Biomolecular simulations in the exascale era
Prerequisiti
Basics in Thermodynamics, Statistical Mechanics, Programming languages (required)
Basics in molecular simulation (suggested)
The course is for PhD students in Chemistry, Condensed Matter Physics, Biology and can also be followed by Master students in chemistry, physics, biology
Programma
- Introduction to molecular dynamics simulations: scopes, foundations, applications
- Structure of biomolecules. Structural databases. Alpha fold.
- Dynamics of biomolecules. Kinetic modeling and analysis.
- Biomolecular simulation: Recall of statistical mechanics/Ergodic hypothesis, Periodic boundary conditions, Long-/short-range interactions, Force fields, Thermostat and barostat algorithms, Applications to biomedicine.
- Biomolecular-based Drug design: Ligand and protein flexibility, Effect of mutations, ligand binding Free-energy predictions.
- Proteins: primary, secondary, tertiary and quaternary structures. Physics basis of the Ramahcandran Plot.
- Soluble proteins. Protein folds. Hydrophobic effect. Intrinsically disordered proteins.
- Membrane proteins and protein-ligand interactions.
- Physical basis of protein function: from enzymatic catalysis to receptor activation
- Nucleic acids.
- Computational training and exercises on molecular visualization and molecular docking
Obiettivi formativi
* Visualizing and analyzing the structural determinants of biomolecules
* Learn biomolecular simulations methods to predict poses and affinities of drugs binding to their target proteins