Our research group works on structure, function and structure-function relationship of biomolecules and materials using advanced computational chemistry methods. The employed computational chemistry techniques are Quantum Mechanics (QM), atomistic and Coarse Grained (CG) Molecular Dynamics (MD) simulations, Brownian Dynamics (BD) simulations combining Quantum Mechanics/Molecular Mechanics (QM/MM) descriptions. Moreover, we use experimental methods to verify our computational results.
Interaction of viruses with materials
This project uses advanced computational chemistry tools to predict the interaction of enveloped viruses with surfaces, and determine the impact of the different properties of the surfaces in their interactions with the virus. MAT4COVID as part of this project has been funded by European Union.
This project is meant to understand the mechanism underlying the extraordinary properties offered by nano-particles and therefore help guide the experiments using computational chemistry methods. Particular attention will be given to explore the interfacial properties between the NP and the surrounding polymer.
Thermodynamics stability and structure-function relationship of beta-lactoglobulin (BLG)
The protein β-lactoglobulin (BLG) is the major protein of whey ruminant milk and it is a member of the family so-called lipocalins. Its ease of purification and importance in the food industry explain in part the huge amount of literature pertaining to it. BLG is a small globular protein with well-known structure. In order for the protein to become biologically active, it must fold and adopt one of an enormous number of possible conformations. In series of relevant studies, the structural changes and function of BLG were investigated in the presence of series of ionic surfactants and natural ligands using experimental (UV-Vis, FT-IR, CD and Fluorescence spectroscopy) and computational (molecular docking, MD simulation and QM/MM) methods. Comparison of the results of these studies paves the way for the determination of some aspects of the structure–function relationship of BLG in different conditions. Also, the obtained information can be useful in the application of the surfactants in dairy food industry. This may also give some guidance as to what could be expected during interactions of charged and neutral lipids with BLG. Furthermore, finding new biologically active ligands to bind BLG is very important, and not only can contribute to a better understanding of the molecular properties of this protein, but also might pave the way for future studies about the transport of drugs to biological sites.
Natural ligand-loaded nanoparticles of beta-lactoglobulin (BLG)
Known as amphiphilic molecules, proteins are capable of incorporating target compounds via various approaches, including hydrophobic interaction, electrostatic attraction, hydrogen bonding, and van der Waals force. This characteristic enables protein nanoparticles to encapsulate nonpolar, polar or charged compounds. In addition, proteins exhibit superior biocompatibility and nutritional value in comparison with synthetic polymers. Because BLG is known for its remarkable resistance against pepsin and moderate digestibility by trypsin, its nanoparticles were anticipated to show controlled-release property, that is, minimal and maximal release in the stomach and small intestine, respectively.
Investigation of interfacial, mechanical, thermal and electrical properties of materials
Although there are many reports on alloys, studies on the relation between their atomic composition and their mechanical and thermodynamic properties, at the same time, are still missing. Given the enormous set of options in terms of alloying, it is impossible to perform experimental screening of all probable combinations in a reasonable timeframe. Hence, in the present study we use first-principles calculations to investigate the feasibility of forming and also the performance of the ternary alloys. The aim is to find an alloy with the optimum behavior. Furthermore, the mechanical, electrical and thermal properties are taken into consideration for the alloys and the H-alloys systems.
Novel metal-Schiff base complexes as anticancer agents and their interaction with biomacromolecules: multi experimental and computational studies
Schiff bases are compounds that fascinate a large number of chemists and biochemists due to their easy formation, high stability, their pharmacological properties and notably anticancer activity. Studying on synthesis, characterization and the interactions of these metal complexes with DNA or HSA is critical to design target specific, more efficient and less toxic drugs. Interaction of candidate drugs with these biomacromolecules were reflected using spectroscopic (fluorescence, UV–Vis, CD and etc.) and computational methods (molecular docking, molecular dynamics simulation and QM/MM)