Seth Blumberg, Feb 2009: Difference between revisions
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=== Schedule === | === Schedule === | ||
* 9:00a: | * 8:45a: Arrival and seminar setup | ||
* 10:00a: | * 9:00a: Seminar, 139 Moore | ||
* 11: | * 10:00a: Niles Pierce (if no jury duty) | ||
* 12:00p: Lunch (host | * 10:45a: Richard Murray, 109 Steele | ||
* 11:30a: Open | |||
* 12:00p: Lunch (host: Paul and Erik) - meet at Ath | |||
* 1:30p: Shuki Bruck, 331 Moore | * 1:30p: Shuki Bruck, 331 Moore | ||
* 2:15p: | * 2:15p: Paul Rothemund, 204 Moore | ||
* 3:00p: | * 3:00p: Erik Winfree, 204 Moore | ||
* 3:45p: Open | * 3:45p: Open (note: there is a faculty meeting from 4-5 pm) | ||
* 4:30p: Open | * 4:30p: Open (note: there is a faculty meeting from 4-5 pm) | ||
=== Seminar === | |||
<center> | |||
'''The Computational Landscape of DNA looping''' | |||
Seth Blumberg, U. Michigan <br> | |||
9:00 am, 139 Moore | |||
</center> | |||
DNA loops form when a protein binds to two operator sites on the same DNA molecule. In the biological world, DNA looping provides an intriguing control mechanism for gene regulation, DNA packaging and other sub-cellular processes. DNA looping is affected by a variety of biochemical and mechanical factors including the strength of DNA-protein interactions, tension in the substrate DNA and intra-operator sequence. In principle, specific looping dynamics can be engineered by manipulating these biomechanical constraints. For instance, it seems plausible to create a tunable AND-XOR-OR gate using a two-loop system under various degrees of tension. Similarly, a multiple loop system can be tuned so that the preferred configuration is responsive to the concentration of looping protein. Besides speculating on the computational landscape of DNA looping, I will review my involvement in single-molecule experiments that characterize simple looping systems. | |||
Latest revision as of 01:33, 22 February 2009
Seth Blumberg is a MD/PhD who is visiting Caltech on 23 Feb (Mon). Use this page to schedule a time to meet with him.
Schedule
- 8:45a: Arrival and seminar setup
- 9:00a: Seminar, 139 Moore
- 10:00a: Niles Pierce (if no jury duty)
- 10:45a: Richard Murray, 109 Steele
- 11:30a: Open
- 12:00p: Lunch (host: Paul and Erik) - meet at Ath
- 1:30p: Shuki Bruck, 331 Moore
- 2:15p: Paul Rothemund, 204 Moore
- 3:00p: Erik Winfree, 204 Moore
- 3:45p: Open (note: there is a faculty meeting from 4-5 pm)
- 4:30p: Open (note: there is a faculty meeting from 4-5 pm)
Seminar
The Computational Landscape of DNA looping
Seth Blumberg, U. Michigan
9:00 am, 139 Moore
DNA loops form when a protein binds to two operator sites on the same DNA molecule. In the biological world, DNA looping provides an intriguing control mechanism for gene regulation, DNA packaging and other sub-cellular processes. DNA looping is affected by a variety of biochemical and mechanical factors including the strength of DNA-protein interactions, tension in the substrate DNA and intra-operator sequence. In principle, specific looping dynamics can be engineered by manipulating these biomechanical constraints. For instance, it seems plausible to create a tunable AND-XOR-OR gate using a two-loop system under various degrees of tension. Similarly, a multiple loop system can be tuned so that the preferred configuration is responsive to the concentration of looping protein. Besides speculating on the computational landscape of DNA looping, I will review my involvement in single-molecule experiments that characterize simple looping systems.
