Kvant-Cheminis ir molekulinės dinamikos modeliavimas

Dalyko anotacija lietuvių kalba

Baigę kursą studentai gebės panaudoti kvantinės molekulių teorijos (kvantchemijos) ir molekulinės dinamikos metodus biologinių sistemų struktūrų (molekulių, jų ansamblių, membranų) geometrijai ir energiniams virsmams modeliuoti, įskaitant aplinkos įtaką norimu artiniu solvataciniuose apvalkaluose, taip pat molekulių ansamblių elgsenai simuliuoti.

Dalyko anotacija užsienio kalba

Students will learn how to use quantum chemical and molecular dynamics simulations for solving of different tasks of modelling structural geometry and energy exchange of biological systems (molecules, their ensembles, membranes), including environmental effects in solvatation shells, as well as to simulate the behaviour of molecular ensembles.

Būtinas pasirengimas dalyko studijoms

General Physics; Biophysics.

Dalyko studijų rezultatai

Understand the principles of molecular modelling.
Understand the proceses of structure geometry simulation of molecules.
Recognize the energetically profitable structure of molecules.
Understands the effects of technological and engineering solutions by quantum chemistry and molecular dynamics methods on the public and environment.

Dalyko turinys

1. Molecular modeling. Approximations. Visualization techniques. Software packages: Gaussview, HyperChem.
2. Electrical charges. Coulomb law. Point charges, dipoles, multipoles. Polarization.
3. Intermolecular forces. Charge- dipole interaction. Dipole-dipole interaction. Induction and dispersion energy. Morse potential.
4. Molecular mechanics.
5. Potential energy surfaces of molecules. Geometry optimization. Conformational search.
6. Monte Carlo simulation. Molecular dynamics.
7. Introduction into Quantum chemistry. Schrödinger equation. 1D and 2D potential function. The hydrogen atom H, molecule H2 and H2 + ion. Bases and methods.
8. Semiempirical models. Huckel theory. ZINDO, PM3, AM1. Density functionals methods.
9. Ab-initio models. Hartree-Fock method.
10. Electron correlation models. Møller-Plesset perturbation theory.
11. Applications. Simulation of electronic and vibrational absorption spectrum by means of quantum chemistry methods.
12. Electron transfer. Fermi golden rule.
13. Physical basics of molecular dynamics (MD) simulations.
14. Applications of molecular dynamics simulations. Simulations of simple systems (water, solutions, molecules)
15. Applications of molecular dynamics simulations. Simulations of complex systems (ensembles of molecules, planar lipid membranes, lipid vesicles)
16. Applications of molecular dynamics simulations. Simulations of membrane electroporation, transfer of small and complex molecules through the membrane, insertion of proteins into the lipid bilayer)
Practical work (contents):
Construction of small molecules, aromatic molecules, large supermolecules. Geometry optimization using different approximations, methods and basisset. Calculation of electronic and vibrational spectra. Calculation of charge redistribution from ground to excited state. Interpretation of spectroscopic state using one-particle transfer approach. Simulation of process parameters of intermolecular charge transfer. Simulation of conformational and tautomeric reaction in macromolcules. MD simulations of water, solutions, and simple molecules. MD simulations of ensembles of molecules, planar lipid membranes, lipid vesicles. MD simulations of membrane electroporation, transfer of small and complex molecules through the membrane, insertion of proteins into the lipid bilayer.

Dalyko studijos valandomis

Lectures – 30 hours, laboratory work – 30 hours, individual work including preparation for mid-term and final examination – 94 hours, examinations– 6 hours. Total 160 hours.

Studijų rezultatų vertinimas

Final assessment sums the assessments of written final examination (50%), written mid-term examination (25%) and assessment of laboratory works (25%).

Literatūra

1. 2007 Ira N. Levine. Quantum Chemistry New Jersey: Prentice Hall
2. 2008 Alytis Gruodis. Liuminescencija Vilnius: Kriventa.
3. 2006 Frank Jensen. Introduction to ComputationalChemistry Chichester: John Wiley and Sons Ltd
4. Furio Ercolessi, A Molecular Dynamics Primer University of Udine, Italy http://www.fisica.uniud.it/~ercolessi/md/md/ (free)
2004 D. C. Rapaport, The Art of Molecular Dynamics Simulation, 2nd Edition Cambridge University Press
Supplementary materials
1. 2000 Volkhard May, Oliver Kuehn. Charge and Energy transfer dynamics in molecular systems Chichester: Wiley-vch
2. 2007 Martin J. Field, A Practical Introduction to the Simulation of Molecular Systems Cambridge University Press