Physical Foundations

Period: First        ECTS: 6


Course contents

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.


Bibliography

  • 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)


Faculty

Coordinator  Rafael Delgado Buscalioni
Email  rafael.delgado@uam.es
Website  http://dep.ftmc.uam.es/members/name/rafael-delgado-buscalioni/


More info on the course official guide (Guía docente)