Prospectus

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Physics and chemistry for biodynamic modeling

Course
2019-2020

Admission requirements

This course is open to all students that have been admitted to the minor ‘Quantitative Biology’.

Contact information

Course coordinator: Dr. S.C. Hille
Email: shille@math.leidenuniv.nl

Description

Physical underpinning of a dynamical mathematical model is essential if the model is used to interpret experimental data of the modeled biological process. In the course the fundamental physics of transport processes like diffusion, osmosis and membrane transport (e.g. facilitated diffusion) are discussed, for example notion of ‘typical time scale’ or ‘typical space scale’ for processes. Thermodynamic aspects of these processes will be touched. Also in relation to the modeling of enzyme-catalyzed chemical reactions (Principle of Detailed Balance). The validity of Mass Action Kinetics and of effective rate expressions is discussed. The electrical activity of cells, due to ion transport over membranes, is considered.

Learning goals

Course objectives:
The students learn the basic concepts from physics that are necessary to understand transport processes and mechanical properties of biological systems. They will get to know and understand the physical assumptions that are made (often implicitly) in modeling decisions, in particular when choices are made for specific functions to represent dependences between variables in the model.

Final qualifications:
• Ability to see the (implicit) physical assumptions that underlie particular mathematical expressions in models
• Ability to assess the validity of effective approximations (e.g. in rate kinetics).
• Understanding of physics of the basic cellular transport processes and their characteristic properties.

Time table

The time table is provisional and provided times are indicative. A detailed final schedule will become available before the start of the minor. It is foreseen that the course runs intensively from the third week of September, until week 9 of the semester. In week 5 a break is foreseen, because of exams for the courses ‘Elementary practical biology and methods for non-biologists’ and ‘Elementary practical mathematics for non-mathematicians’. The course ends with an exam in week 10.

Mode of instruction

Lectures and exercise sessions.

Assessment method

a) Assignments (20%)
b) Written exam (80%)

Blackboard

Blackboard will be used for communication and provision of course material.

Literature

Will be announced.

Registration

Via Usis. Enroll also for the course in Blackboard.
Exchange and Study Abroad students: please see the Prospective students website for information on the application procedure.