Basic Research Needs for Geosciences - Energetics Meetings and ...

PANEL REPORT: MODELING AND SIMULATION OF GEOLOGIC SYSTEMSFigure 20. Integrated constraint-based model of E. coli. Modeling frameworks for metabolism, regulation,transcription, and translation have been developed; connectivity between these models is shown. The model can beused to reconcile diverse “omics” data. (Reed and Palsson 2003; Copyright © 2003, the American Society forMicrobiology. All rights reserved.)Experimental investigations of the mechanisms and rates of energy/electron-transfer across themicrobe-mineral interface have been initiated. These processes can be implemented in numericalmodels to simulate biofilm dynamics in porous media coupled to extracellular geochemicalreactions such as sorption, precipitation, and redox alterations. Other microbial communityresponses such as signaling and motility can be implemented numerically as well to capture thefunctioning of the biofilm as a whole as it interacts with its pore environment. In this way,metabolic activities that take place at the cellular level can be extended via modeling to thebiofilm scale.In silico methods are being developed that allow for the incorporation of “omics” data (seeFigure 20), including genomics, proteomics, transcriptomics and metabolomics (Allen andPalsson 2003; Palsson 2002; Reed and Palsson 2003). The coupled in silico biogeochemicalmodel developed in this research effort will be linked with next-generation pore-scale models forhydrodynamic flow, transport, and geochemical reactions (see Figure 21). Combined withpetascale computing, it will be possible, and increasingly useful, to simulate the interactionsbetween the biotic and abiotic geochemical cycles at increasingly larger spatial scales.62 Basic Research Needs for Geosciences: Facilitating 21 st Century Energy Systems