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Physics and chemistry for biodynamic modeling


Admission requirements

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


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.

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.


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.

You will find the timetables for all courses and degree programmes of Leiden University in the tool MyTimetable (login). Any teaching activities that you have sucessfully registered for in MyStudyMap will automatically be displayed in MyTimeTable. Any timetables that you add manually, will be saved and automatically displayed the next time you sign in.

MyTimetable allows you to integrate your timetable with your calendar apps such as Outlook, Google Calendar, Apple Calendar and other calendar apps on your smartphone. Any timetable changes will be automatically synced with your calendar. If you wish, you can also receive an email notification of the change. You can turn notifications on in ‘Settings’ (after login).

For more information, watch the video or go the the 'help-page' in MyTimetable. Please note: Joint Degree students Leiden/Delft have to merge their two different timetables into one. This video explains how to do this.

Mode of instruction

Lectures and exercise sessions.

Assessment method

The final grade is computed as the weighted average of the result for a computer simulation practical (20%), and the result of the written exam (80%). The result of the written retake exam replaces that of the written exam (80%) only (best result counts).

Reading list

Will be announced.


From the academic year 2022-2023 on every student has to register for courses with the new enrollment tool MyStudyMap. There are two registration periods per year: registration for the fall semester opens in July and registration for the spring semester opens in December. Please see this page for more information. Exemptions are minor students and fall semester for 1st year bachelor students: the student administration will enroll these groups for courses.

Please note that it is compulsory to both preregister and confirm your participation for every exam and retake. Not being registered for a course means that you are not allowed to participate in the final exam of the course. Confirming your exam participation is possible until ten days before the exam.

Extensive FAQ's on MyStudymap can be found here.

Exchange and Study Abroad students: please see the Prospective students website for information on the application procedure.


Course coordinator: Dr. S.C. Hille



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