87995 - Physical Methods of Biology

Learning outcomes

The course will focus on the physical laws that underlie life. At the end of the course the student will acquire a broad understanding of the relation between physics, chemistry, and biology. They will be able to use theoretical and computational methods to predict properties of biomolecules and advanced experimental methods currently available to investigate the relation between genotype and phenotype.

Course contents

The content of the course differs from previous years. Emanuele Paci will focus on the physical principle behind the emergent biological properties of biomolecules and computational and experimental methods to characterize them.

1) Introduction: biology, chemistry and physics; top-down and bottom-up approaches; fundamental physics laws and emergent biological properties; time and length scales.

2) Biological molecules: proteins, DNA, RNA, lipids and their environment.

3) Intramolecular and intermolecular interactions

4) Thermodynamics and statistical mechanics of chemical interactions and biopolymers; chemical and biomolecular kinetics;

5) Atomistic simulation as a computational microscope; molecular dynamics and Monte Carlo simulation; estimation of thermodynamic and kinetic properties; free energy methods.

6) Protein folding; physics-based and knowledge-based methods for protein structure prediction.

7) Experimental biophysics, with a focus on methods to investigate structure and dynamics of proteins (x-ray diffraction; NMR; cryo-EM; SMFS; FRET)

8) Stochastic processes (master equation, Markov processes)

9) Systems biology (law of mass action; Michaelis-Menten equation; Lotke-Volterra equation; Allee effect; toggle-switch model)

Readings/Bibliography

• Van Kampen, Stochastic Processes in Physics and Chemistry, Elsevier 2011
• Frenkel & Smit, Understanding Molecular Simulation, Academic Press 2002
• Nelson, Biological Physics. Energy, Information, Life., Freeman 2008
• Zuckerman, Statistical Physics of Biomolecules: an Introduction, CRC Press, 2010
• Finkelstein & Ptitsyn, Protein Physics, Academic Press, 2002
• Bialek, Biophysics: Searching for Principles, Princeton University Press, 2012
• Leach, Molecular Modelling: Principles and Applications, Pearson 2001
• Zaccai, Serdyuk & Zaccai, Methods in Molecular Biophysics, Cambridge University Press, 2017

Teaching methods

Lectures, tutorials, seminars

Assessment methods

Project-based oral exam.

Teaching tools

Access to computers and virtual reality suite for students choosing specific projects.

Office hours

See the website of Emanuele Paci