Modeling of Chemical Properties of Nano- and Biostructures

Brief description

The graduate study is organized by the department of physical and macromolecular chemistry in collaboration with the Institute of Organic Chemistry and Biochemistry of the Academy of Sciences, covering computational chemistry, quantum chemistry, and molecular modeling. The study is focused on biomacromolecules (DNA and proteins) and complex molecular systems. The following projects can be studied:

1. structure and dynamics of pairs and oligomers of DNA in the ground and excited electronic state,
2. interaction of DNA with proteins and ligands,
3. study of non-covalent interactions, particularly the regular and irregular hydrogen bonds,
4. structural bioinformatics,
5. stabilizing interactions in biomolecules - peptides and proteins and theoretical models of protein folding,
6. theoretical study of chemical reactivity and catalysis,
7. physical and chemical properties of molecular sieves,
8. development of methods for the description of static and dynamic properties of weakly bound systems,
9. study of carbon nanostructures,
10. interaction of biologically relevant ions with hydrated proteins,
11. structure and dynamics of ions in solvents and at interfaces,
12. physical and chemical processes on atmospheric aerosols,
13. Structure, dynamics and function of RNA and DNA.

The concept of the study, which is based on the experience of the advisors, reflects modern trends in computational chemistry and in molecular modeling.

Specialized lectures and seminars

Quantum chemistry
Computational chemistry
Molecular structure and spectroscopy
Vibrational spectroscopy
Chemical thermodynamics
Statistical thermodynamics
Computer simulations in many-body physics
Classical and quantum molecular dynamics
Physics of proteins
Bioinformatics

Additional lectures can be chosen with the approval of the advisor and the committee from graduate and pre-graduate courses on the Faculty of Natural Sciences and other faculties of the Charles University (e.g., Faculty of Mathematics and Physics, medical faculties, etc.) and other Prague universities (ICT, FNPI CTU, etc.).

Research projects at IOCB

• ab initio quantum chemical calculations,
• non-covalent interactions,
• structure and dynamics of biomacromolecules,
• electronically excited states of isolated molecules and other complexes,
• stabilizing interactions in biomolecules,
• thermodynamic description of biochemical processes,
• hydrophobic interactions and their role in structural biology,
• chemical reactivity and catalysis,
• physical and chemical properties of molecular sieves,
• DFT approaches to weakly bound systems,
• Carbon nanostructures,
• Interaction of ions with proteins,
• Structure and dynamics of surfaces of electrolytes.

Subject-area Board

The subject-area board is available in Czech (Oborová rada). The Chairman is highlighted.