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updated last 01/13/06
September 21, 2000 3:00 pm
Sugar Chris Rao
Seminar Room
will bring food.
I am going to discuss the quasi steady-state assumption
(QSSA) applied to stochastic kinetics. The QSSA, or
as known to the rest of the world as singular pertubations,
is one of the few techniques available for reducing the
dimension of a model. I will begin with review of stochastic
kinetics. I will then discuss the QSSA in stochastic as well
as mass action kinetics with an emphasis on enzyme kinetics.
I will discuss an example of gene regulation using the QSSA.
If time permits, I will talk a little bit about stochastic
semi-groups, ergodicity, and the chemical master equation.
August 3, 2000 3:00 pm
Alex Gilman
The activation of SigmaF in B. subtilis sporulation
our sovereign master
the same old place
TBA will bring food.
I will present some results of modelling SigmaF activation in
B. subtilis sporulation. I will then talk about what SigmaF is
and why its activation is significant. The meaning of "activation"
in this context will be presented next. This will be followed by
a discussion of the interesting events of the sporulation process,
and then a definition and overview of sporulation. I will conclude
with vague comments about B. subtilis, the genus Bacillus,
the Eubacteria as a whole, and the kindom prokaryota, followed by
a brief introduction.
July 27, 2000 3:00 pm
Sriram Kosuri
Making Waves
Seminar Room
Alex will bring the donuts will bring food.
The social behavior exhibited by M. xanthus poses an interesting
and novel development system. Under starvation conditions,
these bacteria self-organize to produce visible heterogeneous
opposing wave patterns. Although wave behavior has been
observed and analyzed in other unicellular organisms such as Dictyostelium discoideum,
the patterns that evolve in M. xanthus are quite unique. Individual cell analysis indicates
that cells are constantly reversing, switching between opposing wave crests. Also, observation
of cultures show little or no interference between colliding waves and the role of chemotaxis in
Myxococcus, which is an essential part in Dicytostelium wave formation, is still unclear.
Based on these differences, it has been theorized that these wave patterns are mediated through cell-cell
contact rather than on a reaction-diffusion based system. In order to explore how these waves
arise and to explore the role of chemotaxis, social motility, adventurous motility and
signaling, we have constructed a type of cellular automaton in order to model the wave
formation of these cells. The cellular automaton, CritterSpace, is a Java based computer application
that creates a virtual environment in which simulated bacteria can move and interact. Each
bacterium is a small, movable agent on a triangular grid whose movement behavior is
determined by a few local rules and its internal state. These local rules are created based
upon constants representing contributions of social, reversal, and isolated behaviors for each
bacterium in the model. These rules, properly parameterized, should lead to emergent patterns
that closely resemble the behavior of the actual colony. The constants will be derived from
experimental measurements obtained by analysis of cell rippling movies and other
experiments. Using these results, we can then model the behavior of mutant strains of the
bacterium. Different mutant strains will be expected give rise to different behavioral
constants. By matching automaton behavior with the different mutants we will deduce the
contribution of each gene system to the cell phenotype and to the resultant pattern formation.
July 6, 2000 3:00 pm
Keith Moffat, University of Chicago (Visiting Fleming)
Perturb and probe : Time-resolved macromolecular crystallography
Adam Arkin
Calvin 116
Adam will bring food.
The structural changes that accompany all chemical and
biochemical reactions can occur very fast, on time scales
from femtoseconds to seconds or even longer. It's possible
to initiate structural reaction in a single crystal of a
macromolecule by perturbing the equilibrium structure by,
for example, a brief laser pulse, and then probing the time
evolution of the structural changes by intense X-ray pulses
as the structure relaxes back to the ground state. The
X-ray intensities of each Laue spot and the structure
amplitudes derived from them are then time-dependent but
error-prone. How shall the data be handled to enhance the
signal-to-noise? What form of time-smoothing is
appropriate? Are the structural changes "simple"
or "complex" and how would we know? If simple,
can the underlying chemical kinetic mechanism be derived
and if so, can the time-independent structures of each
intermediate in this mechanism be identified? These
questions will be illustrated by our nanosecond time-
resolved crystallographic studies on carboxymyoglobin and
photoactive yellow protein.
June 22, 2000 3:00 pm
Patrik D'haeseleer
Gene network inference using additive regulation models.
Adam
Calvin Seminar Room
TBA will bring food.
Currently, the most popular method for analyzing
large-scale gene expression data sets is gene clustering,
i.e. finding genes which are co-regulated. Gene network
inference is a somewhat more ambitious approach, in that
it also tries to derive causal relationships between
genes. I will present theoretical estimates of how many
data points are needed for clustering versus network
inference using various network models.
Next, I will show how a simple linear network model fitted
to three data sets on CNS development and injury in rats
can already lead to potentially biologically significant
results. Finally, I will present some initial work on
network inference using a more realistic, nonlinear model.
June 21, 2000 10:00 am
Tarek Elaydi
BSpiceML: An XML specification of the Central Dogma and Beyond
Adam
Calvin Lab Seminar Room
Adam will bring food.
One of the most important facets of design for the
Bio/Spice simulation and analysis tools will be the
how specifications for the biological models and data
are handed around from the user interface to the database
and from these to the simulation and analysis tools.
We have chosen XML as the standard for transporting this
information about. Tarek has been working at making a
refined and extensible specification for the representation
of models and other pathway information in XML.
He will present his results for comments and criticism.
June 7, 2000 3:00 pm
Leor Weinberger
Find the Virus
Proteases 'R' Us
Calvin 116
Tarek will bring food.
Part II!
Note the different time!
June 1, 2000 3:00 pm
Leor Weinberger
Leor and His Amazing Dancing HIV
Brought to you by Nabisco
Calvin Lab Seminar Room
Adam will bring food.
But next time someone else shops for food!
January 1, 2000 1:00 am
nj
mjk
nj
nj
nj will bring food.
nj
