Quantum Chemistry (Petr Nachtigall) Introduction to Quantum Chemistry and Correlation Energy
- Basic approximations used for solving more-electrons stationary Schrodinger equation
- approximations concerning Hamiltonian, approximations concerning wavefunction
- Born-Oppenheimer approximation, perturbation theory, variational principle, MO LCAO approximation, independent electrons model
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Hierarchy of quantum chemistry methods
- ab initio methods, semi-empirical methods, empirical methods
Correlation Energy (Petr Nachtigall)
- Hartree-Fock method
- HF equations for two--electron system, coulombic and exchange integral, SCF equations
- Closed- and open-shell systems, Hartree-Fock-Roothan equation
- Basis for MO-LCAO expansion
- Hartree-Fock limit, correlation energy definition, Koopman's and Brillouin theorem
- Post Hartree-Fock methods
- Configuration interaction method, Moller-Plesset perturbation theory method, coupled-cluster method
Unix for beginners (Daniel Svozil) Linux for Beginners Basic Linux Commands
- Introduction to the system
- Filesystem and basic commands (tree hierarchy, file and directory related commands), Midnight Commander
- Text files commands (more, grep, tail, cat)
- Text editing with mcedit
Vibrational Dynamics (Ota Bludsky) Molecular Symmetry Rotational and vibrational Molecular Spectra
- Molecular symmetry and spectroscopy
- Introduction to group theory, molecular Hamiltonian and its symmetry
- Rovibronic states calculations
- Harmonic approximation and rigid rotor model, normal coordinates
- Anharmonicity and rovibronic interaction, perturbation theory, effective Hamiltonians, spctroscopy constants, variational calculations of rovibronic states, spectra calculations of large molecules and clusters
- Nonrigid molecules, failure of the harmonic approximation
- Current trends in theoretical molecular spectroscopy
Molecular Dynamics (Pavel Jungwirth, Jiri Kolafa) Quantum Molecular Dynamics
- Classical molecular dynamics
- Quantum molecular dynamics
Resonances (Petra Zdanska)
- Resonance phenomenon: open and closed resonator
- Resonances due to wave character of particles (electrons or atoms)
- in spectroscopy
- in collision processes
- Fingerprints of resonance phenomenon in measurables
- Interactions which lead to resonance phenomenon
- Feshbach type of resonance
- Shape type of resonance
- Methods to calculate resonance positions and widths
Proteins (Jiri Vondrasek) Proteins and Life
Statistical Thermodynamics (Anatol Malijevsky)
- What is statistical thermodynamics?
- Axioms, statistical ensembles, partition function and thermodynamic quantities
- Simple models
- Intermolecular interactions
- Pair-additive potentials: models and quantum chemistry results, three-particle potentials
- Real gas
- Virial expansion, pros and cons
- Dense liquid and gas
- Inner structure of liquid - pair distribution function, computer pseudo-experiments, theory of integral equations, perturbation theory, pair-distribution function and thermodynamic quantities
- Some philosophical aspects of statistical thermodynamics
- Probability and entropy, third law of thermodynamics: axiom or proof?, negative absolute temperatures, arrow of time
Visualization (Martin Kabelac) Empirical Potentials and Their Use for The Study of Biomolecules
- How to create (build) a molecule in computer?, structure visualization, 3D visualization (3D glases, virtual reality), rendering and raytracing, computer animations
Quantum Chemistry Codes (Zdenek Havlas) Quantum Chemistry Programs
- General aspcts of programming languages for scientific applications
- Hardware for computational chemistry
- The most often used quantum chemistry codes
- Gaussian program, its computational capabilities, comparison to other codes
DFT (Petr Nachtigall, Vladimir Sychrovsky) Introduction to DFT
- Theorems leading to the formulation of DFT methods
- Exchange and correlation density functionals
- LDA (LSD) approximation
- GGA and hybrid functionals
- Pros and cons of DFT
Energy Hypersurface (Zdenek Havlas) Potential Energy Surface
- Theoretical foundations: Born-Oppenheimer approximation
- Critical points on the energy hypersurface, optimization methods, coordinate systems
- Energy derivatives
- Equilibrium and rate processes
- Critical points on the energy hypersurface occuring during the electronic state change
- Photophysical and photochemistry processes
- Problem of multiple local minima
- Superposition error
- Molecular dynamics and energy hypersurface
NMR, EPR (Vladimir Sychrovsky) Calculations of the NMR Spectra Parameters
Molecular Interactions (Pavel Hobza)
- Covalent and non-covalent interactions
- Non-covalent interactions in natural sciences
- Origin of non-covalent interactions
- Perturbation and variational calculations of non-covalent interactions, their advantages and disadvantages
- Energy, entropy and free (Gibbs) energy and molecular complexes, energy surfaces
- Experimental detection of molecular clusters
Structural Databases (Bohdan Schneider) Structural Database in Chemistry and Biology
RNA (Bohdan Schneider) RNA Functional Diversity
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