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SUMMARY:Simulations of Cellular Processes: From Single Cells to Colonies -
  Zaida Luthey-Schulten (University of Illinois at Urbana-Champaign)
DTSTART:20160622T084500Z
DTEND:20160622T093000Z
UID:TALK66553@talks.cam.ac.uk
CONTACT:INI IT
DESCRIPTION:<span>Co-authors: Michael J. Hallock (University of Illinois  
 at Urbana-Champaign)\, Joseph R. Peterson (University of Illinois at  Urba
 na-Champaign)\, John A. Cole (University of Illinois at  Urbana-Champaign)
 \, Tyler M. Earnest (University of Illinois at  Urbana-Champaign)\, John E
 . Stone (University of Illinois at  Urbana-Champaign) <br></span> <span><b
 r>High-performance computing now allows integration of data from cryoelect
 ron  tomography\, super resolution imaging\, various &ndash\;omics\, and s
 ystems biology  reaction studies into coherent computational models of cel
 ls and cellular  processes functioning under in vivo conditions. Here we a
 nalyze the stochastic  reaction-diffusion dynamics of ribosome biogenesis 
 in slow growing bacterial  cells undergoing DNA replication and probe the 
 metabolic reprogramming that  occurs within dense colonies of Escherichia 
 coli cells over periods of hours.  Using our GPU-based Lattice Microbe sof
 tware\, the some 1300 reactions and 250  species involved in transcription
 \, translation and ribosome assembly are  described in terms of reaction-d
 iffusion master equations and simulated over a  cell cycle of two hours. T
 he ribosome biogenesis simulations account for DNA  replication that takes
  place within the cell cycle\, and the results are compared  to super reso
 lution imaging results. In the case of the c ell colony  simulations\, rea
 ction-diffusion kinetics of the surrounding medium are coupled  with the c
 ellular metabolic networks to demonstrate how small colonies of  interacti
 ng bacterial cells differentially respond to the competition for  resource
 s according to their position in the colony. The predicted metabolic  repr
 ogramming has been observed experimentally. Finally we will report on the 
  progress we have achieved to date and how supercomputers will provide us 
 a  window into cellular dynamics within bacterial and eukaryotic cells.</s
 pan>
LOCATION:Seminar Room 1\, Newton Institute
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