Lab Home | Phone | Search
Center for Nonlinear Studies  Center for Nonlinear Studies
 Home 
 People 
 Current 
 Affiliates 
 Visitors 
 Students 
 Research 
 ICAM-LANL 
 Publications 
 Conferences 
 Workshops 
 Sponsorship 
 Talks 
 Colloquia 
 Colloquia Archive 
 Seminars 
 Postdoc Seminars Archive 
 Quantum Lunch 
 Quantum Lunch Archive 
 CMS Colloquia 
 Q-Mat Seminars 
 Q-Mat Seminars Archive 
 P/T Colloquia 
 Archive 
 Kac Lectures 
 Kac Fellows 
 Dist. Quant. Lecture 
 Ulam Scholar 
 Colloquia 
 
 Jobs 
 Postdocs 
 CNLS Fellowship Application 
 Students 
 Student Program 
 Visitors 
 Description 
 Past Visitors 
 Services 
 General 
 
 History of CNLS 
 
 Maps, Directions 
 CNLS Office 
 T-Division 
 LANL 
 
Monday, February 10, 2020
3:00 PM - 4:00 PM
CNLS Conference Room (TA-3, Bldg 1690)

Colloquium

Continuum and Stochatic Models for Transcription on a Crowded Gene

Dr. Lisa Davis
Department of Mathematical Sciences, Montana State University

In fast-transcribing prokaryotic genes, such as an rrn gene, many RNA polymerases (RNAPs) transcribe the DNA simultaneously. Active elongation of RNAPs involves periods of fast forward motion that are often interrupted by pauses. In some literature, this has been observed to cause RNAP traffic jams. However, other studies indicate that elongation is faster in the presence of multiple RNAPs than elongation by a single polymerase. Over the course of this research project, we have considered several mathematical models to capture the essential behaviors known to this phenomena. I will give a brief overview of the essential biological quantities of interest, and the remainder of the talk will focus on an overview of two mathematical models that have been proposed. The first is a continuum model taking the form of a nonlinear conservation law PDE where transcriptional pausing is incorporated into the flux term with a piecewise continuous density-velocity relationship. The velocity relation is parametrized according to the user-specified (or randomly generated) spatial locations and time duration of the pauses. The second model is a stochastic one that is based on the classical TASEP model but with added complexity to account for the interactions among neighboring RNAPs that can influence local elongation velocities. I'll mention the algorithms that were used for model simulation for a series of parameter studies. If there's time, I'll discuss future directions where sensitivity with respect to model parameters is crucial for developing a better understanding of the validity of these models. In addition, we would like to combine the lessons learned from previous models into the development of a specific second order PDE formulation which allows for a richer, more adaptive density-velocity relationship.

Host: Dr. Kyle Hickmann