BEGIN:VCALENDAR
VERSION:2.0
PRODID:researchseminars.org
CALSCALE:GREGORIAN
X-WR-CALNAME:researchseminars.org
BEGIN:VEVENT
SUMMARY:Stephen Hyde (University of Sydney)
DTSTART:20201106T050000Z
DTEND:20201106T060000Z
DTSTAMP:20260423T004700Z
UID:APATG/11
DESCRIPTION:Title: <a href="https://researchseminars.org/talk/APATG/11/">T
 he simplest 38 (or so) fold-classes of RNA (or DNA) by base-pairing. Knots
  and tangles from string sequences\, and sequences for knots and tangles</
 a>\nby Stephen Hyde (University of Sydney) as part of Asia Pacific Seminar
  on Applied Topology and Geometry\n\n\nAbstract\nRNA is known to fold into
  'pseudo knots' in a variety of viruses.  Though true knots have not been 
 detected\, it is fair to wonder if they are likely in natural or synthetic
  biological systems.  I will explore folding of a single string of RNA int
 o double-helices\, via Watson-Crick duplexing\, allowing the possibility o
 f strand junctions\, found\, for example\, in transient Holliday junctions
  in vivo.  Further\, either parallel or antiparallel double-helices are ad
 mitted. Given some arrangement of complementary base pairs on a strand\, a
 n oriented rigid-vertex graph can be constructed which encodes the resulti
 ng fold.  Conversely\, given a fold\, we can build a graph and deduce the 
 the arrangement of complementary base pairs on the strand.    \n\nSimplest
  folds can be built by winding a single strand on oriented genus-g surface
 s formed by tubifying graphs of cyclomatic number g\, such that a duplexed
  pair of locally parallel strands wrap each tubule of the manifold. More c
 omplex folds have combinations of pairs of of tracks (2-track railways) an
 d single tracks (1\,2-track railways). 2-track railways give relaxed folds
 \, so-named as they be embedded such that all base pairs are duplexed. 1\,
 2-track railways necessarily have unduplexed hairpin-like strands within t
 he fold. It turns out that for g<4\, there are few folds among the 40 or s
 o whose double-helices are all antiparallel - the preferred orientation fo
 r RNA and DNA duplexes.\n\nA connection between folds and knots is possibl
 e via 2-track railways\, whose consequences will be discussed if time perm
 its.\n
LOCATION:https://researchseminars.org/talk/APATG/11/
END:VEVENT
END:VCALENDAR