Biophysics

Introduction and key points

Mechanical forces

• Combinations of mechanical elements: Underdamped, overdamped and critically damped motion
• The molecular basis of elasticity, viscosity and viscoelastic models
• Flexural rigidity and the beam equation: Bending and buckling
• Dynamics of bending and buckling
• Obtaining probability of pore forming in membranes via nanomechanical analysis

Thermal forces

• Boltzmann law, diffusion, Fokker Planck and Einstein equations
• Reactiondiffusion equation
• Fluctuationdissipation theorem
• Jarzynsky equatlity
• Thermal fluctuations in membranes: Power spectral density of passive vs active membranes
• Thermal bending of filaments: persistence length, freely joint chain, wormlike chain

Chemical forces

• Chemical equilibria and effect of external force
• Rate theories of chemical reactions
• Effect of force on chemical rate constants
• Biomolecular reactions (Kramers equation, MichaelisMenten)
• Cycle reactions and free energy transduction

Biological polymers

• Nucleid acids and conformations: DNA and ARN
• Proteins
• Protein folding 

Biological membranes

• Membrane structure
• Self-assembly and phase behavior
• Membrane mechanics
• Membrane fluctuations and active membranes
• Action potential: Hodgkin Huxley vs Heimburg and Jackson models

Information processing in biology

• From single neuron dynamics to neural computation
• The Hopfield Models

• Equilibrium: adhesion-free energies; physical selectivity; limitations to the equilibrium approach
• Host-guest dynamics: detachment times; stickiness of multivalent interactions; motility induced by catalytic activity

Experimental techniques in Biophysics

Understand the interactions within biological building blocks

- Be familiar with the structure, mechanical properties and phase behavior of biopolymers (nucleic acids and proteins), lipid membranes

- Use statistical mechanics to understand thermodynamic potentials and how biological processes can be described by their minimization. Understand the notion of detailed balance and why life operates far-from equilibrium

- Define reaction coordinates and calculate rates of reactions along these

coordinates. Be familiar with Michaelis-Menten enzyme kinetics

- Understand the importance of transport properties (diffusion, viscosity, etc)

and their role in biological processes

- Apply the fundamental physical principles to understand how they govern the

function of important biological phenomena such as nerve pulse propagation,

bacterial adhesion membrane deformation and gene regulation

- Slides
- Support books
- Exercises 
- Visual experiments

Références, bibliographie et lectures recommandées

Glaser, R. (2012). Biophysics: An Introduction (2nd English ed.). Springer Berlin Heidelberg.

Cotterill, R. M. J. (2002). Biophysics: An Introduction. John Wiley & Sons. ISBN: 978-0-471-48538-4

Howard, J. (2001). Mechanics of Motor Proteins and the Cytoskeleton. Sinauer Associates. ISBN: 0-87893-334-4

Phillips, R., Kondev, J., Theriot, J., & Garcia, H. (2012). Physical Biology of the Cell (2nd ed.). Garland Science. https://doi.org/10.1201/9781134111589

Heimburg, T. (2007). Thermal Biophysics of Membranes. Wiley-VCH Verlag GmbH & Co. KGaA. https://doi.org/10.1002/9783527611591

Hertz, J. A., Krogh, A., & Palmer, R. G. (1991). Introduction to the Theory of Neural Computation (1st ed.). CRC Press. https://doi.org/10.1201/9780429499661

Campus

Plaine

Méthode(s) d'évaluation

• Examen oral

Examen oral

• Examen avec préparation

• Question ouverte à développement long
• Question ouverte à réponse courte
• Question visuelle

Langue(s) d'évaluation

• anglais
• (éventuellement français )