Erik Lindahl

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How many states does this correspond to? 1! How many similar states are there? few How many states does this correspond to? How many similar states are there? 1! lots
Helmholtz & Gibbs • Free energy defines most stable state when system exchanges heat with surrounding environment • F is the Helmholtz Free Energy • Valid at constant volume • At constant pressure we have H=E+pV • Gibbs Free Energy G=H-TS=E+pV-TS • For proteins, pV is typically very small Physics: Usually Helmholtz Chemistry: Usually Gibbs Why?
Page 1: Protein Physics 2012 Lecture 2, Jan
Page 6 and 7: Natural amino acids
Page 9 and 10: α R β α L
Page 11 and 12: Outline today • More on interacti
Page 13 and 14: Semi-Empiric Modeling • Use simpl
Page 15 and 16: Bond stretching • Vibration aroun
Page 17 and 18: Torsions/dihedrals Frequently calle
Page 19 and 20: Nonbonded interactions Packing effe
Page 21 and 22: Lennard-Jones • Simpler form than
Page 23 and 24: Hydrophobic effect
Page 25: The Boltzmann Distribution ⇢ / e
Page 28 and 29: Formulating Boltzmann • Clapeyron
Page 30 and 31: Which shape is best energy-wise? Vo
Page 32 and 33: Free Energy • Use V=exp{ln(V)}
Page 36 and 37: Phase Transitions Explained • Sys
Page 38 and 39: Partitioning • Consider transfer

Erik Lindahl

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