Simulation of molecular systems for chemistry, materials and biology
Location: CECAM-IT-SIMUL, Politecnico di Milano, Polo Territoriale di Lecco, Lecco, Italy
Organisers
MISSION AND GOALS
Molecular simulation is a family of powerful computational methods which are widely used in materials science and engineering, biophysics, chemistry, chemical engineering, drug design and many other areas. The aim of the course is to provide a critical understanding of these methods and a practical introduction to their use. The course is aimed in particular at graduate students with an engineering background, such as those who are typically pursuing a Ph.D. at the Politecnico di Milano.
SUBJECT AND PROGRAM
The course aims to provide a broad, rather than in-depth, introduction to computational methods which can be used to study the properties and behaviour of molecular systems, emphasizing their possible applications to engineering problems.
Topics: Introduction to quantum mechanical methods for molecules; Calculation of the spectroscopic response of molecular systems; Methods for the study of chemical kinetics; Atomistic force fields; Molecular Dynamics simulations; Monte Carlo methods; Coarse-grained modelling of synthetic and biological systems; Hybrid quantum/classical simulations; First principles molecular dynamics; Sampling of rare events and free energy calculations.
TEACHING ORGANIZATION
The course includes theoretical lectures, seminars on specific applications and computer practicals to illustrate the use of different codes.
The final exam, held on the last day of the course, consists of an oral discussion on selected scientific papers (journal club).
LINK TO THE OFFICIAL COURSE PAGE AT THE POLITECNICO DI MILANO
DETAILED PROGRAM
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Mon. 10/6 |
Tue. 11/6 |
Wed. 12/6 |
Thu. 13/6 |
Fri. 14/6 |
9:00 – 10:30 |
Famulari |
Milani |
Ganazzoli & Raffaini |
Maestri |
Spare time for self-study |
11:00 – 12:30 |
Tommasini |
Cavallotti |
Raos |
Gautieri |
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14:00 – 17:00 |
QM1 practical |
QM2 practical |
MD1 practical |
MD2 practical |
Exam (Journal Club) |
17:30 – 18:15 |
Seminar 1 |
Seminar 2 |
Seminar 3 |
Seminar 4 |
Topics of lectures and seminars.
Antonino Famulari. Quantum Chemistry 1. Introduction of Born-Oppenheimer and the clamped nuclei Hamiltonian. The potential energy surface and its characterization: minimization and transition state search. Electronic wavefunctions and the independent particle model: spin, antisymmetry, Slater determinants. The Hartree-Fock method and atomic basis sets (LCAO). Ab initio and semiempirical methods.
Matteo Tommasini. Quantum Chemistry 2. Introduction to electron correlation: configuration interaction and excited states. The electron density and its interpretation: dipole moments, molecular electrostatic potential, atomic charges. Introduction to Density Functional Theory: Hohenberg & Kohn theorem and Kohn-Sham method. Extensions to open shell systems. Chemical reactions and the bond-breaking problem.
Alberto Milani. Molecular spectroscopy. Introduction to molecular spectroscopies and observables. Quantum chemical calculation of spectroscopic properties: in-depth discussion of IR and Raman vibrational spectra, elements of molecular excited states and UV-VIS spectra.
Carlo Cavallotti. Chemical Kinetics. Conventional and variational transition state theory (TST); quantum chemical determination of TST parameters in the rigid rotor harmonic oscillator (RRHO) approximation; multi well reactions; beyond the RRHO approximation: hindered rotors and anharmonicities; RRKM/Master equation theory and its numerical solution.
Fabio Ganazzoli & Giuseppina Raffaini. Atomistic force fields. Introduction to molecular simulation and force fields. Intra- and inter-molecular potential energy: force fields for atomistic molecular models. Bond stretching, bending, torsional potentials, etc. Harmonic and anharmonic intramolecular potentials, coupling terms. Inter-molecular potential energy: Coulombic and Lennard-Jones potentials. Force fields parametrization. An example of application.
Guido Raos. Molecular Dynamics. Aims of MD simulations. Algorithms for integration of MD equations. Constraints in simulations. Periodic boundary conditions. Neighbour lists. Treatment of long-range interactions. MD in various ensembles: thermostats and barostats. Observables from MD simulations: correlation functions.
Matteo Maestri. Ab initio MD simulations. Motivation for ab initio MD. Density functional theory for periodic systems: Bloch theorem, plane-wave basis sets. Integration methods: the Car-Parrinello algorithm. Application examples: materials, surfaces and catalysis.
Alfonso Gautieri. Advanced MD methods. Structure and molecular dynamics simulations of biomolecules. Advanced sampling: binding and free energy calculations, metadynamics, accelerated molecular dynamics, replica exchange molecular dynamics, coarse-grained modelling. Biomolecular engineering: protein folding, rational protein engineering, de novo protein structure prediction and design.
Seminar 1: Alessandro Genoni (CNRS & University of Lorraine, France). “Quantum crystallography and its application to macromolecules”
Seminar 2: Gianpietro Moras (Fraunhofer Institute for Mechanics of Materials IWM, Freiburg, Germany). “Friction, wear and lubrication: atomic-scale insights from computer simulation”
Seminar 3: Lynn Kamerlin (Uppsala University, Sweden). “Using Valence Bond Theory to Model (Bio)Chemical Reactivity”
Seminar 4: Matteo Salavalaglio (University College London, UK). “Rare events kinetics from biased sampling”
Topics of practicals
- QM1 and QM2: use of a quantum chemical program to determine geometries and properties of simple molecules, locate transition states and determine reaction rates (supervised by Famulari, Tommasini and Cavallotti).
- MD1 and MD2: use of a molecular dynamics program to simulate a simple protein and analyze the trajectory (supervised by Mosè Casalegno and Alfonso Gautieri).
References
Guido Raos (Politecnico di Milano) - Organiser