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Multiscale Modeling of Nucleic Acids

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  • Full or part time
    Prof J Šponer
    Prof Michal Otyepka
    Dr Miroslav Krepl
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (Students Worldwide)
    Funded PhD Project (Students Worldwide)

Project Description

Nucleic acids (RNA and DNA) belong to the most important biomacromolecules. Studies of structure and dynamics of nucleic acids represent an important task of modern life sciences. Due to fast development of hardware and software, computational and theoretical approaches are frequently used in nucleic acids studies and represent a respected counterpart of experimental techniques. This PhD project will be based on integrated interdisciplinary utilization of a broad spectrum of computational methods (multi-scale modelling) ranging from state-of-the-art quantum-chemical (QM) approaches through modern explicit solvent molecular dynamics (MD) simulation methods up to bioinformatics. Cooperation with established experimental laboratories will provide necessary experimental feedback. State-of-the-art computational facilities are available not only in our laboratory but also in cooperating laboratories abroad. The exact topic will be specified based on the discussion with the applicant and her/his scientific interests and capabilities. Currently available specific themes include for example multiscale studies of protein-RNA complexes, RNA catalysis, structural dynamics and folding of quadruplex DNA and large-scale QM studies of complete nucleic acids building blocks. One of the most ambitious goals is understanding the role of partial disorder in protein-RNA recognition, which allows specific proteins to simultaneously read multiple RNA targets or to separate binding affinity from reactivity. We have wide range of international collaborations with experimental laboratories that are using NMR, X-ray crystallography, Cryo-EM and biochemical techniques. Experienced students may also be involved in parametrization of the AMBER simulation force field for nucleic acids, where we belong to the world-leading laboratories, or to applications of advanced enhanced-sampling methods.

Keywords: nucleic acids, structural dynamics, multiscale modeling, quantum chemistry, molecular dynamics simulations, protein-RNA complexes, RNA catalysis, quadruplex DNA

HOW TO APPLY: Register for this call using the registration form at http://ls-phd.ceitec.cz/http-ls-phd-ceitec-cz/ and submit required documents to receive support with the preparation of the application and all formalities. Your application package will be forwarded to the supervisor for preliminary revision.
Applicants who wish to pursue a degree at the CEITEC PhD program must hold the equivalent of a Master’s degree (MSc) in a similar field (four- or five-year undergraduate degree). The application can be submitted before obtaining the Master’s degree; however, the applicant should obtain a degree within five months after the application deadline.



Funding Notes

Admission for studies, student registration for the full-time study program, and proper fulfillment of student duties constitute the student’s right to a regular income of 22 000 CZK (850 EUR). Information is available at http://ls-phd.ceitec.cz/information-for-students/#fund

Living costs and other practicalities available at http://ls-phd.ceitec.cz/practical-information-for-life-in-brno/



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