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BEGIN:VEVENT
UID:20201031T182310CET-1166s3si7z@ical.php
DTSTAMP:20201031T171010Z
CLASS:PUBLIC
DESCRIPTION:Lisa Davis from Department of Mathematical Sciecnes will give a
n Applied Math Seminar on \nContinuum and Stochastic Models for Transcript
ion on a Crowded Gene\nAbstract: In fast-transcribing prokaryotic genes\,
such as an rrn gene\, many RNA polymerases (RNAPs) transcribe the DNA sim
ultaneously. Active elongation of RNAPs involves periods of fast forward
motion that are often interrupted by pauses. In some literature\, this ha
s been observed to cause RNAP traffic jams. However\, other studies indic
ate that elongation is faster in the presence of multiple RNAPs than elong
ation by a single polymerase. Over the course of this research project\,
we have considered several mathematical models to capture the essential be
haviors known to this phenomena. I will give a brief overview of the esse
ntial biological quantities of interest\, and the remainder of the talk wi
ll focus on an overview of two mathematical models that have been proposed
. The first is a continuum model taking the form of a nonlinear conservat
ion law PDE where transcriptional pausing is incorporated into the flux te
rm with a piecewise continuous density-velocity relationship. The velocit
y relation is parametrized according to the user-specified (or randomly ge
nerated) spatial locations and time duration of the pauses. The second mo
del is a stochastic one that is based on the classical TASEP model but wit
h added complexity to account for the interactions among neighboring RNAPs
that can influence local elongation velocities. I'll mention the algorit
hms that were used for model simulation for a series of parameter studies.
If there's time\, I'll discuss future directions where sensitivity with r
espect to model parameters is crucial for developing a better understandin
g of the validity of these models. In addition\, we would like to combine
the lessons learned from previous models into the development of a specif
ic second order PDE formulation which allows for a richer\, more adaptive
density-velocity relationship.
DTSTART:20200910T150000
DTEND:20200910T160000
LOCATION:Webex Meeting number: 120 556 7048 Password: applied
SUMMARY:Continuum and Stochastic Models for Transcription on a Crowded Gene
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