Model polymers: entropy and conformation. Model of a random (Gaussian) chain, persistence length, Kuhn renormalization, statistics of conformations and gyration radius, entropic elasticity of polymers. Biological polymers: composition and 3D structure. Polysaccharides, lipids, RNA and DNA. Structure and geometry of DNA (physics and chemistry of double helix), RNA vs. DNA. Proteins, chemistry and geometry of peptide bonding, Ramachandran plots, secondary protein structure, alpha-helix and beta-sheets, supersecondary and tertiary structure of proteins, introduction to molecular visualization, determination of protein structure by X-ray methods and phase problem. Elements of thermodynamics of pure systems, mixtures and solutions. A quick overview of thermodynamics with emphasis on the biological systems, thermodynamical potentials, potential minima and the structure of multiphase systems, chemical potentials, partition function of the liquid in the cell model, mixing of ideal gases and liquids, chemical balance and reaction constant. Selected applications of thermodynamics in biological systems. Elementary theory of self-assembly / polymerization / micellization, Michaelis-Menten model of ligand adsorption, helix-coil transition, zip model, Zimm-Bragg model. Physical interactions in biological systems. Ionization of aminoacids and pK factor. Electrostatics in solution, Poisson-Boltzmann (PB) and Debye-Huckel (DH) equations. Electrostatic potentials and electrostatic free energy. Solution of DH equations in simple geometries, introduction to electrostatics of viruses, electrostatic interactions and protein conformations, physics of hydrogen bonding, hydrophobic interactions, van der Waals interactions and DLVO model. Biophysics of cells. Transport processes in cells. Cytoskeleton. Structure, mechanics and dynamics of the of actins, microtubules and intermediate filaments. Force generation by polymerization and depolymerization of macromolecules as building blocks of the cell. Molecular motors: myosin, kinesin and dynein. Mechanochemical coupling of molecular motors and their processivity. Rotary motors. Ion chanells as nonlinear oscillators.
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