The role of topology and chemical composition of zeolites on their biomedical characteristics

• Thesis title in Czech: Význam topologie a chemického složení zeolitů pro jejich využití v biomedicíně
• Thesis title in English: The role of topology and chemical composition of zeolites on their biomedical characteristics
• Key words: zeolity, strojové učení, biomedicína, p-kresol, CAN
• English key words: zeolites, machine learning, biomedicine, p-cresol, CAN
• Academic year of topic announcement: 2022/2023
• Thesis type: Bachelor's thesis
• Thesis language: angličtina
• Department: Department of Physical and Macromolecular Chemistry (31-260)
• Supervisor: doc. RNDr. Lukáš Grajciar, Ph.D.
• Author: hidden - assigned and confirmed by the Study Dept.
• Date of registration: 25.10.2022
• Date of assignment: 25.10.2022
• Confirmed by Study dept. on: 01.02.2023
• Date of electronic submission: 22.05.2023
• Date of proceeded defence: 13.06.2023
• Opponents: Mgr. Miroslav Rubeš, Ph.D.
• Advisors: Dr. rer. nat. Andreas Erlebach

Guidelines

The project requires learning of various concept of atomic simulations (structure optimization, molecular dynamics) and machine learning algorithms for simulations of biomaterials. This work will also overlap with other collaborative projects of the group including collaboration with experimental colleagues measuring QENS (quasielastic neutron scattering) spectra in zeolites giving the student insights into the synergetic interaction of theory and experiment. The student will collaborate within a computational group and gain experience in presenting data orally and in written form.
Student will learn techniques of machine learning and molecular dynamics within internal workshops organized within the group of (Nano)materials modeling.

References

1 H. Serati-Nouri, A. Jafari, L. Roshangar, M. Dadashpour, Y. Pilehvar-Soltanahmadi and N. Zarghami, Biomedical applications of zeolite-based materials: A review, Materials Science and Engineering: C, 2020, 116, 111225.
2 P. Zarrintaj, G. Mahmodi, S. Manouchehri, A. H. Mashhadzadeh, M. Khodadadi, M. Servatan, M. R. Ganjali, B. Azambre, S.-J. Kim, J. D. Ramsey, S. Habibzadeh, M. R. Saeb and M. Mozafari, Zeolite in tissue engineering: Opportunities and challenges, MedComm, 2020, 1, 5–34.
3 L. Bacakova, M. Vandrovcova, I. Kopova and I. Jirka, Applications of zeolites in biotechnology and medicine – a review, Biomaterials Science, 2018, 6, 974–989.
4 B. Sels and L. M. Kustov, Zeolites and zeolite-like materials, Elsevier, Amsterdam, 2016.
5 D. Frenkel and B. Smit, Understanding Molecular Simulations, Academic Press, London, 2002.
6 K. E. Gubins et al.,The role of molecular modeling in confined systems: impact and prospects, PCCP, 2011, 13, 58–85.
7 Bussai et al, On the diffusion of water in silicalite-1: MD simulations using ab initio fitted potential and PFG NMR measurements, Applied Catalysis A:General, 2002, 232, 59-66
Annotation: The literature provides a broad overview of zeolites as biomaterials and the zeolite structure and properties. Additionally, the resources give a comprehensive introduction to the concepts of machine learning and molecular simulations.

Preliminary scope of work

Motivace výzkumu: Zeolity jsou mikroporézní hlinitokřemičitany, které mají hojné využití v několika biomedicinálních aplikací od drug delivery po využití jako materiály na kostní implantáty. Topologie a chemické složení (zejména koncetrace a typ mimomřížkových kationtů) zeolitů ve spojitosti s charakterem rozpouštědla (zejména voda) velice ovlivňuje reaktivitu a difúzi molekul v pórech zeolitu a tedy jejich medicinální vlastnosti.
Anotace: Bakalářská práce je zaměřena na zeolity jako inertní adsorbent využívaný pro kontrolované uvolňování léků a jiných medicinálních molekul, zejména se zaměřením na porozumění efektu topologie a chemického složení (zejména koncetrace a typ mimomřížkových kationtů) na jejich absorpční vlastnosti. Budeme objasňovat charakter a energetiku solvatace (ve vodě) mimomřížkových kationtů a (bio)molekul v kanálech zeolitů za relevantních experimentálních podmínek včetně uvažování efektu teploty, topologie zeolitu a poměru Si/Al. Toto umožní realistické modelování komplexních a industriálně významných zeolitů (např. MFI) a jejich interakcí s (bio)molekulami na úrovni atomů.
Metodika: Budeme používat nejmodernější modely strojového učení (potenciály založené na neuronových sítích) pro aproximaci povrchu potenciální energie, který využijeme pro přesné (blízké ab initio kvalitě) a realistické simulace zeolitů, zejména na molekulové dynamiky ve velkém měřítku.

Preliminary scope of work in English

Research Motivation: Zeolites are microporous aluminosilicates widely used for several biomedical applications ranging from drug delivery to bone implant materials. Zeolite topologies and their chemical composition (mainly concentration and type of extra-framework cations) significantly affects the binding and diffusion of molecules in the zeolite pores and, therefore, the zeolites’ biomedical properties.
Annotation: The thesis is focused on zeolites as inert adsorbent used for the controlled release of drugs and other medicinal molecules. In particular, understanding of effect of zeolite topology and chemical composition on the adsorption properties is targeted. We will elucidate the character and energetics of extra-framework cation solvation (in water) and solvation of (bio)molecules under relevant experimental conditions, considering effects of temperature, zeolite topology and Si/Al ratio. This allows realistic atomic-level modeling of complex and industrially relevant zeolites, such as MFI, and their interaction with (bio)molecules.
Methodologies: We will use state-of-the-art machine learning models (neural network potentials) to approximate the potential energy surface for accurate and realistic zeolite simulations. This enables large-scale molecular dynamics simulations with ab initio quality.