Thursday, December 12, 2013 - 10:15am - 11:05am
Mariel Vazquez (San Francisco State University)
Newly replicated circular chromosomes are topologically linked. Controlling these topological changes, and returning the chromosomes to an unlinked monomeric state is essential to cell survival. XerCD-dif-FtsK recombination acts in the replication termination region of the Escherichia coli chromosome to remove links introduced during replication. We use topological methods to show definitively that there is a unique shortest pathway of unlinking by XerCD-dif-FtsK that strictly reduces the complexity of the links at every step.
Wednesday, December 11, 2013 - 10:15am - 11:05am
Alexander Vologodskii (New York University)
The talk will review the development in the field of DNA-related topological problems, knots and links formed by double-stranded DNA molecules. It will start from purely theoretical problem of calculating the equilibrium probability of knots in a polymer chain. Although solving this problem was an achievement in polymer statistical physics, it did not look useful for anything else at that time. Eventually, however, it helped greatly in the studies of DNA general properties and its topological transformations catalyzed by site-specific recombinases and DNA topoisomerases.
Monday, November 14, 2011 - 4:30pm - 5:30pm
Nevenka Dimitrova (Philips Research Laboratory)
Within only a decade since the first draft of the human genome, we’ve witness astonishing pace of development of technologies for high throughput molecular profiling that probe various aspects of genome biology and its relationship to tumorigenesis and cancer treatment. There have been giant steps towards cataloging massive amounts of data and providing fairly good annotation information.
Monday, October 29, 2007 - 2:30pm - 3:00pm
Niles Pierce (California Institute of Technology)
DNA and RNA are versatile construction materials.
By appropriately designing the sequence of bases in each strand, synthetic nucleic acid
systems can be programmed to self-assemble into complex structures that implement dynamic mechanical
tasks. Motivated by the challenge of encoding arbitrary mechanical function into
nucleic acid sequences, we are developing a suite of computational algorithms for
analyzing the underlying free energy landscapes that control the
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