W. C. K. Poon, D. Andelman

INTRODUCTION: Coarse graining in biological soft matter The atomistic description of globular proteins: the tertiary structure Coarse-graining : level 1 Secondary structure; Coarse-graining : level 2 Domains Coarse-graining : level 3 Proteins as colloids Further coarse-graining I. SOFT MATTER BACKGROUND Introduction to colloidal systems Colloidal phase behaviour; Colloid dynamics The physics of floppy polymers Statistical physics of single chains Statistical physics of many chains Polymer dynamics Self-assembly and properties of lipid membranes The constituents of lipid bilayer membranes Self assembly Bilayer membrane phases Membrane energies Fluctuations Domains, shapes and other current issues Some aspects of membrane elasticity Gibbs' description Description in terms of microscopic properties Equations of equilibrium and shape of interfaces Introduction to electrostatics in soft and biological matter The Poisson-Boltzmann theory Poisson-Boltzmann equation: planar geometry; Poisson-Boltzmann equation: cylindrical coordinates; Poisson-Boltzmann equation: spherical coordinates -- Charged colloids Beyond the Poisson-Boltzmann treatment Thermal Barrier Hopping in Biological Physics A preliminary: Diffusion on a flat landscape First passage times: an exact result Landscapes and intermediate states Higher-dimensional barrier crossing II. BIOLOGICAL APPLICATIONS Elasticity and dynamics of cytoskeletal filaments and their networks Single-filament properties Solutions of semi-flexible polymer Network elasticity Nonlinear response Twisting and stretching DNA: Single-molecule studies Micromanipulation techniques Stretching DNA DNA under torsion DNA-protein interactions Interactions and conformational fluctuations in DNA arrays Electrostatic interactions Equation of state: No thermal fluctuations; Effect of thermal fluctuations (1) Effect of thermal fluctuations (2) Sequence-structure relationships in proteins Energy functions for fold recognition The evolutionary capacity of