Coursebooks 2018-2019

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Computational cell biology

BIOENG-455

Lecturer(s) :

Shillcock Julian Charles

Language:

English

Summary

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.

Content

 

 

 

 

 

 

 

 

 

 



 

Keywords

Cell Biology, Soft Matter, Thermodynamics, Self-Assembly, Differential equations, Numerical algorithms, Computer simulations, Dissipative Particle Dynamics, Diffusion, Langevin equation

 

 

Learning Prerequisites

Required courses

Phys-101

Math-106

Bio-205

Recommended courses

CS-111

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:

Transversal skills

Teaching methods

Lectures

Exercises

Tests

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, writing a scientific report summarising the semester project

Assessment methods

DPD simulation project and report - 50%

Numerical modelling of chosen cellular functions - 25%

5 x class tests - 25%

Resources

Bibliography

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

 

In the programs

Reference week

 MoTuWeThFr
8-9     
9-10     
10-11     
11-12     
12-13  BC04  
13-14    
14-15  BC04  
15-16    
16-17     
17-18     
18-19     
19-20     
20-21     
21-22     
 
      Lecture
      Exercise, TP
      Project, other

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  • Autumn semester
  • Winter sessions
  • Spring semester
  • Summer sessions
  • Lecture in French
  • Lecture in English
  • Lecture in German