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SUMMARY:Coarse-grained modelling of DNA for biophysics and nanotechnology 
 - Dr Ard Louis\, Rudolph Peierls Centre for Theoretical Physics\, Universi
 ty of Oxford\, UK
DTSTART:20121019T130000Z
DTEND:20121019T140000Z
UID:TALK40397@talks.cam.ac.uk
CONTACT:Tracy Inman
DESCRIPTION:The remarkable ability of biological matter to robustly self-a
 ssemble into\nwell defined composite objects excites the imagination\, sug
 gesting that\nthese processes could perhaps be emulated through the judici
 ous design of\nsynthetic building blocks.  DNA is a particularly promising
  candidate for\nlarge-scale self-assembly because the specific binding of 
 DNA bases can be\naccurately designed to build dynamic structures at the n
 anoscale.\n\nWe have developed a coarse-grained model of DNA [1\,2\,3] tha
 t is simple\nenough to be tractable\, but complex enough to capture struct
 ural\,\nthermodynamic and mechanical properties of DNA that are crucial to
  DNA\nnanotechnology. We have used it to study basic biophysical propertie
 s of\nDNA such as hybridization and the stacking transition in single-stra
 nded\nDNA [3]\, the response of DNA to tension  leading to overstretching 
 of\ndouble-stranded DNA and unstacking in single-stranded DNA [4]\, the re
 sponse\nof DNA to twist\, leading to bubble\, cruciform [5] and plectoneme
  formation\,\nand (4) the effect of topology on self-assembly processes [6
 ]. Applications\nto nanotechnology include DNA nanotweezers [1]\,  DNA dis
 placement\nreactions\,  A two-footed DNA walker\, and DNA origami.  Our co
 de is publicly\naccessible at: http://dna.physics.ox.ac.uk/\n\nReferences\
 n\n[1] DNA nanotweezers studied with a coarse-grained model of DNA\, T.E.\
 nOuldridge\, A.A. Louis and J.P.K. Doye\, Phys. Rev. Lett. 104\, 178101 (2
 010)\n\n[2] Structural\, mechanical and thermodynamic properties of a coar
 se-grained\nDNA model\, T.E. Ouldridge\, A.A. Louis and J.P.K. Doye\, J. C
 hem. Phys\, 134\,\n085101 (2011)\n\n[3] Sequence-dependent thermodynamics 
 of a coarse-grained DNA model\, P.\nSulc\, F. Romano\, T.E. Ouldridge\, L.
  Rovigatti\, J.P.K. Doye and A.A. Louis\,\narXiv:1207.3391.\n\n[4] Coarse-
 grained simulations of DNA overstretching Flavio Romano\, Debayan\nChakrab
 orty\, Jonathan P. K. Doye\, Thomas E. Ouldridge\, Ard. A. Louis\,\narXiv:
 1209.5892\n\n[5] DNA cruciform arms nucleate through a correlated but non-
 synchronous\ncooperative mechanism\, C. Matek\, T.E. Ouldridge\, A. Levy\,
  J.P.K. Doye\, and\nA.A. Louis\, arXiv:1206.2636.\n\n[6] The effect of top
 ology on the structure and free energy landscapes of\nDNA kissing complexe
 s\, F. Romano\, A. Hudson\, J.P.K. Doye\, T.E. Ouldridge\nand A.A. Louis\,
  J. Chem. Phys. 136\, 215102 (2012)
LOCATION:Small Lecture Theatre\, Cavendish Laboratory
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