This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The Resource has begun development of a new software package for efficient simulation of the reaction-diffusion master equation, named """"""""Lattice Microbes"""""""". Development is focused on optimizing the software for the simulation of whole-cell models including approximated in vivo crowding. Through the use of graphics processing units (GPUs) we have been able to extend simulation sizes and times to the scale of cells and cell cycles. The new software will allow computational biologists to take advantage of data regarding the cellular architecture now being collected from experiments such as cryoelectron tomography (CET) and single-molecule, singlecell fluorescence. In collaboration with Julio Ortiz and Wolfgang Baumeister at the Max Planck Institute in Martinsreid, Resource researchers have used single-cell CET reconstructions as the basis for building a three-dimensional model of an E. coli cell. Using this model they studied the effect of spatial heterogeneity on gene expression in bacteria [1].

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
5P41RR005969-22
Application #
8363668
Study Section
Special Emphasis Panel (ZRG1-BCMB-E (40))
Project Start
2011-08-01
Project End
2012-09-09
Budget Start
2011-08-01
Budget End
2012-07-31
Support Year
22
Fiscal Year
2011
Total Cost
$49,734
Indirect Cost
Name
University of Illinois Urbana-Champaign
Department
Type
Organized Research Units
DUNS #
041544081
City
Champaign
State
IL
Country
United States
Zip Code
61820
Decker, Karl; Page, Martin; Aksimentiev, Aleksei (2017) Nanoscale Ion Pump Derived from a Biological Water Channel. J Phys Chem B 121:7899-7906
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Belkin, Maxim; Aksimentiev, Aleksei (2016) Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores. ACS Appl Mater Interfaces 8:12599-608
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Chaudhry, Jehanzeb Hameed; Comer, Jeffrey; Aksimentiev, Aleksei et al. (2014) A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow Through a Nanopore. Commun Comput Phys 15:

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