Instructor: Georgios Archontis
Theoretical topics: Elements of protein and nucleic acid structure. Intra- and intermolecular interactions in biomolecular systems. Thermodynamics of biomolecular systems. The effect of solvent on the thermodynamic stability of biopolymers. Implicit solvent models (from liquid state theory and continuum electrostatics). Statistical mechanical theories of protein stability and folding.
Computational topics: Hamiltonians employed in atomic-detail simulations of biomolecules. Molecular Dynamics (MD) simulations. Basic concepts (MD algorithms; MD in various ensembles; Langevin dynamics). MD simulation methods for the efficient sampling of biomolecular phase space. Monte Carlo (MC) simulations; General methodology. MC simulation methods for the efficient sampling of biomolecular phase space. Protein folding simulations in implicit and explicit solvent. Free-energy calculations in biomolecular systems. Theory and implementation.
Computational applications: This part is carried out as a set of computational exercises, utilizing specialized software (e.g., CHARMM, UHBD). Energy minimization methods and determination of normal modes of vibration in biomolecular systems. MD simulations in vacuum; Heating, equilibration and production stages. MD simulations with implicit solvent models. MD simulations in explicit solvent; periodic boundary conditions; stochastic boundary conditions. Principal Component Analysis of MD trajectories. Free-Energy Perturbation calculations; application in biomolecular systems. Determination of the electrostatic field of a solvated biomolecule by finite-difference solution of the Poisson-Boltzmann equation.
Assesment: Project and/or final exam