Science and Engineering at The University of Edinburgh

Soft Condensed Matter, Biological Physics Experiment & Statistical Physics Seminars

Explanatory note

This is a weekly series of informal talks given primarily by members of the soft condensed matter and statistical mechanics groups, but is also open to members of other groups and external visitors. The aim of the series is to promote discussion and learning of various topics at a level suitable to the broad background of the group. Everyone is welcome to attend.

Speakers should read this note

Week beginning 16 October 2016

Monday 17 Oct 16 - 1:00pm

Topological Patterns in Gel Electrophoresis of DNA Knots

Davide Michieletto (University of Edinburgh)

Agarose gels are broadly employed across the biophysical community. Beyond being an ideal environment for the growth of bacterial colonies, agarose gels are also commonly used to identify and classify biomolecules based on their physical properties. Electrophoresis of charged biopolymers through agarose gels is in fact an important tool to discriminate their weight, length or topology. Although the patterns of bands and spots emerging from 1D and 2D gel electrophoresis are empirically widely accepted, at present there is no theoretical model that can explain all the observed "topological patterns" from first principles. Particularly complicated and puzzling patterns have been observed for viral DNA, which is known to be heavily knotted. In order to shed some light into this problem, I will describe a crude model for agarose gels which improves previous attempts to capture its porous structure and then show that accounting for the gel's microscopic disorder (under the form of "dangling ends") crucially allows one to capture some of the unexplained topological patterns observed for gel electrophoresis of circular and knotted DNA.

Upcoming meetings

Monday 24 Oct 16 - 1:00pm - Room 2511

To be confirmed

Joost de Graff (University of Edinburgh)

Monday 31 Oct 16 - 1:00pm - Room 2511

To be confirmed

Ana Fialho (University of Edinburgh)

Monday 7 Nov 16 - 1:00pm - Room 2511

To be confirmed

Will Trewby (Durham University)

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Note for speakers

  • We try to encourage an informal atmosphere.
  • To encourage discussion, talks are limited to 30/40 mins plus up to 20/10 mins for questions.
  • Almost any style of talk is allowed and resident speakers are encouraged to give a variety of different types of talk during their stay at Edinburgh. Examples include talks about the speaker's research, a particular paper or publication (`Journal Club' talks), pedagogical talks, question-and-answer sessions, etc.
  • Speakers are encouraged to pitch their seminars to the whole group.
  • I would be grateful if the next speaker on the list could inform me of the title and short abstract (it should fit onto the usual advertising poster) of his/her talk by Wednesday of the week before, to allow me to do the advertising.
  • Anyone unable to give their talk on the scheduled date should in the first instance try to rearrange with someone else on the list, and only then inform me of the final outcome so that I can change the rota.
  • Talks of soft condensed matter students can only be cancelled with permission from Prof. Cates, and should be done as far in advance as possible to give some chance of finding a replacement.
  • If anyone would like to volunteer a seminar themselves, knows of a visitor or new arrival who might be willing to give a talk, or for any other queries, please contact the seminar organiser (see below for email address).