Seminars & Discussions
Week beginning 22 May 2016
Monday 23 May 16 - 1:00pm
A Single Nucleotide Resolution Model of Double Stranded DNA
Yair Fossado (University of Edinburgh)
We explore some of the structural, topological and mechanical features of a coarse-grained model of double stranded DNA. We validate its physical properties by measuring correlation lengths and by reproducing in silico single molecule experiments which provide an independent way of verifying the parameters of the model. Furthermore, we show that our model captures some dynamical processes of double stranded DNA such as denaturation and supercoiling. Finally, we show how this model can be extended to include base pair specificity and we discuss possible applications to other problems.
Wednesday 25 May 16 - 11:30am
Mean-field approach for random close packings of non-spherical particles
Random packings of objects of a particular shape are ubiquitous in science and engineering. However, such jammed matter states have eluded any systematic theoretical treatment due to the strong positional and orientational correlations involved. Here, a mean field theory based on a statistical treatment of the Voronoi volume is discussed, which allows for the calculation of the random close packing fractions of spherical as well as non-spherical particles . This approach captures in particular the density peaks observed in simulations of different classes of non-spherical shapes. A phase diagram is presented that describes packings of elongated shapes such as spherocylinders and dimers in terms of an analytic continuation from the spherical random close packing .
 A. Baule, R. Mari, L. Bo, L. Portal, and H. A. Makse, Nature Commun. 4, 2194 (2013)
 A. Baule and H. A. Makse, Soft Matter 10, 4423 (2014)
Friday 27 May 16 - 11:30am
Loss of lamin A function increases chromatin dynamics in the nuclear interior
Authors: I. Bronshtein, E. Kepten, I. Kanter, S. Berezin, M. Lindner, Abena B. Redwood, S Mai, S. Gonzalo, R. Foisner, Y. Shav-Tal, Y. Garini
Speaker: Davide Marenduzzo
Chromatin is organized in a highly ordered yet dynamic manner in the cell nucleus, but the principles governing this organization remain unclear. Similarly, it is unknown whether, and how, various proteins regulate chromatin motion and as a result influence nuclear organization. Here by studying the dynamics of different genomic regions in the nucleus of live cells, we show that the genome has highly constrained dynamics. Interestingly, depletion of lamin A strikingly alters genome dynamics, inducing a dramatic transition from slow anomalous diffusion to fast and normal diffusion. In contrast, depletion of LAP2a, a protein that interacts with lamin A and chromatin, has no such effect on genome dynamics. We speculate that chromosomal inter-chain interactions formed by lamin A throughout the nucleus contribute to chromatin dynamics, and suggest that the molecular regulation of chromatin diffusion by lamin A in the nuclear interior is critical for the maintenance of genome organization.
Nature Communications 6
Article number 8044 (2015) pdf version
Additional Reading Exploring chromatin organization mechanisms through its dynamic properties
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