Prof. Denis Garoli
University of Modena and Reggio Emilia – Department of Science and Engineering, Italy
Aim of this project is optimising, validating and exploiting hybrid biosystems based on aptamers as biosensors. This will be based on the application of machine learning and molecular dynamics simulations for the design and analysis of aptamers (Stuber et al. ACS Nano 2023, Douaki et al. Chem. Comm. 2023, Douaki et al. Biosensors 2022). The PhD candidate will mainly work on the design and simulation of the nucleic acid sequences, considering applications towards highly selective and sensitive sensing. The results of the design will be then synthesised and integrated in hybrid systems where a solid- state device will be modified with the aptamers. Moreover, the model to be developed within this project will be used by the PhD student as a powerful tool to investigate the interaction between artificial nucleic acid sequences and DNA:RNA origami and hybrid biosystems comprising proteins of different size. The optimised aptamers developed by the PhD student will be also used in collaboration with other partners in the demonstration of the integration of optimised aptamers in silicified DNA origami and for the highly specific reaction in biohybrid cargo that can be modified with the aptamers.
Requirements: Potential candidates must have a master degree in one of the following disciplines: Physics, Chemistry, Biotechnology. Experience in machine learning and molecular dynamics simulations is a plus.
Planned secondments: Jungmann lab, Keyser/Mela lab
Salary: Gross salary € 3,821.53 + € 710.00 mobility allowance (+ €495.00 family allowance, if applicable).
The salary (36 months) is directly based on Marie Sklodowska-Curie Actions (MSCA) Doctoral Network budgeting (including a country-specific living allowance and a fixed mobility allowance for a doctoral candidate, as well as a possible family allowance).