Admission requirements
(Python skills at the level of) Programming NA
Description
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
Brownsian movement
The Stokes-Einstein relation
Fick's law and the diffusion equation
Entropy en free energy
The Boltzmann distribution
Course Objectives
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
Transferable Skills
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
Timetable
See timetable in Brightspace
In MyTimetable, you can find all course and programme schedules, allowing you to create your personal timetable. Activities for which you have enrolled via MyStudyMap will automatically appear in your timetable.
Additionally, you can easily link MyTimetable to a calendar app on your phone, and schedule changes will be automatically updated in your calendar. You can also choose to receive email notifications about schedule changes. You can enable notifications in Settings after logging in.
Questions? Watch the video, read the instructions, or contact the ISSC helpdesk.
Note: Joint Degree students from Leiden/Delft need to combine information from both the Leiden and Delft MyTimetables to see a complete schedule. This video explains how to do it.
Mode of Instruction
See Brightspace
Assessment method
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).
Reading list
Available on Brightspace
Registration
As a student, you are responsible for enrolling on time through MyStudyMap.
In this short video, you can see step-by-step how to enrol for courses in MyStudyMap.
Extensive information about the operation of MyStudyMap can be found here.
There are two enrolment periods per year:
Enrolment for the fall opens in July
Enrolment for the spring opens in December
See this page for more information about deadlines and enrolling for courses and exams.
Note:
It is mandatory to enrol for all activities of a course that you are going to follow.
Your enrolment is only complete when you submit your course planning in the ‘Ready for enrolment’ tab by clicking ‘Send’.
Not being enrolled for an exam/resit means that you are not allowed to participate in the exam/resit.
Contact
Lecturer: Prof.dr.ir. John van Noort
Remarks
Your presence at the programming classes is mandatory.
Software
Starting from the 2024/2025 academic year, the Faculty of Science will use the software distribution platform Academic Software. Through this platform, you can access the software needed for specific courses in your studies. For some software, your laptop must meet certain system requirements, which will be specified with the software. It is important to install the software before the start of the course. More information about the laptop requirements can be found on the student website.