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Biological Physics Candidacy Exam Topics

This list covers many topics in biological physics and the student is not expected to master them all.  The student will agree on relevent topics to be covered in the exam with his/her committee.

Biomolecular Structure: The chemical structures of peptides, nucleic acids, lipids, and saccharides, as well as their basic structural motifs such as bilayers and secondary structures of proteins.

Biomolecular Interactions:  Guoy-Chapman theory, van der Waals interactions, the hydrophobic effect, and hydrogen bonds.  Chemical equilibrium and cooperative effects.

Hydrodynamics:  Reynolds number and the differences between lamellar and turbulent flow. Viscosity and pressure propagation, and the effects of low Reynolds number.

Interfacial Phenomena:  Surface tension, osmotic pressure, line tension, the Gibbs and Langmuir isotherms, and humidity.

Elasticity: Normal and Gaussian curvature, spontaneous curvature, persistence length, polymer elasticity models.

Diffusion:  diffusion equation, random walks.

Fundamental Techniques: Light scattering, X-ray and neutron diffraction, traditional and multiphoton microscopy, sedimentation, absorption spectroscopies, fluorometry, and vibrational spectroscopies.

Specialized Techniques (for experimental students):  Near field optics, scanned probe microscopy, small angle X-ray scattering

Statistical Mechanics (for theory students): Monte Carlo and molecular dynamics methods, random energy models, spin glass systems, GNK model, basic features of the immune system