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Dr S Krivov
Dr R Tuma
No more applications being accepted
Competition Funded PhD Project (European/UK Students Only)
About the Project
Computational experiments became a vital component of researches arsenal, as was highlighted by the 2013 Nobel prize awarded to three computational chemists: Martin Karplus, Michael Levitt and Arieh Warshel. Advances in simulation algorithms made it possible to obtain detailed dynamical picture of real-life biological processes on a computer. Likewise single molecule imaging is at the forefront of contemporary experimental science. This project will use state of the art simulation and analysis methods coupled with single molecule experiments to elucidate the dynamics of molecular motors which are used by viruses to package their genome. The final aim is the usage of the obtained models to re-engineer the motors to translocate specific RNA with the aim to combat viral diseases.
Funding Notes
4 year BBSRC studentship, under the White Rose Mechanistic Biology DTP. The successful applicant will receive fees and stipend (c.£13863 for 2014-15). The PhD will start in Oct 2015. Applicants should have, or be expecting to receive, a 2.1 Hons degree in a relevant subject. EU candidates must have been resident in the UK for 3 years in order to receive full support. There are 2 stages to the application process. Please see our website for more information:
http://www.fbs.leeds.ac.uk/gradschool/keywords/mnuFindaphd.php
http://www.fbs.leeds.ac.uk/gradschool/keywords/mnuFindaphd.php
References
Mancini, E. J., Kainov, D. E., Grimes, J. M., Tuma R., Bamford, D. H. and Stuart. D. I. (2004) “Atomic Snapshots of an RNA Packaging Motor Reveal Conformational Changes Linking ATP Hydrolysis to RNA Translocation.” Cell 118, 743.
Krivov, S. V. and Karplus, M. (2008) Diffusive reaction dynamics on invariant free energy profiles. Proc. Natl. Acad. Sci. USA 105, 13841.
Krivov, S. V. (2011) The Free Energy Landscape Analysis of Protein (FIP35) Folding Dynamics. J. Phys. Chem. B 115, 12315.
Borodavka, A., R.Tuma, and P. G. Stockley (2012). Evidence that viral RNAs have evolved for efficient, two-stage packaging. Proc. Natl. Acad. Sci. U S A 109:15769-15774.
Krivov, S. V. and Karplus, M. (2008) Diffusive reaction dynamics on invariant free energy profiles. Proc. Natl. Acad. Sci. USA 105, 13841.
Krivov, S. V. (2011) The Free Energy Landscape Analysis of Protein (FIP35) Folding Dynamics. J. Phys. Chem. B 115, 12315.
Borodavka, A., R.Tuma, and P. G. Stockley (2012). Evidence that viral RNAs have evolved for efficient, two-stage packaging. Proc. Natl. Acad. Sci. U S A 109:15769-15774.
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