Admission requirements
This course is open to all students that have been admitted to the minor ‘Quantitative Biology’. Students have to select either this course or the course ‘Elementary practical biology and methods for non-biologists’, depending on their background. Please consult the course or minor coordinator when there is uncertainty about which course is the most appropriate.
Description
In the course the students will become acquainted with mathematical concepts and methods involved in the modeling of dynamical processes in terms of ordinary differential equations (ODEs). These type of equations have been used successfully in various branches of Science, after their invention by Isaac Newton. The modeling approach will be explained by means of application motivated examples: e.g. from chemical reaction networks, electrophysiology, membrane transport. It is discussed what is the meaning of solving such equations. The concept of ‘state’ of the modeled system is introduced. Typically, a model in terms of ODEs cannot be solved explicitly, i.e. there does not exist an easy functional expression that describes the state of the system at any point of time. Instead, the students will be introduced to the technique of ‘phase plane analysis’: a graphical method that allows one to gain insight into the dynamics represented by the model. It is particularly handy in analyzing models when no explicit solution is available. Basic concepts like steady state, stability of steady states and periodic solutions are introduced. The freely available software tool for phase plane analysis, XPPAUT by Bart Ermentrout, will be demonstrated by which one can examine moderately complicated mathematical models.
Course objectives
Students with a Life Science background will learn fundamental concepts and methods from mathematics needed in other courses in the minor to enable effective communication with mathematicians. They will get acquainted with the type of research questions considered in applied mathematics, in particular within the context of analysis of dynamic mathematical models using ordinary differential equations. Attention is given to interpreting the mathematical expressions in a model as representing particular physical, chemical or biological processes. Moreover, in exercise sessions the students will increase their practical skills in manipulating with mathematical expressions and work with various concepts. The use of particular software tools in the analysis of models will be demonstrated and examined in exercise sessions.
Final qualifications:
Ability to effectively communicate about mathematical models.
Ability to interpret mathematical models in terms of underlying processes.
Skilled in manipulating with a selection of types of mathematical expressions and concepts.
Ability to analyze basic mathematical models, combining explicit elementary computations with the use of software tools for more complicated problems.
Understanding what type of information can be obtained from mathematical analysis and simulation of the discussed types of mathematical models.
Timetable
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 he course starts intensively in the first two weeks of September, then less intensively in the next two weeks. In week 5 the course is closed by a written exam.
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. Instruction in the use of computational software tools is provided.
Assessment method
Written exam (100%). The retake is also a written exam.
Reading list
Will be announced.
Registration
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.
Contact
Course coordinator: Dr. S.C. Hille
Email: shille@math.leidenuniv.nl
Remarks
Brightspace will be used for communication and provision of course material.