Modeling complex bacterial cell systems through development of segregated models with spatial localization
EMSL Project ID
3570
Abstract
Systems of cells can exhibit behavior that is more complex than is expressed by individuals within the population. An example here might the be the formation of biofilms on surfaces. Because of the spatial structure of biofilms, spatial gradients of the cell environment are induced, and this in turn can influence genetic expression and protein expression in the cells as they adapt to the different environmental conditions. The characteristic sizes of cells and processes that can affect the cellular environment can be disparate. For example, bacterial cells themselves are about 1 ?m in diameter, but their cell walls (where much of the cell function is posited to occur) might be on the order of 50 to 100 nm thick, depending upon the cell. Conversely, a biofilm might be on the order of millimeters thick. The ratio of the two primary length-scales of interest then, is on the order of (1x10^-3 m for biofilm thickness) / (50x10^-9 m for cell walls) = 20,000. To simultaneously resolve the interacting physical and chemical processes occurring at these two disparate scales required enormous computational resources.
We propose to begin applications of NWGrid and NWPhys to relevant problems of bacterial cell systems using the EMSL computational facilities. These computations will be performed in concert with existing experimental efforts on the metabolic processes of the bacterium S. oneidensis MR-1, currently being studied as part of projects supported by the DOE Genomes to Life program and by LDRD. Our focus will be on modeling the spatial gradients of oxygen concentration with S. oneidensis cell aggregates as measured by Fredrickson?s group (J. Fredrickson, Y. Gorby, J. McLean), ultimately progressing toward an understanding (both in laboratory measurement and modeling) of these processes at the level of the proteome. The goal of this effort is to provide ?proof of principle? applications of advanced scientific computing tools (i.e., NWGrid and NWPhys) to biological systems where new understanding can be developed as a direct result of the use of these tools. Additionally, we seek to begin to ?bridge the gap? between biologists, engineers, and computational scientists by involving researchers from each of these groups who have inter-disciplinary skills and interests (e.g., members who have some expertise in biology and computations and mathematics will be involved). One objective of this work is to produce a publication that will help establish our expertise in the area of computational functional biology so that we can use this as leverage to further this area of research in a future call from the Genomes to Life (or other appropriate) program.
Project Details
Project type
Exploratory Research
Start Date
2003-06-26
End Date
2005-08-02
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members