(emsl2419)Large Scale Code Development Applied to Building A Geometry Based Computational Framework for Biology and Ecology Applications
EMSL Project ID
2419
Abstract
The time is right to apply high-performance, parallel computing and modeling techniques to the area of geometry based computational biology and ecology. These biology applications involve scale lengths in time and space that span many orders of magnitude, making them truly multi-scale and very difficult to model as a whole. The whole area of computational biology could benefit by having access to a geometry based modeling capability that is adaptive in space and time such that it could capture aspects of multi-scale features. Here we propose to use the parallel computational framework of NWGrid and NWPhys codes to provide adaptive, computational engines as the basis of geometry based simulator. Here are the principle areas that will be addressed: 1) Transforming experimental biology image data into computational meshes that can be computed on. 2)Computational cell simulations that account for explicit cell geometry coupled to hydrodynamics, continuum mechanics, reaction-diffusion, and discrete particle transport. This would include cell signaling and reaction network modeling as well as gross cell phenomena like locomotion. 3)Organ modeling that takes into account explicit organ geometry coupled to hydrodynamics, continuum mechanics, reaction-diffusion, radiation and discrete particle transport. 4)Multi-scale computations for transport and mechanical properties in biological systems. On of the features of this modeling effort would be upscaling to capture the characteristics of sub-grid features, like cell complexes that make up tissues and tissue that make up organs. 5)Modeling of ecology systems that takes into account explicit organ geometry coupled to hydrodynamics, continuum mechanics, and discrete particle transport. 6)Testing new grid generation and computational physics algorithms, scaling of algorithms, optimization of algorithms that might be incorporated in NWGrid/NWPhys. This would involve the Terascale Simulation Tools and Technologies (TSTT) Center partners.
Project Details
Project type
Capability Research
Start Date
2002-01-28
End Date
2002-12-31
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members