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CATEGORIES:Isaac Newton Institute Seminar Series
SUMMARY:Simulations of Cellular Processes: From Single Cel
ls to Colonies - Zaida Luthey-Schulten (University
of Illinois at Urbana-Champaign)
DTSTART;TZID=Europe/London:20160622T094500
DTEND;TZID=Europe/London:20160622T103000
UID:TALK66553AThttp://talks.cam.ac.uk
URL:http://talks.cam.ac.uk/talk/index/66553
DESCRIPTION:Co-authors: Michael J. Hallock (University o
f Illinois at Urbana-Champaign)\, Joseph R. Peter
son (University of Illinois at Urbana-Champaign)\
, John A. Cole (University of Illinois at Urbana-
Champaign)\, Tyler M. Earnest (University of Illin
ois at Urbana-Champaign)\, John E. Stone (Univers
ity of Illinois at Urbana-Champaign)
High-performance computing now allows in
tegration of data from cryoelectron tomography\,
super resolution imaging\, various &ndash\;omics\,
and systems biology reaction studies into cohere
nt computational models of cells and cellular pro
cesses functioning under in vivo conditions. Here
we analyze the stochastic reaction-diffusion dyna
mics of ribosome biogenesis in slow growing bacter
ial cells undergoing DNA replication and probe th
e metabolic reprogramming that occurs within dens
e colonies of Escherichia coli cells over periods
of hours. Using our GPU-based Lattice Microbe sof
tware\, the some 1300 reactions and 250 species i
nvolved in transcription\, translation and ribosom
e assembly are described in terms of reaction-dif
fusion master equations and simulated over a cell
cycle of two hours. The ribosome biogenesis simul
ations account for DNA replication that takes pla
ce within the cell cycle\, and the results are com
pared to super resolution imaging results. In the
case of the c ell colony simulations\, reaction-
diffusion kinetics of the surrounding medium are c
oupled with the cellular metabolic networks to de
monstrate how small colonies of interacting bacte
rial cells differentially respond to the competiti
on for resources according to their position in t
he colony. The predicted metabolic reprogramming
has been observed experimentally. Finally we will
report on the progress we have achieved to date a
nd how supercomputers will provide us a window in
to cellular dynamics within bacterial and eukaryot
ic cells.
LOCATION:Seminar Room 1\, Newton Institute
CONTACT:INI IT
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