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
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
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 registering on time, i.e. 14 days before the start of the course. This can be done via Mystudymap. You do this twice a year: once for the courses you want to take in semester 1 and once for the courses you want to take in semester 2. Please note: late registration is not possible.
Registration for courses in the first semester is possible from July; registration for courses in the second semester is possible from December. First-year bachelor students are registered for semester 1 by the faculty student administration; they do not have to do this themselves. For more information, see this page
In addition, it is mandatory for all students, including first-year bachelor students, to register for exams. This can be done up to and including 10 calendar days prior to the exam or up to five calendar days in case of a retake exam. You cannot participate in the exam or retake without a valid registration in My Studymap.
Contact
Lecturer: Prof.dr.ir. John van Noort
Remarks
Your presence at the programming classes is mandatory.