Fall 2013 Colloquia



Tuesday, September 3

Open

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Tuesday, September 10

Open

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Tuesday, September 17 (Brandeis Thursday)

Robert Holyst, Polish Academy of Sciences
Biologistics:Mobility in cytoplasm of the eukaryotic and prokaryotic cells

Biologistics and biochemistry in a crowded environment are two emerging interdisciplinary fields of science. They provide  quantitative analysis of transport of proteins and their interactions involved in gene expression and regulation. These processes inside living cells strongly depend on the physics of liquids at the nanoscale. As I will try to convince you during my talk, the length-scale dependent nanoviscosity [1-4] characterizing motion of proteins at the nanoscale is a key to quantitative analysis of biochemical reactions in living cells.  Genes are activated and repressed by proteins referred to as transcription factors (TF). The binding of TFs to the operator region on DNA is diffusion limited. TFs search for operators by performing a combination of three-dimensional (3D) diffusion in a defined volume and one-dimensional (1D) diffusion along DNA molecule. The diffusion coefficients for 3D diffusion, D, and 1D diffusion, D1, are inversely proportional to the viscosity. For the model Gram-negative bacterium Escherichia coli, the nanoviscosity of the cytoplasm depends on the size of diffusing objects[2]. This scale dependent nanoviscosity changes by a factor of >104 between 0.001 Pas for water molecules (size 0.14 nm) and 18 Pas for large plasmids (size 300 nm). Accordingly D for biomolecules in E. coli varies by a factor of ~108. An understanding of how D, D1 and the reaction rates for gene expression depend on the length-scale dependent nanoviscosity and non-specific interactions between DNA and proteins is an essential step for understanding metabolic and proteomic networks.  The final outcome of the work of my group is a database (6600 records) of diffusion coefficients for all proteins and their complexes from the proteome of E.coli. This is the first such database for any organism. Only 10-20 measurements of diffusion coefficients are needed to construct the databases for any cell or its organelles (nucleus, mitochondria).

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Tuesday, September 24

David Huse, Princeton University
Title: TBA

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Tuesday,  October 1

Open

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Tuesday, October 8

Greg Bearman, Snapshot Spectra, USC Keck School of Medicine and the Israeli Antiquities Authority
Title: TBA

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Tuesday, October 15

Marin Soljacic, MIT
Title: TBA
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Tuesday, October 22

Patrick Charbonneau, Duke University
Title: TBA

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Tuesday, October 29

Gabriella Sciolla, Brandeis University
Title: TBA

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Tuesday, November 5

Open

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Tuesday, November 12

Open

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Tuesday, November 19

Mark Reid, Harvard University
Measuring the Cosmos

Abstract:  Over 2000 years ago, Hipparcus measured the distance to the Moon by triangulation from two locations across the Mediterranean Sea. However, determining distances to stars proved much more difficult.  Many of the best scientists of the 16th through 18th centuries attempted  to measure stellar parallax, not only to determine the scale of the cosmos but also to test Heliocentric cosmologies.  While these efforts failed, along the way they lead to many discoveries, including atmospheric refraction, precession, and aberration of light.  It was not until the 19th century that Bessel measured the first stellar parallax.  Distance measurement in astronomy remained a difficult problem even into the early 20th century, when the nature of galaxies ("spiral nebulae") was still debated.  While we now know the distances of galaxies at the edge of the Universe, we have only just begun to measure distances accurately throughout the Milky Way.  Using the Very Long Baseline Array, we now can achieve positional accuracy approaching 10 micro-arcseconds!  I will present new results on parallaxes and motions of star forming regions.  These measurements address the nature of the spiral structure, size, rotation speed, and mass of the Milky Way.
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Tuesday, December 3

Open