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PhD position on multiscale simulations to unders ... (No replies)
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A PhD position is available as collaborative project between the group of Alberta Ferrarini in Padova (Italy) and the group of Marialore Sulpizi at the Ruhr University Bochum (Germany). The project aims to understand the interplay between pairing and stacking with a multiscale computer simulation approach including ab initio as well as classical molecular dynamics (MD) models on the high-resolution side and coarse-grained, machine-learnt potentials for large scale simulations.
A question still puzzling researchers working on the origin of life is how polymeric RNA and DNA could arise within the original prebiotic broth of molecules. An intriguing hypothesis, suggested by recent experimental findings [De Michele 2016, Fraccia 2015, 2016, Todosco 2018] is that the key information for the assembly and polymerization is already present within the single building-blocks, namely the nucleobases with their sugar and phosphate groups, able to selectively pair, stack and eventually react.
What are the critical interactions which guide the self-assembly and ultimately lead to life?
To answer this question, we will use multiscale approach, where the detailed insights from AIMD simulations, including geometries and free energies of binding and pairing, will be used to develop coarse grained models tailored for the mononucleotides under investigation, which will allow us to investigate the formation of linear aggregates of nucleotides and to characterize their morphology.
For the most promising base pairs, the phase diagram will be investigated as a function of density and temperature, using both MD simulations and theoretical approaches.
YOUR PROFILE:
You hold an A-grade (“very good”) qualifying degree at either the level of Master or Diploma; degrees in physics, chemistry or a related discipline will be accepted.
You have good knowledge in quantum mechanics and statistical mechanics. Experience with molecular simulations and scripting languages (e.g. python) is a plus.
You have very good English language skills (equal to B2, oral and writing).
Please submit your application (motivation letter, CV, diplomas, transcripts with grades, contact details for a reference letter via email to [email protected] or [email protected].
Application deadline: November 15th, 2022