BIOENG-455 / 4 credits

Teacher: Shillcock Julian Charles

Language: English


Computer modelling is increasingly used to study dynamic phenomena in cell biology. This course shows how to identify common mathematical features in cell biological mechanisms, and become proficient in selecting numerical algorithms to model them and predict their behaviour.



Cell Biology, Soft Matter, Thermodynamics, Self-Assembly, Differential equations, Numerical algorithms, Computer simulations, Dissipative Particle Dynamics, Protein Aggregation, Biomolecular Condensates

Learning Prerequisites

Required courses




Recommended courses


Important concepts to start the course

Students should have a basic knowledge of cellular anatomy, calculus and ordinary differential equations, probability and statistics, mechanics and thermodynamics. They will be required to write short programmes using a programming language of their choice (python, matlab, C, C++, etc) to solve mathematical problems relevant to the topics in the course, and should be familiar with running programmes from the command line (or within matlab or ipython). A laptop or access to a computer on which the student can execute their own programmes is mandatory for this course.


Learning Outcomes

By the end of the course, the student must be able to:

  • Describe selected cellular structures and dynamical mechanisms
  • Choose a numerical technique for simulating models of cellular dynamics
  • Create a programme to solve numerical problems
  • Justify applying a simulation technique to a problem
  • Explore consequences of parameter changes on model results
  • Estimate the accuracy of a numerical routine
  • Explain the common elements in different simulation types
  • Perform a series of DPD simulations of a complex fluid
  • Organize the data produced by a series of simulations

Transversal skills

  • Demonstrate a capacity for creativity.
  • Plan and carry out activities in a way which makes optimal use of available time and other resources.
  • Write a scientific or technical report.

Teaching methods




Journal club

Semester Project

Expected student activities

Attending lectures, completing in-class tests, writing short programmes to solve mathematical models, selecting and working on a simulation-based semester project, presenting a paper in a journal club, writing a scientific report summarising the semester project

Assessment methods

DPD simulation project and report - 50%

2 x Homework exercises on numerical modelling and simulation data management - 15%

3 x in class tests - 30%

Journal club presentation - 5%



Biological Physics, Philip Nelson, W. H. Freeman and Co. New York, USA, 2014

Molecular Biology of the Cell, Bruce Alberts, et al., 2nd ed., Garland Publ. Inc. New York and London, 1989


Ressources en bibliothèque


User Guide to the Dissipative Particle Dynamics simulation code is provided

In the programs

  • Semester: Fall
  • Exam form: During the semester (winter session)
  • Subject examined: Computational cell biology
  • Lecture: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks
  • Semester: Fall
  • Exam form: During the semester (winter session)
  • Subject examined: Computational cell biology
  • Lecture: 2 Hour(s) per week x 14 weeks
  • Exercises: 2 Hour(s) per week x 14 weeks

Reference week

12-13  BC04  
14-15  BC04  

Wednesday, 12h - 14h: Lecture BC04

Wednesday, 14h - 16h: Exercise, TP BC04