Petascale simulations of Complex Biological Behavior in Fluctuating Environments

University Of California-Davis, Davis CA

Investigators

Abstract

This award is for a provisional allocation of time on the Blue Waters computer system, due to become operational in 2011, and for travel funds to support technical coordination by various collaborators with the Blue Waters project team and vendor technical team. The project involves studies in bacterial ecology, gene regulatory networks and intracellular biochemical networks with a view to understanding the way in which populations of unicellular organisms evolve and adapt as their environment changes. This involves multi-scale biological systems where processes ranging from gene expression and intracellular biochemistry to ecosystem dynamics are in play. A key aim is to understand how, by considering the genetic and biochemical processes within a cell, unicellular organisms evolve to develop adaptive responses to recurring changes in their environments. The study will look at the influence of parameters such as nutrient concentrations and mutation on adaptation, compare the efficacy of different strategies for survival in static and fluctuating environments, and examine how unicellular organisms internalize the correlation structure of their environment by modifying their internal networks to facilitate such changes. The role of genetic and molecular information transfer processes will also be studied. The modeling approach has been developed and previously used for scientific research using an implementation on contemporary computing systems. It is inherently multi-scale, including representations of molecular processes within cells and scaling up to ecosystems of unicellular organisms. In prior work, the limitations of computer power have necessitated a number of simplifying assumptions. It is anticipated that the use of Blue Waters will allow some of these to be relaxed, so that more biological processes can be included in the simulations. Results will be tested against the outcomes of in vivo experiments in the UC Davis Genome Center. The principal investigator is a recent Ph.D. Progress in this research area could find application in bioengineering and biotechnology.