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This course explores the physical principles of life at the molecular and cellular level, with some examples up to multicellular. It examines how these principles shape the behaviour of cells, enabling them to sense and react to their environment as they grow and divide. The course aims to demonstrate how a description of living systems in terms of complex physical systems complements the traditional experimental investigations of biologists, and can ultimately reveal a deep understanding of the design principles of life.
The course begins with an overview of quantitative cell biology including a lecture aimed at connecting cell biology to background physical knowledge, and a primer on networks [module A]. This is followed by an examination of how populations grow and evolve [module B].
Neurons play a key role in higher organisms, and we discuss the basics of neural transport which underpin aspects of vision, hearing and information processing [module C].
From there, we turn to the study of the cell as a crowded and disordered environment and explore the effects of this environment on physical models of cellular processes. This leads on to lectures on the cytoskeletal assembly and molecular motors with an emphasis on statistical approaches to modeling dynamical processes within cells [module D].
A quantitative insight into how organisms differentiate spatially for example to form specific organs, or more simply to acquire stripes, comes from reaction-diffusion models [module E].
Regulating protein production is a key aspect of how a cell functions; this is looked at first at the level of modeling the reaction with stochastic equations, and then to describe quantitatively activation and repression of gene expression in terms of stat mech models [module F]. These come together in a "dynamical systems" description of regulatory networks to understand transcriptional decisions such as switches and oscillatory behaviour [module G].
During the course there will be four guest lectures connecting aspects of the course to active research in Cambridge.
The
Part II thermal and statistical physics (or equivalent) course is a
requirement, and exposure to material from Part II Soft Condensed Matter (or
equivalent) will be very beneficial.
The physical characteristics of living matter;
Examples and roles of thermal fluctuations and stochastic processes in biological systems;
The use of physical concepts and laws to model biological systems;
Quantitative and physically based models, and their analysis;
The biological significance and key features of the model systems introduced;
Modern
experimental techniques for quantitative studies at single cell resolution.
"Physical Biology of the cell (2nd Edition)", Phillips, Kondev, Theriot and Garcia
"Physical Models of Living Systems", Freeman Press, Philip Nelson
"Models of Life", CUP (available online through http://www.lib.cam.ac.uk/), Sneppen
"An Introduction to Systems Biology (2nd Edition)", Chapman and Hall, Uri Alon
"Molecular Biology of the Cell", Garland Science, Alberts et al. (cell biology reference textbook)
"Biological Physics", Freeman Press, Philip Nelson
“Mathematical
population genetics: Theoretical introduction”, Springer, Warren Ewens
These lecture notes are made available here as PDF files. They will be online in their final form after the end of each course module.
Module A (updated on 6/10/23)
Module
B (updated
on 13/10/23)
Module
C (updated
on 13/11/23)
Module
D (updated
on 13/11/23)
1. Motors Notes
Module
E (updated
on 13/11/23)
Module
F/G (updated
on 13/11/23)
The question sheet will be covered in 3 supervisions. Please, put your name down for all time-slots you would be available. Note: there are multiple sheets, check them all! Use your cam google account to edit the document (not your personal gmail). Solutions and Jupiter notebook are courtesy of Tom Parton. Please, put down your crsid in the sign-up sheet so that we can assign students to supervisors (there are three sheets there! Check them all!)
Supervision 1: week of 23/10. Solutions Jupyter notebook
Supervision 2: week of 13/11. Solutions and notebook
Supervision 3: week of 27/11 Solutions and notebook
Answers to parts of the QS will be posted a couple of days before each supervision.
To
post questions about lectures or problems, or to report any typo you might
find, please sign up to the course Slack (please, use your cam email).
These are added in the directories you will see visible here. You can find the scripts discussed in lectures in the corresponding folder, and scripts/files related to question sheet material in those folders.
Fascinating description of the early days discovering the genetic machineries.
Concise 2 page overview on cell size control; many references, and it's an open question.
Huxley Hodgkin short letter to Nature showing recording of action potential.
Hopfield seminar paper for neuroscience, in Science 1986 .
Movie of voltage clamping to measure action potential.
Key paper on intrinsic and extrinsic noise, with bacteria experiments.
Nice paper with data on measuring production of single proteins.
Berg
and Purcell important paper on distribution of receptors on cell membrane.
This course is only in its fifth year; as well as the January 2016-2021 exam papers, it may be useful to you to see one more example of question structure, and how we try to balance between coursework and quantitative problems. Obviously, this is just intended to help, and there is no guarantee on how similar or dissimilar the actual exam will be, since it is officially not actually set by the course lecturers. We are providing a file with just the questions, and another file including solutions.
1. Mock exam
2. Solutions
A database of useful biological numbers.
NEW!!! Great introductory lecture to biological physics by Rob Phillips
Biological and Soft Systems Sector | Cavendish Laboratory | University of Cambridge
Maintained by webmaster
File last modified Sept 27 2020