Biology Simulation Models

Application Point of Contact: Rick Corley (PNNL), Jim Fredrickson (PNNL)

TSTT Point of Contact: H. Trease (PNNL)

An emerging DOE application area for mesh-based modeling is in the area of computational biology. The face of biology is changing as new methods are brought to bear on the study of living systems. In fact, it is the transition from viewing biology as a set of components to treating it by a systems approach that will truly revolutionize the field. Biology does not occur at any one scale, rather it occurs from scales as small as an atomic ion, e.g., Ca2+ to scales as large as complex human populations and their interactions with the environment. A key element in any study of modern biology and the impact of understanding it in terms of human health or in terms of the impact of microbial systems on the environment is the ability to cross many temporal and spatial scales in order to connect diverse data and predict biological behavior at the systems level.

In addition to the five primary SciDAC application areas that the TSTT Center supports, we are also incorporating TSTT meshing and discretization capabilities into DOE-funded computational biology applications. This activity is designed to coordinate and cultivate a relationship between TSTT capabilities and DOE's biology areas. Specifically, this was done by incorporating TSTT (NWGrid/NWPhys) mesh technology and CCA-compliant component technology into two ongoing DOE programmatic areas in Microbial Cell Biology (DOE LAB 01-20) and Computational Biology (DOE LAB 01-21). In addition, application support was provided to several internal PNNL LDRD projects that are directed toward multi-scale computational biology, like the Virtual Lung Project and Nano-biology projects. The main focus of these efforts is in image reconstruction and feature extraction of computational geometry and meshes representing complex biological systems that include everything from individual cells (procaryotic and eucaryotic) to organs (like lungs, upper respiratory systems, whole organisms). The figure on the left represents the process of extracting the meshed geometry of a lung and arterial branching tree from the volume image data for a CT scan of a human chest. The figure on the right represents the process of extracting the computational geometry and mesh for the upper respiratory tract of a rat based on volume NMR images. The following two figures are simulations of microbial cell communities (left) and microbial cell biofilms (right) using the TSTT NWGrid/NWPhys mesh generation and discretization codes. The figure on the left is of the diffusion of oxygen into a community of Shewanella bacteria (images are from confocal microscopy where the microbes have been stained using GFP. The figure on the right is the growth of a biofilm within a bioreactor (imaged using NMR).

Spiral CT Images

NMR Data