Topic 1 Introduction: physical units, molecules and biological systems
Topic 2 Basic concepts in thermodynamics and statistical physics
- Thermodynamics: energy, work, constraints and entropy, free energy. Osmotic pressure, Second Law and stability.
- Distributions and their meanings (Poisson, Gaussian, Binomial). Entropy and density of states, thermal unit. Ideal gas, fluctuations, Bolzmann distribution, free energy.
- Biological applications: many body systems, membranes, ionic gradients, permeability. Ionic gradients, Electro motrix force. Ionic gradients. Ligand-receptor statistics, two system state.
Topic 3 Diffusion and transport
- Macroscopic view: conservation equations, Onsager relations (affinities). Mass flow, advection and diffusion. Friction (Stokes), Einstein relation. Diffusion and chemical potential.
- Microscopic view: Brownian motion. Langevin dynamics.
- Applications in biology. Active and passive transport. Kinetic equations. Turing patterns, activator-repressor dynamics.
Topic 4 Molecular interactions and forces
- Forces of quantum origin: dispersion (van der Waals), hydrogen bond, ionic and covalent bonds. Relevance of hydrogen bond in biology. Energetic bonds: ATP, NADH, etc.
- Entropic forces: Entropic spring, depletion, solvation, hydrophobic forces. Entropic forces in crowded systems (proteins). Electrostatic forces (Debye lenght, Nernst equation, Poisson-Boltzmann equation).
- Applications: membrane potential, ionic channels. Patch clamp. Transmission of electric impulse in neurons.
Topic 5 Polymers
- Types of polymers: analogies with Brownian motion, entropic spring, excluded volume, globular polymers. Diffusion and relaxation times.
- Flexibility. Worm-like chain model. Bending energy. Free energy of proteins and stability. Role of hydrophobic forces in proteins. DNA origami.
Topic 6 Membranes
- Types of lipids and their effect in the membrane structure. Model systems.
- Membrane elasticity: stretching, bending. Morphologies.
- Experiments to study the mechanical properties of membranes: micropipette aspiration, optic tweezers, fluctuations.
Topic 7 Hydrodynamics
- Navier Stokes equation: stress, viscosity and inertia. Non-dimensional numbers: Peclet and Reynolds
- Applications: Swimming at different Reynolds numbers. Flying with different mass. Purcell. A brief revew of microfluidics.
Topic 8 Molecular motors
- Citoskeleton proteins (strucure and dynamics) ATP-ase. Experimental techniques.
- Probabilistic description of molecular engines.
Topic 9 Energy transduction in living systems
- Cellular respiration. Photosyntesis (quantum description). Hydrogenases. Applications in nanotechnology.
Topic 10 Self-assembly
- Some seminars including some of the following subjects. Entropy production as creator of order (dissipative structures) bio: actine microtubules (creation and destruction). Active soft matter. Nano-structured inorganic systems.
- Howard Reiss, Methods of Thermodynamics, Dover
- Rob Phillips, Jane Kondev, Julie Theriot, Physical Biology of the Cell, Second Edition, Garland Science, 2008 . (http://microsite.garlandscience.com/pboc2/)
- J. Israelachvili, Intermolecular and Surface Forces (Academic Press, London, 1992)
- D. Boal, Mechanics of the Cell (Cambridge University Press, 2002)
- M. Daune, Molecular Biophysics (Oxford University Press, 2006)
- R. A. L. Jones, Soft Condensed Matter (Oxford Master Series in Physics, 2002)
Coordinator Rafael Delgado Buscalioni
More info on the course official guide (Guía docente)