5. Methods of physiological control systems identification, experiments with Starling heart-lungs preparate. Kaov's experiments with crossed circulation, controlled perfusion of brain for central and peripheral chemoreceptors separation, galvanic clamp, pupilar reflex loop opening, rebreathing techniques. Minimal model of glucose control, identification of parameters of breathing regulation.
6. Physiological processes stability testing: analysis of pupilar reflex stability, Cheyne-Stokes breathing model, homeostasis.
7. Optimization problems in biological systems: normal breathing pattern control, aortal pulse wave control, adaptive control of physiological variables- adaptive attenuation of arterial PCO2 fluctuations.
8. Methods of nonlinear analysis of physiological regulation systems - heart arrhythmia modelling, periodic breathing with apnoea. Neuron dynamics models: Hodgkin-Huxley model, Bonhoeffer-van der Pol model.
9. Description of complex dynamics in physiological control systems - spontaneous variability, logistics equation, neutrophile density control, cardiovascular variability model, circadian rhythms model. Sleep apnoea model.
10. Fuzzy modelling use and definition given incomplete information on physiological processes.
11. Modelling of physiological systems and processes by neural networks.
12. A review of models on the cell, organ and system levels. Discussion of its usability.
13. The structure and expandability of an interactive catalogue of biomedical models.
14. Reserve.

Exercises outline:

An addition to regular demonstration of models during seminars each student will be given an individual exercise based on measurements on a biological object, processing of collected data, model design, identification, verification, and interpretation. Real-time mode of models might be required. Progress will be checked three times during the term. A necessary documentation should be submitted and the model should be presented to the fellow students. Exam grade will depend on activity points collected during the term as well as on the results of oral and written exams.


[1] Jang, J.S.R., Sun, C.T., Mizutani E.: Neuro-fuzzy and Soft Computing, 1997. Prentice Hall.
[2] Biomedical Engineering - Handbook,1995, CRC Press, Inc.
[3] Biomedical Modeling and Simulation on PC, Springer - Verlag, New York, 1993.
[4] Murray, J.D.:Mathematical Biology I,II, Spatial Models and Biomedical Applicatios, Springer, 2002, 2003.
[5] Michael C. K. Kho: Physiological Control Systems. Analysis, Simulation and Estimation. IEE Press, New York, 2000, ISBN 0-7803-3408-6.
[6] Hugh R. Wilson: Spikes, Decisions and Actions. Dynamical foundation of neuroscience. Oxford University Press, Oxford, 1999, ISBN 0-19-852430-7.
[7] Frank C. Hoppensteadt, Charles S. Peskin: Modeling and Simulation in Medicine and the Life Sciences. Springer 2000,ISBN 0-387-95072-9.
[8] Robert D. Strum, Donald E. Kirk: Contemporary Linear Systems using Matlab. PWS Publishing Company, Boston, 1999, ISBN: 0-534-94710-7.
[9] Keener,J Sneyd,J: Mathematical Physiology. Springer, New York, Berlin, 1998, ISBN 0-387-98381-3.


No prerequisities.



Simulation, Modelling

Subject is included into these academic programs:

Program Branch Role Recommended semester
MPBIO1 Biomedical Informatics P 3
MPBIO2 Biomedical Engineering P 3

Page updated 8.7.2020 07:51:52, semester: Z,L/2020-1, L/2019-20, Send comments about the content to the Administrators of the Academic Programs Proposal and Realization: I. Halaška (K336), J. Novák (K336)