(gc3603)Image Processing, Modeling and Simulation of Complex Biological Systems Using Volume Filling and Boundary Fitted Mesh Based Methods
EMSL Project ID
3603
Abstract
Terascale hardware and software capabilities represent a large increment in our ability to apply modeling and simulation to solving biology problems that include both spatially and temporally evolving concentration fields, bio-chemical reaction networks, and geometry. This new hardware capability coupled with advanced mathematical methods and algorithms enable our ability capture the multi-scale nature inherent in complex biological systems. Being able to capture these phenomena allows us to create virtual biological systems which can be used as numerical laboratories to predict virtual biology experiments. This capability helps biologists understand what might be going on in real experiments or ?better yet? will help expose new fundamental knowledge about the biology that is going on. The DOE is engaged in several biological programs that would benefit from having access to such a virtual biology simulation framework running on a massive parallel computer system. One specific program, called the Microbial Cell Project (A Genomes-to-Life project relevant to DOE OBER and PNNL) will be able to take advantage of such a computational simulation framework for studying the bioremediation of heavy metal radioactive waste. It?s main focus is to characterize Shewanella bacteria at all levels from the genome  proteome  individual cells multi-cell communities/biofilms. Another DOE/NIH related problem involves the modeling and simulation of the virtual respiratory tract of various species (rat, mouse, monkey, and human) with respect to the transport of reactive gases and discrete particles throughout the system.This project aims to use mesh based modeling and simulation methods to support the building and use of a computational biology framework for capturing the space and time dependent variations of complex biological systems in a virtual laboratory environment. Mesh based methods have there uses in three main areas related to computational biology, which are: 1) Image processing, 2) Data representation and data analysis and 3) Predictive modeling and simulation. But these methods tend to be computer cycle, computer memory and disk storage intensive, where the accuracy and the fidelity of the physical system being represented depends the size of the computer system you run on. Of course the larger the computer system the more accuracy and fidelity you will get. Mesh based methods map well onto distributed memory parallel architectures in that they exhibit approximate linear scaling as the number of processors and the problem size increases. This means that computer models that use meshes are highly efficient on parallel machines. These modeling efforts will be based on the NWGrid/NWPhys suite of codes, which runs on all classes of parallel machines.
Project Details
Project type
Capability Research
Start Date
2003-10-01
End Date
2006-10-08
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members