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Dipoloma Project in Theoretical ChemistryTheoretical studies of biomolecular complexes.The overall project objective is to use computational simulations to study biomolecular recognition and complex forming mechanisms. Biomolecular recognition that involves recognition and non-covalent binding of pairs of molecules is one of key processes by which cells are able to survive and function. Timely binding of correct molecular partners is critical in controlling various biomolecular processes. Recognition and binding of different small molecules to their biomolecular targets constitutes the basis for treating diseases by drugs. Hence understanding the basis of recognition is important in deciphering the laws that governs life at the molecular level. Molecular Dynamics simulations of different biomolecules free in water and in complex with different binding partners will increase our understanding of biomolecular recognition and complex forming mechanisms. The driving force behind biomolecular recognition with hydrophobic interactions together with other important factors including electrostatic interactions, hydrogen bonding, release of bound solvent and ions upon binding of partners, decreased conformational flexibility in the bound complex, formation of water bridges etc. can be studied in details using computational simulations. Molecular Dynamics simulations of different biomolecules free in water and in complex give us knowledge of the structure and dynamics of these biomolecules and complex forming mechanisms can be studied in details at an atomic level. Also other computational methods, such as a combined quantum mechanics and molecular mechanics (QM/MM) method or the current implementations of density functional theory (DFT), are used when needed and especially when different proteins enzymatic mechanisms are studied in details.
Used model systems (when free in solution):
Used model systems (biomolecular recognition and complex forming processes):
If you are interested in doing your diploma project at the Department of Theoretical Chemistry, or would like to have more information, you are welcome to contact us:
Dr. Pekka Mark: pekka-at-theochem-kth-se
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