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Computer simulations of knotted DNA and proteins

Tuesday 4th September 2012 - 13:30 to 14:10
INI Seminar Room 1
When mature bacteriophages such as P2 or P4 are assembled in infected cells, a long linear DNA molecule is loaded into the phage capsid and arranges itself in a toroidal, nematic phase. Intriguingly, experiments show that the DNA is not only highly knotted, but also exhibits a rather uncommon knot spectrum. Observation that DNA molecules in bacteriophage capsids preferentially form torus knots provide a sensitive gauge to evaluate various models of DNA arrangement in phage heads. We demonstrate with computer simulations of a simple bead-spring model that an increasing chain stiffness not only leads to nematic ordering and a (somewhat counter-intuitive) increase of knottedness, it is also the decisive factor in promoting formation of DNA torus knots in phage capsids. In the second part of my presentation I will review recent and not so recent advances in the understanding and modelling of protein knots.
University of Cambridge Research Councils UK
    Clay Mathematics Institute London Mathematical Society NM Rothschild and Sons