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Lipid Nanoparticles in Drug Delivery
Doctoral study program
Life Sciences (Faculty of Science, Masaryk University)
Supervisor
Annotation
With nearly 10 million lives claimed annually, cancer remains one of the leading causes of mortality worldwide, highlighting the urgent need for more effective treatments. One promising strategy involves mRNA-based cancer immunotherapy vaccines, which require a drug delivery system capable of reliably reaching the cytosol. Developing such delivery systems is challenging: they must ensure cytosolic delivery and therapeutic efficacy while maintaining safety, long-term stability, and compliance with scalable manufacturing standards—including high mRNA loading efficiency and uniform particle size. This project will investigate the intermolecular protein interactions that control key properties of protein-RNA liquid droplets, including size, stability, and loading capacity, as well as their responsiveness to environmental cues such as pH, temperature, or ionic strength. Using a combination of computational and biophysical approaches, the project aims to elucidate design principles for tuning the delivery systems based on protein droplets toward controlled release and selective targeting. The outcomes are expected to yield mechanistic insights and provide a foundation for the rational design of next-generation responsive delivery vehicles.
Recommended literature
- Paunovska K., et al.: Nat Rev Genet 2022, 23, 265–280, Doi: 10.1038/s41576-021-00439-4
- Hou X., et al.: Nat Rev Mater 2021, 6, 1078–1094, Doi: 10.1038/s41578-021-00358-0
- Yasuda I. et al.: J. Chem. Theory Comput. 2025, 21, 5, 2766–2779, Doi: 10.1021/acs.jctc.4c01646
- Chew P.Y., et al.: Chem. Sci., 2023,14, 1820-1836, Doi: 10.1039/D2SC05873A
Research area
Computational biophysics
Keywords
Computer simulations, Coarse-grained model, Molecular dynamics, protein-protein interactions, protein design
Funding of the PhD candidate
National Institute of Virology and Bacteriology, ERC, GACR grants
In the academic year 2026/27 the net income of the CEITEC PhD School student is expected to be at least CZK 29,400 (approx. EUR 1215)
Requirements for candidate
- MSc in computational biophysics/chemistry/physics and related fields
- Experience with Molecular Dynamics using coarse grained or atomistic models
- Advantage is experience with simulations of disordered proteins/polymers and membranes
- Excellent track record
- Good English language – spoken and written
- Motivated person with collaborative mind set
Information about the supervisor
Current group: 9 postdocs, 3 PhD students, 2 Master students, 4 technicians
Current projects are:
National Institute of Virology and Bacteriology, ERC consolidator grant, ERC proof of concept grant, Czech Science Foundation grant, TACR Proof of Concept, INTER-COST
In total 84 publications with more than 4700 citations (WoS) and H-index 37.
Recent publications:
- Kroutil, O.; Bartoš, L.; Kabelka, I.; Vácha, R.: Martini 3 Limitations in Phospholipid Flip-Flop. Journal of Chemical Theory and Computation 2025, 21, 19, 9227–9233, link
- Bartoš, L.; Pajtinka, P.; Vácha, R.: gorder: Comprehensive tool for calculating lipid order parameters from molecular simulations. SoftwareX 2025, 31, 102254
- Bartoš, L.; Lund, M.; Vácha, R.: Enhanced Diffusion through Multivalency. Soft Matter 2025, 21, 179-185,
- Linhartova, K.; Falginella, F.L.; Matl, M.; Šebesta, M.; Vácha, R.; Štefl, R.: Sequence and structural determinants of RNAPII CTD phase-separation and phosphorylation by CDK7. Nature Communications 2024, 15, 9163
- Deb, R.; Torres, M.D.T.; Boudný, M.; Koběrská, M.; Cappiello, F.; Popper, M.; Dvořáková Bendová, K.; Drabinová, M.; Hanáčková, A.; Jeannot, K.; Petřík, M.; Mangoni, M.L.; Balíková Novotná, G.; Mráz, M.; de la Fuente-Nunez, C.; Vácha, R.: Computational Design of Pore-Forming Peptides with Potent Antimicrobial and Anticancer Activities. Journal of Medicinal Chemistry 2024, 67, 16, 14040–14061
- Blasco S.; Sukeník, L.; Vácha, R.: Nanoparticle induced fusion of lipid membranes. Nanoscale 2024, 16, 10221-10229