(Python skills at the level of) Programming NA
In this course you will learn the physics behind elementary processes in living cells. The stochastic movement of molecules, and how this is used to drive biological reactions, takes a central place.
After an introduction of the physical and biological concepts in the weekly lecture you will make programming excercises to get a better grasp of the statistical physics behind the problem, making use of probability theory, statistics and conbinatorics.
Numerical programing excercises, to be done in experimental class from the hart of this course. By wrtiing a host of Python scripts you'll compute simulations of a number of stochastic and/or biological processes. Together with a partner, who will change on a weekly basis, you will hand in assignments, benefit from each others insights and learn to work in a small team.
Thes topics from biophysics will be discussed:
Contents of the cell
The Stokes-Einstein relation
Fick's law and the diffusion equation
Entropy en free energy
The Boltzmann distribution
After this course, you can employ probability theory, statistics and conbinatorics to quantify a variety of (bio-)physical problems.
You learn to:
use of Python for computations and simulations
to apply simple numerical techniques to physical problems
relate analytical solutions to numerical simulations and critically test these
describe essential parts of the cell
extract statistical parameters from “random walks”
explain the concepts of entropy and frree energy
After this course you can:
Provide constructive feedback on the work of others
independently convert abstract problems to quantitative solutions
critically evaluate the accuracy of experimental results
See timetable in Brightspace
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
The final grade is calculated from: 1+0.6programming assignments+0.3final assignment. The final assignment will be done individually and at home (take home exam).
Available on Brightspace
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. An exemption is the fall semester for 1st year bachelor students, the student administration will enroll this group.
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.
Lecturer: Prof.dr.ir. John van Noort
Your presence at the programming classes is mandatory.