Computational cell biology

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

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Keywords

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

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.  A Dissipative Paricle Dynamics simulation code is provided (https://github.com/Osprey-DPD/osprey-dpd), which forms the basis of the project, and students should be familiar with running programmes from the command line. 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

Lectures

Exercises

Tests

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 / simulations - 15%

3 x in class / take home tests - 30%

Journal club presentation - 5%

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

 

Ressources en bibliothèque

• Biological Physics, Philip Nelson
• Molecular Biology of the Cell, Bruce Alberts,

Notes/Handbook

User Guide to the Dissipative Particle Dynamics simulation code is provided

Moodle Link

• https://go.epfl.ch/BIOENG-455